Starting phenix.real_space_refine on Wed Mar 4 14:11:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ugd_20761/03_2026/6ugd_20761_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ugd_20761/03_2026/6ugd_20761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ugd_20761/03_2026/6ugd_20761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ugd_20761/03_2026/6ugd_20761.map" model { file = "/net/cci-nas-00/data/ceres_data/6ugd_20761/03_2026/6ugd_20761_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ugd_20761/03_2026/6ugd_20761_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 186 atoms to isotropic. 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 18 5.49 5 Mg 5 5.21 5 S 63 5.16 5 C 8800 2.51 5 N 2438 2.21 5 O 2604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13928 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2239 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 9, 'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2273 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2297 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 12, 'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2318 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 5, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2306 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2186 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 151 Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 118 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.19 Number of scatterers: 13928 At special positions: 0 Unit cell: (132.84, 139.32, 118.8, 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 63 16.00 P 18 15.00 Mg 5 11.99 O 2604 8.00 N 2438 7.00 C 8800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 619.3 milliseconds 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 48.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.202A pdb=" N ILE A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.611A pdb=" N ARG A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.956A pdb=" N LEU A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 removed outlier: 4.343A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.232A pdb=" N ARG A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 348 through 353' Processing helix chain 'A' and resid 363 through 375 removed outlier: 4.053A pdb=" N LYS A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 397 through 415 removed outlier: 4.160A pdb=" N VAL A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.517A pdb=" N ALA A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 removed outlier: 4.089A pdb=" N PHE A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'B' and resid 159 through 163 removed outlier: 4.261A pdb=" N ASP B 163 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.790A pdb=" N VAL B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.661A pdb=" N ILE B 195 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.605A pdb=" N LEU B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.510A pdb=" N GLU B 344 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.562A pdb=" N LYS B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 392 Processing helix chain 'B' and resid 400 through 415 Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.981A pdb=" N GLU B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.546A pdb=" N GLY C 162 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 163 " --> pdb=" O SER C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 198 through 207 Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.746A pdb=" N LEU C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.549A pdb=" N ARG C 223 " --> pdb=" O GLN C 220 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 224 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 269 through 285 removed outlier: 3.698A pdb=" N ILE C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.958A pdb=" N LYS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 376 removed outlier: 3.578A pdb=" N LYS C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 392 removed outlier: 3.618A pdb=" N LEU C 389 " --> pdb=" O ASN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 411 Processing helix chain 'C' and resid 425 through 434 removed outlier: 4.082A pdb=" N GLU C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 448 removed outlier: 3.828A pdb=" N PHE C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.630A pdb=" N GLY D 162 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 163 " --> pdb=" O SER D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 171 through 180 removed outlier: 4.061A pdb=" N VAL D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 removed outlier: 3.547A pdb=" N ASP D 194 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 195 " --> pdb=" O LEU D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 195' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.803A pdb=" N LEU D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 removed outlier: 3.793A pdb=" N ILE D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 250 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 285 removed outlier: 4.319A pdb=" N ALA D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.999A pdb=" N LEU D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 321 removed outlier: 4.001A pdb=" N ARG D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 removed outlier: 3.587A pdb=" N GLU D 344 " --> pdb=" O ILE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 353 removed outlier: 4.055A pdb=" N ARG D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 375 Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.039A pdb=" N ALA D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 450 removed outlier: 4.011A pdb=" N PHE D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN D 448 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'E' and resid 159 through 163 removed outlier: 4.121A pdb=" N ASP E 163 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 180 removed outlier: 3.699A pdb=" N VAL E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.631A pdb=" N ASP E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 195' Processing helix chain 'E' and resid 198 through 207 Processing helix chain 'E' and resid 210 through 215 removed outlier: 4.049A pdb=" N LEU E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.847A pdb=" N ARG E 223 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER E 224 " --> pdb=" O GLY E 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 220 through 224' Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 269 through 285 removed outlier: 4.454A pdb=" N ALA E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 Processing helix chain 'E' and resid 309 through 322 removed outlier: 4.501A pdb=" N ASP E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 363 through 375 Processing helix chain 'E' and resid 385 through 393 removed outlier: 3.627A pdb=" N LEU E 389 " --> pdb=" O ASN E 385 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 416 removed outlier: 3.756A pdb=" N SER E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR E 416 " --> pdb=" O VAL E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 436 removed outlier: 3.796A pdb=" N ALA E 435 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 449 removed outlier: 3.847A pdb=" N PHE E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 469 Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.762A pdb=" N GLY F 162 " --> pdb=" O ASN F 159 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP F 163 " --> pdb=" O SER F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 173 through 180 Processing helix chain 'F' and resid 198 through 209 removed outlier: 3.797A pdb=" N LYS F 202 " --> pdb=" O MET F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 215 removed outlier: 4.093A pdb=" N LEU F 214 " --> pdb=" O THR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.823A pdb=" N SER F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 284 removed outlier: 3.827A pdb=" N VAL F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 removed outlier: 4.188A pdb=" N LEU F 297 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 323 removed outlier: 4.324A pdb=" N ASP F 322 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY F 323 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 375 removed outlier: 3.622A pdb=" N LYS F 369 " --> pdb=" O ASP F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 392 Processing helix chain 'F' and resid 399 through 412 Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.721A pdb=" N GLU F 431 " --> pdb=" O THR F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 450 removed outlier: 3.710A pdb=" N PHE F 443 " --> pdb=" O ARG F 439 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 450 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 467 removed outlier: 4.121A pdb=" N MET F 459 " --> pdb=" O GLY F 455 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 231 removed outlier: 3.510A pdb=" N ILE A 289 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 338 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 338 through 339 removed outlier: 6.737A pdb=" N LEU B 231 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 230 " --> pdb=" O ILE B 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 290 removed outlier: 6.847A pdb=" N ILE B 289 " --> pdb=" O LEU B 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.370A pdb=" N ILE C 289 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA C 338 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE C 291 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 228 through 232 removed outlier: 6.189A pdb=" N ILE D 289 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA D 338 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE D 291 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE D 255 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP D 292 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL D 257 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 254 through 257 removed outlier: 6.529A pdb=" N PHE E 255 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASP E 292 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL E 257 " --> pdb=" O ASP E 292 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 289 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA E 338 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE E 291 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 254 through 257 removed outlier: 7.011A pdb=" N PHE F 255 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASP F 292 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL F 257 " --> pdb=" O ASP F 292 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER F 287 " --> pdb=" O PHE F 334 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU F 336 " --> pdb=" O SER F 287 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE F 289 " --> pdb=" O LEU F 336 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ALA F 338 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE F 291 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU F 231 " --> pdb=" O THR F 339 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL F 230 " --> pdb=" O ILE F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 483 hydrogen bonds defined for protein. 1428 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: 1.92 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4490 1.34 - 1.46: 2008 1.46 - 1.57: 7544 1.57 - 1.69: 30 1.69 - 1.81: 109 Bond restraints: 14181 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.69e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.09e+01 ... (remaining 14176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.57: 19158 4.57 - 9.15: 97 9.15 - 13.72: 7 13.72 - 18.30: 5 18.30 - 22.87: 8 Bond angle restraints: 19275 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 117.00 22.87 1.00e+00 1.00e+00 5.23e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 119.04 20.83 1.00e+00 1.00e+00 4.34e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 116.23 20.60 1.00e+00 1.00e+00 4.24e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.37 19.50 1.00e+00 1.00e+00 3.80e+02 ... (remaining 19270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7690 18.00 - 35.99: 774 35.99 - 53.99: 119 53.99 - 71.99: 32 71.99 - 89.98: 12 Dihedral angle restraints: 8627 sinusoidal: 3258 harmonic: 5369 Sorted by residual: dihedral pdb=" CA THR C 296 " pdb=" C THR C 296 " pdb=" N LEU C 297 " pdb=" CA LEU C 297 " ideal model delta harmonic sigma weight residual 180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR B 284 " pdb=" C TYR B 284 " pdb=" N ALA B 285 " pdb=" CA ALA B 285 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASP C 295 " pdb=" C ASP C 295 " pdb=" N THR C 296 " pdb=" CA THR C 296 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 8624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1529 0.045 - 0.090: 534 0.090 - 0.135: 139 0.135 - 0.180: 29 0.180 - 0.225: 7 Chirality restraints: 2238 Sorted by residual: chirality pdb=" CB ILE F 441 " pdb=" CA ILE F 441 " pdb=" CG1 ILE F 441 " pdb=" CG2 ILE F 441 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL B 401 " pdb=" CA VAL B 401 " pdb=" CG1 VAL B 401 " pdb=" CG2 VAL B 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB ILE A 288 " pdb=" CA ILE A 288 " pdb=" CG1 ILE A 288 " pdb=" CG2 ILE A 288 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2235 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C 212 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 285 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 286 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 211 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO F 212 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 212 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 212 " -0.037 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 150 2.65 - 3.21: 11468 3.21 - 3.77: 19620 3.77 - 4.34: 25547 4.34 - 4.90: 43627 Nonbonded interactions: 100412 Sorted by model distance: nonbonded pdb=" O3B ATP C 501 " pdb="MG MG C 502 " model vdw 2.082 2.170 nonbonded pdb=" O3G ATP B 501 " pdb="MG MG B 502 " model vdw 2.117 2.170 nonbonded pdb=" OG1 THR C 240 " pdb="MG MG C 502 " model vdw 2.124 2.170 nonbonded pdb=" O2B ATP D 501 " pdb="MG MG D 502 " model vdw 2.126 2.170 nonbonded pdb=" O3G ATP D 501 " pdb="MG MG D 502 " model vdw 2.127 2.170 ... (remaining 100407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 21 \ 6 or (resid 217 and (name N or name CA or name C or name O or name CB )) or resi \ d 218 through 219 or (resid 220 and (name N or name CA or name C or name O or na \ me CB )) or resid 221 through 243 or (resid 244 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 245 through 248 or (resid 249 and ( \ name N or name CA or name C or name O or name CB )) or resid 250 through 259 or \ (resid 260 and (name N or name CA or name C or name O or name CB )) or resid 261 \ through 294 or (resid 295 and (name N or name CA or name C or name O or name CB \ )) or resid 296 through 303 or (resid 304 and (name N or name CA or name C or n \ ame O or name CB )) or resid 305 through 322 or resid 332 through 343 or (resid \ 344 and (name N or name CA or name C or name O or name CB )) or resid 345 throug \ h 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) or \ resid 362 or (resid 363 and (name N or name CA or name C or name O or name CB )) \ or resid 364 through 366 or (resid 367 and (name N or name CA or name C or name \ O or name CB )) or resid 368 or (resid 369 and (name N or name CA or name C or \ name O or name CB )) or resid 370 through 371 or (resid 372 through 373 and (nam \ e N or name CA or name C or name O or name CB )) or resid 374 or (resid 375 and \ (name N or name CA or name C or name O or name CB )) or resid 376 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 9 or (resid 380 and (name N or name CA or name C or name O or name CB )) or resi \ d 381 or (resid 382 through 385 and (name N or name CA or name C or name O or na \ me CB )) or resid 386 or (resid 387 through 394 and (name N or name CA or name C \ or name O or name CB )) or resid 395 through 399 or (resid 400 and (name N or n \ ame CA or name C or name O or name CB )) or resid 401 through 405 or (resid 406 \ and (name N or name CA or name C or name O or name CB )) or resid 407 through 41 \ 3 or (resid 414 and (name N or name CA or name C or name O or name CB )) or resi \ d 415 through 417 or (resid 418 through 419 and (name N or name CA or name C or \ name O or name CB )) or resid 420 or (resid 421 through 422 and (name N or name \ CA or name C or name O or name CB )) or resid 423 through 436 or (resid 437 and \ (name N or name CA or name C or name O or name CB )) or resid 438 or (resid 439 \ and (name N or name CA or name C or name O or name CB )) or resid 440 through 44 \ 3 or (resid 444 through 446 and (name N or name CA or name C or name O or name C \ B )) or resid 447 or (resid 448 through 449 and (name N or name CA or name C or \ name O or name CB )) or resid 450 through 457 or (resid 458 through 464 and (nam \ e N or name CA or name C or name O or name CB )) or resid 465 through 466 or (re \ sid 467 through 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 501)) selection = (chain 'B' and (resid 156 through 167 or (resid 168 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 182 or (resid 188 through 191 and (name N or name CA or name C or name \ O or name CB )) or resid 192 or (resid 193 through 194 and (name N or name CA o \ r name C or name O or name CB )) or resid 195 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 216 or (re \ sid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 th \ rough 222 or (resid 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 226 or (resid 227 through 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 243 or (resid 244 and (nam \ e N or name CA or name C or name O or name CB or name CG )) or resid 245 through \ 248 or (resid 249 and (name N or name CA or name C or name O or name CB )) or r \ esid 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 268 or (resid 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 or (resid 271 and (name N or name CA or name C or n \ ame O or name CB )) or resid 272 through 278 or (resid 279 and (name N or name C \ A or name C or name O or name CB )) or resid 280 through 294 or (resid 295 and ( \ name N or name CA or name C or name O or name CB )) or resid 296 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 \ or (resid 306 and (name N or name CA or name C or name O or name CB )) or resid \ 307 or (resid 308 through 309 and (name N or name CA or name C or name O or nam \ e CB )) or resid 310 through 314 or (resid 315 through 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 318 or (resid 319 and ( \ name N or name CA or name C or name O or name CB )) or resid 320 through 322 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 333 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 or (resid 346 through 348 and (name N or name CA or name C or n \ ame O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 through 360 or (res \ id 361 and (name N or name CA or name C or name O or name CB )) or resid 362 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 through 387 or \ (resid 388 through 394 and (name N or name CA or name C or name O or name CB )) \ or resid 395 through 399 or (resid 400 and (name N or name CA or name C or name \ O or name CB )) or resid 401 through 405 or (resid 406 and (name N or name CA or \ name C or name O or name CB )) or resid 407 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 417 or (res \ id 418 through 419 and (name N or name CA or name C or name O or name CB )) or r \ esid 420 or (resid 421 through 422 and (name N or name CA or name C or name O or \ name CB )) or resid 423 through 435 or (resid 436 through 437 and (name N or na \ me CA or name C or name O or name CB )) or resid 438 through 443 or (resid 444 t \ hrough 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ or (resid 448 through 449 and (name N or name CA or name C or name O or name CB \ )) or resid 450 through 452 or (resid 453 through 454 and (name N or name CA or \ name C or name O or name CB )) or resid 455 through 457 or (resid 458 through 4 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 465 through \ 466 or (resid 467 through 468 and (name N or name CA or name C or name O or nam \ e CB )) or resid 469 through 471 or (resid 472 and (name N or name CA or name C \ or name O or name CB )) or resid 501)) selection = (chain 'C' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 through 193 or (resid 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 222 or (resid 223 and (name N or name CA or name C or name O or na \ me CB )) or resid 224 through 229 or (resid 230 and (name N or name CA or name C \ or name O or name CB )) or resid 231 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 245 through 248 or \ (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 \ through 258 or (resid 259 through 260 and (name N or name CA or name C or name \ O or name CB )) or resid 261 through 268 or (resid 269 and (name N or name CA or \ name C or name O or name CB )) or resid 270 or (resid 271 and (name N or name C \ A or name C or name O or name CB )) or resid 272 through 278 or (resid 279 and ( \ name N or name CA or name C or name O or name CB )) or resid 280 through 294 or \ (resid 295 and (name N or name CA or name C or name O or name CB )) or resid 296 \ through 303 or (resid 304 and (name N or name CA or name C or name O or name CB \ )) or resid 305 or (resid 306 and (name N or name CA or name C or name O or nam \ e CB )) or resid 307 or (resid 308 through 309 and (name N or name CA or name C \ or name O or name CB )) or resid 310 through 314 or (resid 315 through 316 and ( \ name N or name CA or name C or name O or name CB )) or resid 317 through 318 or \ (resid 319 and (name N or name CA or name C or name O or name CB )) or resid 320 \ through 322 or (resid 332 and (name N or name CA or name C or name O or name CB \ )) or resid 333 through 343 or (resid 344 and (name N or name CA or name C or n \ ame O or name CB )) or resid 345 or (resid 346 through 348 and (name N or name C \ A or name C or name O or name CB )) or resid 349 through 354 or (resid 355 throu \ gh 356 and (name N or name CA or name C or name O or name CB )) or resid 357 thr \ ough 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 through 366 or (resid 367 and (name N or name CA or name C or name \ O or name CB )) or resid 368 or (resid 369 and (name N or name CA or name C or n \ ame O or name CB )) or resid 370 through 371 or (resid 372 through 373 and (name \ N or name CA or name C or name O or name CB )) or resid 374 or (resid 375 and ( \ name N or name CA or name C or name O or name CB )) or resid 376 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 and (name N or name CA or name C or name O or name CB )) or resid \ 381 through 382 or (resid 383 through 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 387 or (resid 388 through 394 and (name \ N or name CA or name C or name O or name CB )) or resid 395 through 405 or (res \ id 406 and (name N or name CA or name C or name O or name CB )) or resid 407 thr \ ough 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 420 or (resid 421 through 422 and (name N or name CA or nam \ e C or name O or name CB )) or resid 423 through 435 or (resid 436 through 437 a \ nd (name N or name CA or name C or name O or name CB )) or resid 438 or (resid 4 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 440 through \ 443 or (resid 444 through 446 and (name N or name CA or name C or name O or nam \ e CB )) or resid 447 or (resid 448 through 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 through 452 or (resid 453 through 454 and ( \ name N or name CA or name C or name O or name CB )) or resid 455 through 456 or \ (resid 457 through 464 and (name N or name CA or name C or name O or name CB )) \ or resid 465 through 467 or (resid 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 through 501)) selection = (chain 'D' and (resid 156 through 175 or (resid 176 through 177 and (name N or n \ ame CA or name C or name O or name CB )) or resid 178 through 189 or (resid 190 \ through 191 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 2 or (resid 193 through 194 and (name N or name CA or name C or name O or name C \ B )) or resid 195 through 199 or (resid 200 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 219 or (resid 220 and (name N or name \ CA or name C or name O or name CB )) or resid 221 through 222 or (resid 223 and \ (name N or name CA or name C or name O or name CB )) or resid 224 through 229 or \ (resid 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 243 or (resid 244 and (name N or name CA or name C or name O or name C \ B or name CG )) or resid 245 through 248 or (resid 249 and (name N or name CA or \ name C or name O or name CB )) or resid 250 or (resid 251 and (name N or name C \ A or name C or name O or name CB )) or resid 252 through 258 or (resid 259 throu \ gh 260 and (name N or name CA or name C or name O or name CB )) or resid 261 thr \ ough 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) \ or resid 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C or n \ ame O or name CB )) or resid 280 through 294 or (resid 295 and (name N or name C \ A or name C or name O or name CB )) or resid 296 through 303 or (resid 304 and ( \ name N or name CA or name C or name O or name CB )) or resid 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 or (resid 3 \ 08 through 309 and (name N or name CA or name C or name O or name CB )) or resid \ 310 through 314 or (resid 315 through 316 and (name N or name CA or name C or n \ ame O or name CB )) or resid 317 through 318 or (resid 319 and (name N or name C \ A or name C or name O or name CB )) or resid 320 through 322 or (resid 332 and ( \ name N or name CA or name C or name O or name CB )) or resid 333 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 345 \ through 346 or (resid 347 through 348 and (name N or name CA or name C or name \ O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name N o \ r name CA or name C or name O or name CB )) or resid 357 through 360 or (resid 3 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 362 or (res \ id 363 and (name N or name CA or name C or name O or name CB )) or resid 364 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 or (resid 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 381 or (resid 3 \ 82 through 385 and (name N or name CA or name C or name O or name CB )) or resid \ 386 or (resid 387 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 or (resid 421 through 422 and (name N or name CA or name C or n \ ame O or name CB )) or resid 423 through 436 or (resid 437 and (name N or name C \ A or name C or name O or name CB )) or resid 438 or (resid 439 and (name N or na \ me CA or name C or name O or name CB )) or resid 440 through 447 or (resid 448 t \ hrough 449 and (name N or name CA or name C or name O or name CB )) or resid 450 \ through 457 or (resid 458 through 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 467 or (resid 468 and (name N or name CA or \ name C or name O or name CB )) or resid 469 through 501)) selection = (chain 'E' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 226 or (resid 227 \ through 228 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 9 or (resid 230 and (name N or name CA or name C or name O or name CB )) or resi \ d 231 through 243 or (resid 244 and (name N or name CA or name C or name O or na \ me CB or name CG )) or resid 245 through 248 or (resid 249 and (name N or name C \ A or name C or name O or name CB )) or resid 250 or (resid 251 and (name N or na \ me CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 t \ hrough 260 and (name N or name CA or name C or name O or name CB )) or resid 261 \ through 268 or (resid 269 and (name N or name CA or name C or name O or name CB \ )) or resid 270 or (resid 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 294 or (resid 295 and (name N or na \ me CA or name C or name O or name CB )) or resid 296 through 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 through 314 \ or (resid 315 through 316 and (name N or name CA or name C or name O or name CB \ )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C or n \ ame O or name CB )) or resid 320 through 322 or (resid 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 343 or (resid 344 and ( \ name N or name CA or name C or name O or name CB )) or resid 345 through 346 or \ (resid 347 through 348 and (name N or name CA or name C or name O or name CB )) \ or resid 349 through 354 or (resid 355 through 356 and (name N or name CA or nam \ e C or name O or name CB )) or resid 357 through 360 or (resid 361 and (name N o \ r name CA or name C or name O or name CB )) or resid 362 through 366 or (resid 3 \ 67 and (name N or name CA or name C or name O or name CB )) or resid 368 or (res \ id 369 and (name N or name CA or name C or name O or name CB )) or resid 370 thr \ ough 371 or (resid 372 through 373 and (name N or name CA or name C or name O or \ name CB )) or resid 374 or (resid 375 and (name N or name CA or name C or name \ O or name CB )) or resid 376 through 377 or (resid 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 through 383 or (resid 384 through 3 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 386 through \ 388 or (resid 389 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 through 436 or (resid 437 and (name N or name CA or name C or n \ ame O or name CB )) or resid 438 or (resid 439 and (name N or name CA or name C \ or name O or name CB )) or resid 440 through 452 or (resid 453 through 454 and ( \ name N or name CA or name C or name O or name CB )) or resid 455 through 457 or \ (resid 458 through 464 and (name N or name CA or name C or name O or name CB )) \ or resid 465 through 467 or (resid 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 through 501)) selection = (chain 'F' and (resid 156 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 192 or (resid 193 through 194 and (name N or name CA or name C or name \ O or name CB )) or resid 195 through 219 or (resid 220 and (name N or name CA o \ r name C or name O or name CB )) or resid 221 through 222 or (resid 223 and (nam \ e N or name CA or name C or name O or name CB )) or resid 224 through 226 or (re \ sid 227 through 228 and (name N or name CA or name C or name O or name CB )) or \ resid 229 or (resid 230 and (name N or name CA or name C or name O or name CB )) \ or resid 231 through 258 or (resid 259 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 270 or (resid 271 and (name N \ or name CA or name C or name O or name CB )) or resid 272 through 303 or (resid \ 304 and (name N or name CA or name C or name O or name CB )) or resid 305 throug \ h 314 or (resid 315 through 316 and (name N or name CA or name C or name O or na \ me CB )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 322 or resid 332 through 345 or (r \ esid 346 through 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 through 354 or (resid 355 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 through 399 or (resid 400 and (name N or \ name CA or name C or name O or name CB )) or resid 401 through 417 or (resid 418 \ through 419 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 20 or (resid 421 through 422 and (name N or name CA or name C or name O or name \ CB )) or resid 423 through 443 or (resid 444 through 446 and (name N or name CA \ or name C or name O or name CB )) or resid 447 or (resid 448 through 449 and (na \ me N or name CA or name C or name O or name CB )) or resid 450 through 452 or (r \ esid 453 through 454 and (name N or name CA or name C or name O or name CB )) or \ resid 455 through 501)) } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.840 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 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 : 0.006 0.083 14181 Z= 0.364 Angle : 1.002 22.873 19275 Z= 0.710 Chirality : 0.050 0.225 2238 Planarity : 0.007 0.080 2448 Dihedral : 14.945 89.984 5135 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer: Outliers : 0.23 % Allowed : 7.96 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.14), residues: 1829 helix: -3.33 (0.11), residues: 802 sheet: -2.68 (0.38), residues: 170 loop : -3.32 (0.16), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 352 TYR 0.011 0.001 TYR C 173 PHE 0.017 0.002 PHE A 254 TRP 0.012 0.001 TRP F 343 HIS 0.007 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00572 (14181) covalent geometry : angle 1.00179 (19275) hydrogen bonds : bond 0.15174 ( 483) hydrogen bonds : angle 5.91987 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 179 ARG cc_start: 0.6990 (ttt-90) cc_final: 0.6633 (ttm-80) REVERT: D 190 MET cc_start: 0.6256 (ptp) cc_final: 0.5993 (ptp) REVERT: E 194 ASP cc_start: 0.9055 (t0) cc_final: 0.8802 (t0) REVERT: E 227 LYS cc_start: 0.8457 (ptmt) cc_final: 0.7959 (pttm) REVERT: E 246 ILE cc_start: 0.8670 (tp) cc_final: 0.8338 (tp) REVERT: E 265 LYS cc_start: 0.7899 (tttt) cc_final: 0.7671 (tttm) REVERT: F 346 ASP cc_start: 0.8858 (t0) cc_final: 0.8625 (m-30) outliers start: 3 outliers final: 0 residues processed: 206 average time/residue: 0.1050 time to fit residues: 32.7271 Evaluate side-chains 147 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 307 HIS A 340 ASN A 440 ASN B 300 GLN E 220 GLN E 320 GLN E 411 ASN F 176 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111325 restraints weight = 21247.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113194 restraints weight = 13576.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114287 restraints weight = 8809.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114568 restraints weight = 7508.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114682 restraints weight = 6999.415| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14181 Z= 0.103 Angle : 0.501 10.037 19275 Z= 0.264 Chirality : 0.039 0.143 2238 Planarity : 0.005 0.054 2448 Dihedral : 8.752 83.675 2193 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.65 % Allowed : 12.62 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.17), residues: 1829 helix: -1.47 (0.17), residues: 812 sheet: -2.23 (0.37), residues: 182 loop : -2.93 (0.17), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 352 TYR 0.013 0.001 TYR B 173 PHE 0.023 0.001 PHE E 218 TRP 0.025 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00233 (14181) covalent geometry : angle 0.50097 (19275) hydrogen bonds : bond 0.03593 ( 483) hydrogen bonds : angle 4.19188 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.435 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 190 MET cc_start: 0.6978 (tpp) cc_final: 0.6762 (tpp) REVERT: B 179 ARG cc_start: 0.7683 (ttt-90) cc_final: 0.6943 (ttm-80) REVERT: D 461 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7817 (mtpp) REVERT: E 246 ILE cc_start: 0.9233 (tp) cc_final: 0.8859 (tp) outliers start: 22 outliers final: 10 residues processed: 172 average time/residue: 0.0981 time to fit residues: 26.1371 Evaluate side-chains 152 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 72 optimal weight: 0.9990 chunk 178 optimal weight: 0.0010 chunk 155 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN B 293 GLN D 340 ASN D 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099577 restraints weight = 21881.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102020 restraints weight = 12770.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104249 restraints weight = 7843.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103971 restraints weight = 6395.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104268 restraints weight = 6345.462| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14181 Z= 0.088 Angle : 0.454 9.352 19275 Z= 0.236 Chirality : 0.038 0.141 2238 Planarity : 0.004 0.049 2448 Dihedral : 8.086 86.579 2193 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.03 % Allowed : 14.80 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.18), residues: 1829 helix: -0.56 (0.18), residues: 802 sheet: -1.93 (0.37), residues: 184 loop : -2.62 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 406 TYR 0.005 0.001 TYR E 173 PHE 0.014 0.001 PHE B 353 TRP 0.026 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00200 (14181) covalent geometry : angle 0.45378 (19275) hydrogen bonds : bond 0.03008 ( 483) hydrogen bonds : angle 3.74255 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.570 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 179 ARG cc_start: 0.7399 (ttt-90) cc_final: 0.6397 (ttm-80) REVERT: B 242 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7294 (mt) REVERT: D 459 MET cc_start: 0.7557 (tmm) cc_final: 0.7306 (tmm) REVERT: D 461 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7956 (mtpp) REVERT: E 194 ASP cc_start: 0.8565 (t0) cc_final: 0.8135 (t0) REVERT: E 246 ILE cc_start: 0.8696 (tp) cc_final: 0.8362 (tp) REVERT: F 292 ASP cc_start: 0.8271 (t70) cc_final: 0.7337 (p0) REVERT: F 293 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7758 (mm-40) outliers start: 27 outliers final: 11 residues processed: 177 average time/residue: 0.0896 time to fit residues: 25.6262 Evaluate side-chains 156 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 73 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 116 optimal weight: 0.0770 chunk 135 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN D 340 ASN F 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098793 restraints weight = 21841.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101453 restraints weight = 13022.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103241 restraints weight = 7786.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103095 restraints weight = 6715.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103515 restraints weight = 6627.653| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14181 Z= 0.098 Angle : 0.464 8.765 19275 Z= 0.236 Chirality : 0.039 0.168 2238 Planarity : 0.003 0.046 2448 Dihedral : 7.864 86.874 2193 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.10 % Allowed : 16.15 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1829 helix: -0.14 (0.19), residues: 797 sheet: -1.70 (0.37), residues: 183 loop : -2.40 (0.18), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 406 TYR 0.006 0.001 TYR C 284 PHE 0.016 0.001 PHE F 358 TRP 0.029 0.001 TRP F 343 HIS 0.003 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00233 (14181) covalent geometry : angle 0.46400 (19275) hydrogen bonds : bond 0.03065 ( 483) hydrogen bonds : angle 3.62804 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.546 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 173 TYR cc_start: 0.7966 (p90) cc_final: 0.7617 (p90) REVERT: A 190 MET cc_start: 0.6320 (tpp) cc_final: 0.5816 (tpp) REVERT: B 179 ARG cc_start: 0.7468 (ttt-90) cc_final: 0.6491 (ttm-80) REVERT: B 242 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7292 (mt) REVERT: E 194 ASP cc_start: 0.8584 (t0) cc_final: 0.8141 (t0) REVERT: E 246 ILE cc_start: 0.8699 (tp) cc_final: 0.8370 (tp) REVERT: E 249 GLU cc_start: 0.8265 (tt0) cc_final: 0.7941 (tt0) REVERT: F 346 ASP cc_start: 0.8825 (t0) cc_final: 0.8287 (m-30) REVERT: F 400 ASP cc_start: 0.6713 (m-30) cc_final: 0.6422 (m-30) outliers start: 28 outliers final: 15 residues processed: 175 average time/residue: 0.0941 time to fit residues: 26.1597 Evaluate side-chains 156 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 77 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 411 ASN D 340 ASN F 176 GLN F 448 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099739 restraints weight = 22027.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103022 restraints weight = 13129.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103980 restraints weight = 8009.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105204 restraints weight = 6310.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105310 restraints weight = 5700.785| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14181 Z= 0.087 Angle : 0.453 8.474 19275 Z= 0.231 Chirality : 0.038 0.135 2238 Planarity : 0.003 0.047 2448 Dihedral : 7.689 88.419 2193 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.18 % Allowed : 16.98 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1829 helix: 0.17 (0.19), residues: 798 sheet: -1.50 (0.37), residues: 183 loop : -2.24 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 406 TYR 0.006 0.000 TYR E 173 PHE 0.025 0.001 PHE E 218 TRP 0.031 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00201 (14181) covalent geometry : angle 0.45301 (19275) hydrogen bonds : bond 0.02776 ( 483) hydrogen bonds : angle 3.49943 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.428 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 173 TYR cc_start: 0.7877 (p90) cc_final: 0.7574 (p90) REVERT: A 203 GLN cc_start: 0.7863 (tt0) cc_final: 0.6997 (tp-100) REVERT: B 179 ARG cc_start: 0.7405 (ttt-90) cc_final: 0.6436 (ttm-80) REVERT: C 430 MET cc_start: 0.7833 (mmm) cc_final: 0.7104 (mmm) REVERT: E 194 ASP cc_start: 0.8652 (t0) cc_final: 0.8300 (t0) REVERT: E 246 ILE cc_start: 0.8699 (tp) cc_final: 0.8392 (tp) REVERT: E 249 GLU cc_start: 0.8294 (tt0) cc_final: 0.7961 (tt0) REVERT: E 359 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8606 (mm) REVERT: F 292 ASP cc_start: 0.8284 (t70) cc_final: 0.7355 (p0) REVERT: F 346 ASP cc_start: 0.8824 (t0) cc_final: 0.8311 (m-30) outliers start: 29 outliers final: 16 residues processed: 175 average time/residue: 0.0887 time to fit residues: 24.9083 Evaluate side-chains 158 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 163 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 108 optimal weight: 0.0270 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 320 GLN D 340 ASN D 411 ASN D 440 ASN F 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099231 restraints weight = 21785.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102306 restraints weight = 13043.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103196 restraints weight = 8077.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104630 restraints weight = 6416.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104666 restraints weight = 5623.673| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14181 Z= 0.097 Angle : 0.460 10.803 19275 Z= 0.233 Chirality : 0.039 0.140 2238 Planarity : 0.003 0.048 2448 Dihedral : 7.614 88.589 2193 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.33 % Allowed : 17.88 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.19), residues: 1829 helix: 0.37 (0.19), residues: 799 sheet: -1.36 (0.38), residues: 183 loop : -2.07 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 406 TYR 0.006 0.001 TYR C 284 PHE 0.017 0.001 PHE F 358 TRP 0.030 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00229 (14181) covalent geometry : angle 0.45951 (19275) hydrogen bonds : bond 0.02926 ( 483) hydrogen bonds : angle 3.48740 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.476 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 173 TYR cc_start: 0.7901 (p90) cc_final: 0.7585 (p90) REVERT: A 190 MET cc_start: 0.6287 (tpp) cc_final: 0.5797 (tpp) REVERT: A 203 GLN cc_start: 0.7852 (tt0) cc_final: 0.7027 (tp-100) REVERT: B 179 ARG cc_start: 0.7551 (ttt-90) cc_final: 0.6490 (ttm-80) REVERT: C 430 MET cc_start: 0.7853 (mmm) cc_final: 0.7023 (mmm) REVERT: E 194 ASP cc_start: 0.8638 (t0) cc_final: 0.8290 (t0) REVERT: E 246 ILE cc_start: 0.8764 (tp) cc_final: 0.8452 (tp) REVERT: E 249 GLU cc_start: 0.8281 (tt0) cc_final: 0.7947 (tt0) REVERT: E 359 ILE cc_start: 0.8819 (mm) cc_final: 0.8522 (mm) REVERT: F 156 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8020 (mt) REVERT: F 292 ASP cc_start: 0.8314 (t70) cc_final: 0.7405 (p0) REVERT: F 346 ASP cc_start: 0.8802 (t0) cc_final: 0.8256 (m-30) outliers start: 31 outliers final: 19 residues processed: 169 average time/residue: 0.0914 time to fit residues: 24.9255 Evaluate side-chains 162 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 33 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 411 ASN D 340 ASN F 176 GLN F 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.095362 restraints weight = 21951.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098111 restraints weight = 13629.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099325 restraints weight = 8339.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099444 restraints weight = 6973.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099730 restraints weight = 6588.352| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14181 Z= 0.160 Angle : 0.516 10.911 19275 Z= 0.263 Chirality : 0.041 0.138 2238 Planarity : 0.004 0.050 2448 Dihedral : 8.014 84.384 2193 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.48 % Allowed : 18.18 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.19), residues: 1829 helix: 0.36 (0.19), residues: 790 sheet: -1.50 (0.37), residues: 191 loop : -2.04 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 406 TYR 0.013 0.001 TYR C 284 PHE 0.012 0.001 PHE B 353 TRP 0.032 0.001 TRP F 343 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00394 (14181) covalent geometry : angle 0.51595 (19275) hydrogen bonds : bond 0.03832 ( 483) hydrogen bonds : angle 3.75590 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.6302 (tpp) cc_final: 0.5836 (tpp) REVERT: A 203 GLN cc_start: 0.7894 (tt0) cc_final: 0.7039 (tp-100) REVERT: B 179 ARG cc_start: 0.7665 (ttt-90) cc_final: 0.6655 (ttp-170) REVERT: C 430 MET cc_start: 0.7897 (mmm) cc_final: 0.7069 (mmm) REVERT: E 194 ASP cc_start: 0.8617 (t0) cc_final: 0.8271 (t0) REVERT: E 246 ILE cc_start: 0.8841 (tp) cc_final: 0.8518 (tp) REVERT: E 249 GLU cc_start: 0.8291 (tt0) cc_final: 0.7936 (tt0) REVERT: E 359 ILE cc_start: 0.8945 (mm) cc_final: 0.8678 (mm) REVERT: F 292 ASP cc_start: 0.8327 (t70) cc_final: 0.7460 (p0) REVERT: F 293 GLN cc_start: 0.8491 (mm-40) cc_final: 0.7942 (mm-40) REVERT: F 346 ASP cc_start: 0.8800 (t0) cc_final: 0.8254 (m-30) outliers start: 33 outliers final: 19 residues processed: 164 average time/residue: 0.0878 time to fit residues: 23.2091 Evaluate side-chains 159 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 0.0870 chunk 152 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 411 ASN D 340 ASN D 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096240 restraints weight = 21777.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098243 restraints weight = 13143.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099867 restraints weight = 8382.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099978 restraints weight = 7135.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100500 restraints weight = 6963.009| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14181 Z= 0.133 Angle : 0.494 10.815 19275 Z= 0.251 Chirality : 0.040 0.141 2238 Planarity : 0.003 0.049 2448 Dihedral : 7.959 85.051 2193 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.33 % Allowed : 18.56 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1829 helix: 0.45 (0.19), residues: 790 sheet: -1.48 (0.37), residues: 186 loop : -1.96 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 406 TYR 0.015 0.001 TYR A 173 PHE 0.011 0.001 PHE B 353 TRP 0.034 0.001 TRP F 343 HIS 0.003 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00325 (14181) covalent geometry : angle 0.49432 (19275) hydrogen bonds : bond 0.03484 ( 483) hydrogen bonds : angle 3.67330 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.552 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 190 MET cc_start: 0.6500 (tpp) cc_final: 0.6012 (tpp) REVERT: A 203 GLN cc_start: 0.7866 (tt0) cc_final: 0.7020 (tp-100) REVERT: B 179 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.6599 (ttp-170) REVERT: C 430 MET cc_start: 0.7861 (mmm) cc_final: 0.6977 (mmm) REVERT: C 436 GLU cc_start: 0.7374 (tp30) cc_final: 0.6971 (tp30) REVERT: E 194 ASP cc_start: 0.8667 (t0) cc_final: 0.8345 (t0) REVERT: E 246 ILE cc_start: 0.8788 (tp) cc_final: 0.8450 (tp) REVERT: E 249 GLU cc_start: 0.8292 (tt0) cc_final: 0.7934 (tt0) REVERT: E 359 ILE cc_start: 0.8915 (mm) cc_final: 0.8628 (mm) REVERT: E 375 MET cc_start: 0.8518 (tpp) cc_final: 0.8242 (tpp) REVERT: F 156 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7994 (mt) REVERT: F 292 ASP cc_start: 0.8337 (t70) cc_final: 0.7457 (p0) REVERT: F 293 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7929 (mm-40) REVERT: F 346 ASP cc_start: 0.8799 (t0) cc_final: 0.8246 (m-30) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.0858 time to fit residues: 23.1074 Evaluate side-chains 165 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 132 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 174 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 100 optimal weight: 0.0770 chunk 137 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 150 optimal weight: 0.0370 chunk 80 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100372 restraints weight = 21767.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101997 restraints weight = 13205.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103787 restraints weight = 8379.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103761 restraints weight = 6954.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104155 restraints weight = 6795.523| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14181 Z= 0.084 Angle : 0.455 10.516 19275 Z= 0.229 Chirality : 0.039 0.140 2238 Planarity : 0.003 0.045 2448 Dihedral : 7.551 88.994 2193 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.58 % Allowed : 19.31 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.20), residues: 1829 helix: 0.74 (0.19), residues: 791 sheet: -1.32 (0.38), residues: 183 loop : -1.85 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 406 TYR 0.006 0.000 TYR E 173 PHE 0.013 0.001 PHE E 218 TRP 0.033 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00192 (14181) covalent geometry : angle 0.45531 (19275) hydrogen bonds : bond 0.02588 ( 483) hydrogen bonds : angle 3.39872 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.391 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. REVERT: A 173 TYR cc_start: 0.8150 (p90) cc_final: 0.7700 (p90) REVERT: A 190 MET cc_start: 0.6361 (tpp) cc_final: 0.5896 (tpp) REVERT: A 203 GLN cc_start: 0.7832 (tt0) cc_final: 0.7028 (tp-100) REVERT: B 179 ARG cc_start: 0.7594 (ttt-90) cc_final: 0.6540 (ttm-80) REVERT: C 430 MET cc_start: 0.7773 (mmm) cc_final: 0.6825 (mmm) REVERT: C 436 GLU cc_start: 0.7362 (tp30) cc_final: 0.6952 (tp30) REVERT: E 194 ASP cc_start: 0.8626 (t0) cc_final: 0.8373 (t0) REVERT: E 246 ILE cc_start: 0.8779 (tp) cc_final: 0.8444 (tp) REVERT: E 249 GLU cc_start: 0.8262 (tt0) cc_final: 0.7934 (tt0) REVERT: E 359 ILE cc_start: 0.8895 (mm) cc_final: 0.8618 (mm) REVERT: E 375 MET cc_start: 0.8392 (tpp) cc_final: 0.8103 (tpp) REVERT: F 156 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7935 (mt) REVERT: F 292 ASP cc_start: 0.8264 (t70) cc_final: 0.7442 (p0) REVERT: F 293 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7897 (mm-40) REVERT: F 346 ASP cc_start: 0.8744 (t0) cc_final: 0.8219 (m-30) outliers start: 21 outliers final: 17 residues processed: 173 average time/residue: 0.0913 time to fit residues: 25.1769 Evaluate side-chains 160 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 117 optimal weight: 6.9990 chunk 179 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 54 optimal weight: 0.0970 chunk 90 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 104 optimal weight: 0.0570 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS D 340 ASN E 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101713 restraints weight = 21579.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103897 restraints weight = 12862.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105640 restraints weight = 8037.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105771 restraints weight = 6741.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106313 restraints weight = 6649.424| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14181 Z= 0.080 Angle : 0.451 10.553 19275 Z= 0.226 Chirality : 0.038 0.134 2238 Planarity : 0.003 0.046 2448 Dihedral : 7.362 88.595 2193 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.43 % Allowed : 19.76 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1829 helix: 0.92 (0.20), residues: 794 sheet: -1.06 (0.38), residues: 185 loop : -1.76 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 406 TYR 0.006 0.000 TYR E 173 PHE 0.020 0.001 PHE F 358 TRP 0.036 0.001 TRP F 343 HIS 0.004 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00183 (14181) covalent geometry : angle 0.45136 (19275) hydrogen bonds : bond 0.02535 ( 483) hydrogen bonds : angle 3.30454 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.545 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. REVERT: A 173 TYR cc_start: 0.8153 (p90) cc_final: 0.7691 (p90) REVERT: A 190 MET cc_start: 0.6317 (tpp) cc_final: 0.5817 (tpp) REVERT: A 203 GLN cc_start: 0.7792 (tt0) cc_final: 0.7035 (tp-100) REVERT: B 179 ARG cc_start: 0.7573 (ttt-90) cc_final: 0.6537 (ttm-80) REVERT: B 307 HIS cc_start: 0.8304 (t-90) cc_final: 0.7759 (t-90) REVERT: C 430 MET cc_start: 0.7795 (mmm) cc_final: 0.6865 (mmm) REVERT: C 436 GLU cc_start: 0.7387 (tp30) cc_final: 0.6921 (tp30) REVERT: D 459 MET cc_start: 0.7704 (tmm) cc_final: 0.7405 (tmm) REVERT: E 194 ASP cc_start: 0.8514 (t0) cc_final: 0.8111 (t0) REVERT: E 246 ILE cc_start: 0.8768 (tp) cc_final: 0.8439 (tp) REVERT: E 249 GLU cc_start: 0.8245 (tt0) cc_final: 0.7918 (tt0) REVERT: E 359 ILE cc_start: 0.8883 (mm) cc_final: 0.8600 (mm) REVERT: E 375 MET cc_start: 0.8412 (tpp) cc_final: 0.8121 (tpp) REVERT: F 156 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7945 (mt) REVERT: F 292 ASP cc_start: 0.8242 (t70) cc_final: 0.7413 (p0) REVERT: F 293 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7913 (mm-40) REVERT: F 346 ASP cc_start: 0.8723 (t0) cc_final: 0.8187 (m-30) outliers start: 19 outliers final: 15 residues processed: 163 average time/residue: 0.0899 time to fit residues: 23.5988 Evaluate side-chains 164 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 153 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 0.0370 chunk 97 optimal weight: 0.0870 chunk 89 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 overall best weight: 3.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS C 411 ASN D 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.094434 restraints weight = 22064.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.095867 restraints weight = 13669.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097713 restraints weight = 8856.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097709 restraints weight = 7236.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098091 restraints weight = 7064.386| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14181 Z= 0.210 Angle : 0.574 10.651 19275 Z= 0.291 Chirality : 0.043 0.147 2238 Planarity : 0.004 0.054 2448 Dihedral : 8.235 82.385 2193 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.65 % Allowed : 19.46 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1829 helix: 0.56 (0.19), residues: 790 sheet: -1.35 (0.37), residues: 194 loop : -1.83 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 406 TYR 0.016 0.001 TYR C 284 PHE 0.015 0.002 PHE E 218 TRP 0.037 0.001 TRP F 343 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00515 (14181) covalent geometry : angle 0.57363 (19275) hydrogen bonds : bond 0.04470 ( 483) hydrogen bonds : angle 3.91719 ( 1428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1966.55 seconds wall clock time: 34 minutes 37.30 seconds (2077.30 seconds total)