Starting phenix.real_space_refine on Sat Jun 21 01:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh1_34748/06_2025/8hh1_34748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh1_34748/06_2025/8hh1_34748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh1_34748/06_2025/8hh1_34748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh1_34748/06_2025/8hh1_34748.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh1_34748/06_2025/8hh1_34748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh1_34748/06_2025/8hh1_34748.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24280 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.56, per 1000 atoms: 0.60 Number of scatterers: 24280 At special positions: 0 Unit cell: (124.96, 127.6, 155.76, 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 77 16.00 P 19 15.00 Mg 5 11.99 O 4673 8.00 N 4219 7.00 C 15287 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: 6.26 Conformation dependent library (CDL) restraints added in 3.1 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 19 sheets defined 48.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.566A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.603A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.556A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.807A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 4.047A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.827A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 406 through 421 removed outlier: 3.586A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.634A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.647A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.674A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.576A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.855A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.026A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.639A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.600A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.610A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.607A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.595A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.746A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.646A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.562A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.954A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.687A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 381 through 395 Processing helix chain 'C' and resid 403 through 420 removed outlier: 3.702A pdb=" N ALA C 411 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.630A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 478 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 243 removed outlier: 4.785A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.840A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.619A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 3.596A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.658A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.600A pdb=" N LYS D 467 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.544A pdb=" N LEU E 128 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 5.022A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.673A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.631A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 355 through 360 removed outlier: 3.538A pdb=" N GLY E 360 " --> pdb=" O PRO E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 380 Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.646A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.572A pdb=" N PHE E 453 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.972A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.590A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 180 removed outlier: 4.595A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 243 removed outlier: 4.906A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.935A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.635A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 325 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 388 removed outlier: 4.450A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.669A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.800A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 4.030A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.550A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.954A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.551A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 162 removed outlier: 4.167A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 205 removed outlier: 3.943A pdb=" N GLU G 204 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE G 205 " --> pdb=" O VAL G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 283 removed outlier: 4.012A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.530A pdb=" N ASP G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.004A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA E 29 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN E 28 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.408A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.170A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.098A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.641A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.222A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA D 29 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN D 28 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.968A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.327A pdb=" N VAL C 108 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB2, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.289A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.155A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.427A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.406A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.685A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY F 216 " --> pdb=" O GLY F 187 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.196A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 133 through 137 removed outlier: 6.584A pdb=" N VAL G 133 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE G 115 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU G 135 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) 1186 hydrogen bonds defined for protein. 3372 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: 9.37 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4187 1.32 - 1.44: 5900 1.44 - 1.56: 14416 1.56 - 1.68: 31 1.68 - 1.81: 154 Bond restraints: 24688 Sorted by residual: bond pdb=" C LYS B 377 " pdb=" O LYS B 377 " ideal model delta sigma weight residual 1.235 1.406 -0.171 1.26e-02 6.30e+03 1.84e+02 bond pdb=" C ARG B 383 " pdb=" O ARG B 383 " ideal model delta sigma weight residual 1.236 1.321 -0.084 1.15e-02 7.56e+03 5.35e+01 bond pdb=" C GLY B 380 " pdb=" O GLY B 380 " ideal model delta sigma weight residual 1.234 1.319 -0.086 1.20e-02 6.94e+03 5.11e+01 bond pdb=" CA TYR F 341 " pdb=" C TYR F 341 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.26e-02 6.30e+03 2.17e+01 bond pdb=" C LEU G 224 " pdb=" O LEU G 224 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.15e-02 7.56e+03 2.11e+01 ... (remaining 24683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 33203 2.94 - 5.88: 248 5.88 - 8.82: 30 8.82 - 11.76: 4 11.76 - 14.70: 1 Bond angle restraints: 33486 Sorted by residual: angle pdb=" C TYR F 341 " pdb=" N PRO F 342 " pdb=" CA PRO F 342 " ideal model delta sigma weight residual 119.56 109.44 10.12 1.01e+00 9.80e-01 1.00e+02 angle pdb=" N ALA A 369 " pdb=" CA ALA A 369 " pdb=" C ALA A 369 " ideal model delta sigma weight residual 113.23 102.47 10.76 1.24e+00 6.50e-01 7.53e+01 angle pdb=" N ALA B 379 " pdb=" CA ALA B 379 " pdb=" C ALA B 379 " ideal model delta sigma weight residual 111.36 119.34 -7.98 1.09e+00 8.42e-01 5.36e+01 angle pdb=" N PRO F 342 " pdb=" CA PRO F 342 " pdb=" C PRO F 342 " ideal model delta sigma weight residual 113.86 104.73 9.13 1.25e+00 6.40e-01 5.34e+01 angle pdb=" N TYR F 341 " pdb=" CA TYR F 341 " pdb=" C TYR F 341 " ideal model delta sigma weight residual 109.81 124.51 -14.70 2.21e+00 2.05e-01 4.43e+01 ... (remaining 33481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13833 17.66 - 35.31: 901 35.31 - 52.97: 270 52.97 - 70.63: 77 70.63 - 88.28: 35 Dihedral angle restraints: 15116 sinusoidal: 6191 harmonic: 8925 Sorted by residual: dihedral pdb=" N TYR F 341 " pdb=" C TYR F 341 " pdb=" CA TYR F 341 " pdb=" CB TYR F 341 " ideal model delta harmonic sigma weight residual 122.80 142.36 -19.56 0 2.50e+00 1.60e-01 6.12e+01 dihedral pdb=" C TYR F 341 " pdb=" N TYR F 341 " pdb=" CA TYR F 341 " pdb=" CB TYR F 341 " ideal model delta harmonic sigma weight residual -122.60 -141.45 18.85 0 2.50e+00 1.60e-01 5.69e+01 dihedral pdb=" C GLN F 217 " pdb=" N GLN F 217 " pdb=" CA GLN F 217 " pdb=" CB GLN F 217 " ideal model delta harmonic sigma weight residual -122.60 -133.19 10.59 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 15113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 3838 0.197 - 0.394: 17 0.394 - 0.591: 0 0.591 - 0.788: 0 0.788 - 0.985: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA TYR F 341 " pdb=" N TYR F 341 " pdb=" C TYR F 341 " pdb=" CB TYR F 341 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA ALA B 379 " pdb=" N ALA B 379 " pdb=" C ALA B 379 " pdb=" CB ALA B 379 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA LYS B 377 " pdb=" N LYS B 377 " pdb=" C LYS B 377 " pdb=" CB LYS B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 376 " 0.033 2.00e-02 2.50e+03 6.21e-02 3.86e+01 pdb=" C LYS B 376 " -0.108 2.00e-02 2.50e+03 pdb=" O LYS B 376 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS B 377 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 378 " -0.033 2.00e-02 2.50e+03 6.08e-02 3.70e+01 pdb=" C VAL B 378 " 0.105 2.00e-02 2.50e+03 pdb=" O VAL B 378 " -0.036 2.00e-02 2.50e+03 pdb=" N ALA B 379 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 381 " -0.025 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C THR B 381 " 0.087 2.00e-02 2.50e+03 pdb=" O THR B 381 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU B 382 " -0.031 2.00e-02 2.50e+03 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 4 1.84 - 2.61: 173 2.61 - 3.37: 31398 3.37 - 4.14: 57872 4.14 - 4.90: 110025 Nonbonded interactions: 199472 Sorted by model distance: nonbonded pdb=" CB ASN G 55 " pdb=" CG2 VAL G 202 " model vdw 1.081 3.860 nonbonded pdb=" CG ASN G 55 " pdb=" CG2 VAL G 202 " model vdw 1.567 3.690 nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 601 " model vdw 1.708 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1G ATP D 602 " model vdw 1.767 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 2.016 2.170 ... (remaining 199467 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 57.330 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 24688 Z= 0.255 Angle : 0.655 14.704 33486 Z= 0.423 Chirality : 0.051 0.985 3856 Planarity : 0.005 0.116 4363 Dihedral : 14.404 88.283 9404 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.01 % Allowed : 0.90 % Favored : 98.09 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.15), residues: 3115 helix: 1.70 (0.15), residues: 1249 sheet: 1.23 (0.23), residues: 522 loop : 0.07 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 363 PHE 0.023 0.001 PHE F 322 TYR 0.036 0.001 TYR F 341 ARG 0.005 0.000 ARG D 240 Details of bonding type rmsd hydrogen bonds : bond 0.15240 ( 1186) hydrogen bonds : angle 6.11261 ( 3372) covalent geometry : bond 0.00379 (24688) covalent geometry : angle 0.65530 (33486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8396 (mtt90) REVERT: B 60 MET cc_start: 0.9269 (mmp) cc_final: 0.9051 (mmp) REVERT: C 466 GLN cc_start: 0.8588 (tp40) cc_final: 0.8374 (mm-40) REVERT: D 386 ILE cc_start: 0.8423 (mm) cc_final: 0.8173 (mt) REVERT: G 58 LEU cc_start: 0.4792 (OUTLIER) cc_final: 0.4551 (tp) REVERT: G 198 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7265 (ptmm) REVERT: G 200 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5568 (mmp-170) REVERT: G 206 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6686 (tp30) REVERT: G 207 PRO cc_start: 0.6134 (Cg_endo) cc_final: 0.5452 (Cg_exo) outliers start: 26 outliers final: 9 residues processed: 295 average time/residue: 1.6861 time to fit residues: 558.5837 Evaluate side-chains 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 219 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN D 177 GLN D 179 HIS E 372 GLN F 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.064823 restraints weight = 43436.562| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.04 r_work: 0.2634 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 24688 Z= 0.409 Angle : 0.738 11.211 33486 Z= 0.392 Chirality : 0.056 0.423 3856 Planarity : 0.006 0.072 4363 Dihedral : 9.825 87.372 3634 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.41 % Allowed : 8.49 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3115 helix: 1.03 (0.14), residues: 1246 sheet: 0.69 (0.22), residues: 534 loop : -0.16 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS F 363 PHE 0.021 0.002 PHE F 257 TYR 0.041 0.002 TYR F 341 ARG 0.006 0.001 ARG D 240 Details of bonding type rmsd hydrogen bonds : bond 0.07268 ( 1186) hydrogen bonds : angle 5.38141 ( 3372) covalent geometry : bond 0.01020 (24688) covalent geometry : angle 0.73781 (33486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 3.006 Fit side-chains revert: symmetry clash REVERT: A 404 LYS cc_start: 0.8005 (tttt) cc_final: 0.7698 (ttmt) REVERT: B 451 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: C 89 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8033 (mtp85) REVERT: C 409 LYS cc_start: 0.8429 (mmtt) cc_final: 0.7774 (tmtt) REVERT: D 177 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7940 (mp-120) REVERT: D 201 GLU cc_start: 0.8800 (tp30) cc_final: 0.8593 (tp30) REVERT: D 352 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8144 (mpt90) REVERT: D 386 ILE cc_start: 0.8479 (mm) cc_final: 0.8174 (mt) REVERT: G 58 LEU cc_start: 0.5136 (OUTLIER) cc_final: 0.4733 (tp) REVERT: G 200 ARG cc_start: 0.6546 (mmm160) cc_final: 0.5394 (mmp-170) REVERT: G 219 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7644 (mt0) outliers start: 62 outliers final: 20 residues processed: 196 average time/residue: 1.6516 time to fit residues: 366.7982 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 219 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 297 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN G 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.069435 restraints weight = 42602.465| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.05 r_work: 0.2726 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24688 Z= 0.114 Angle : 0.502 10.655 33486 Z= 0.270 Chirality : 0.044 0.264 3856 Planarity : 0.004 0.045 4363 Dihedral : 8.691 88.175 3615 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.06 % Allowed : 10.44 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3115 helix: 1.52 (0.15), residues: 1247 sheet: 0.78 (0.23), residues: 521 loop : -0.00 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.013 0.001 PHE G 205 TYR 0.028 0.001 TYR G 203 ARG 0.003 0.000 ARG D 240 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 1186) hydrogen bonds : angle 4.86945 ( 3372) covalent geometry : bond 0.00243 (24688) covalent geometry : angle 0.50247 (33486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 150 time to evaluate : 2.932 Fit side-chains REVERT: A 95 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8126 (tpt) REVERT: A 404 LYS cc_start: 0.7998 (tttt) cc_final: 0.7784 (ttmt) REVERT: B 451 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: D 177 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7992 (mp-120) REVERT: D 352 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8038 (mpt90) REVERT: D 386 ILE cc_start: 0.8392 (mm) cc_final: 0.8085 (mt) REVERT: D 469 MET cc_start: 0.7778 (mtm) cc_final: 0.7252 (mmt) REVERT: G 58 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4503 (tp) REVERT: G 67 MET cc_start: 0.7465 (mtp) cc_final: 0.6381 (mmt) REVERT: G 191 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7638 (mt) REVERT: G 200 ARG cc_start: 0.6432 (mmm160) cc_final: 0.5491 (mmp-170) outliers start: 53 outliers final: 14 residues processed: 189 average time/residue: 1.4604 time to fit residues: 316.9738 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 197 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 56 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068775 restraints weight = 43163.653| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.06 r_work: 0.2713 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24688 Z= 0.144 Angle : 0.511 10.286 33486 Z= 0.272 Chirality : 0.044 0.249 3856 Planarity : 0.004 0.047 4363 Dihedral : 8.268 88.668 3610 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.26 % Allowed : 11.45 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3115 helix: 1.60 (0.15), residues: 1249 sheet: 0.80 (0.23), residues: 529 loop : 0.04 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.014 0.001 PHE F 257 TYR 0.028 0.001 TYR G 203 ARG 0.002 0.000 ARG D 240 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 1186) hydrogen bonds : angle 4.78808 ( 3372) covalent geometry : bond 0.00342 (24688) covalent geometry : angle 0.51147 (33486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 134 time to evaluate : 2.873 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8839 (tpt) cc_final: 0.8093 (tpt) REVERT: A 404 LYS cc_start: 0.8000 (tttt) cc_final: 0.7632 (ttmt) REVERT: B 451 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8137 (pt0) REVERT: C 376 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8636 (ttmm) REVERT: D 352 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8035 (mpt90) REVERT: D 386 ILE cc_start: 0.8415 (mm) cc_final: 0.8097 (mt) REVERT: D 469 MET cc_start: 0.7721 (mtm) cc_final: 0.7259 (mmt) REVERT: E 59 VAL cc_start: 0.9190 (OUTLIER) cc_final: 0.8969 (m) REVERT: G 58 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4454 (tp) REVERT: G 67 MET cc_start: 0.7498 (mtp) cc_final: 0.6406 (mmt) REVERT: G 182 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8187 (mm-30) REVERT: G 191 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7670 (mt) REVERT: G 200 ARG cc_start: 0.6520 (mmm160) cc_final: 0.5771 (mmp-170) outliers start: 58 outliers final: 23 residues processed: 179 average time/residue: 1.3817 time to fit residues: 285.6003 Evaluate side-chains 159 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 197 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 176 optimal weight: 6.9990 chunk 279 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 172 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.069904 restraints weight = 43005.748| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.06 r_work: 0.2735 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24688 Z= 0.115 Angle : 0.480 10.472 33486 Z= 0.256 Chirality : 0.043 0.196 3856 Planarity : 0.004 0.048 4363 Dihedral : 7.846 87.664 3610 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.87 % Allowed : 11.99 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.15), residues: 3115 helix: 1.73 (0.15), residues: 1255 sheet: 0.83 (0.23), residues: 528 loop : 0.09 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.014 0.001 PHE A 398 TYR 0.025 0.001 TYR G 203 ARG 0.007 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 1186) hydrogen bonds : angle 4.64243 ( 3372) covalent geometry : bond 0.00260 (24688) covalent geometry : angle 0.48032 (33486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 2.937 Fit side-chains REVERT: A 95 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8041 (tpt) REVERT: A 404 LYS cc_start: 0.8056 (tttt) cc_final: 0.7694 (ttmt) REVERT: B 451 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: C 376 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8463 (ttmm) REVERT: D 201 GLU cc_start: 0.8668 (tp30) cc_final: 0.8245 (tp30) REVERT: D 352 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7976 (mpt90) REVERT: D 386 ILE cc_start: 0.8439 (mm) cc_final: 0.8078 (mt) REVERT: D 469 MET cc_start: 0.7696 (mtm) cc_final: 0.7261 (mmt) REVERT: F 383 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8633 (mt) REVERT: G 58 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4500 (tp) REVERT: G 67 MET cc_start: 0.7482 (mtp) cc_final: 0.6411 (mmt) REVERT: G 191 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7772 (mt) REVERT: G 200 ARG cc_start: 0.6515 (mmm160) cc_final: 0.5682 (mmp-170) outliers start: 48 outliers final: 19 residues processed: 173 average time/residue: 1.3994 time to fit residues: 279.7815 Evaluate side-chains 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 152 optimal weight: 4.9990 chunk 153 optimal weight: 0.2980 chunk 228 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 280 optimal weight: 0.0170 chunk 200 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 overall best weight: 2.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN G 209 GLN G 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.088303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.067967 restraints weight = 42821.972| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.04 r_work: 0.2697 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24688 Z= 0.181 Angle : 0.531 10.287 33486 Z= 0.281 Chirality : 0.046 0.234 3856 Planarity : 0.004 0.049 4363 Dihedral : 8.021 87.434 3606 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.10 % Allowed : 12.62 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3115 helix: 1.60 (0.15), residues: 1255 sheet: 0.75 (0.23), residues: 529 loop : 0.08 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 363 PHE 0.016 0.001 PHE F 257 TYR 0.037 0.001 TYR G 203 ARG 0.003 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 1186) hydrogen bonds : angle 4.75140 ( 3372) covalent geometry : bond 0.00445 (24688) covalent geometry : angle 0.53080 (33486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 2.816 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8866 (tpt) cc_final: 0.8075 (tpt) REVERT: B 451 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: C 376 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8574 (ttmm) REVERT: D 201 GLU cc_start: 0.8649 (tp30) cc_final: 0.8393 (tp30) REVERT: D 352 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8048 (mpt90) REVERT: D 386 ILE cc_start: 0.8446 (mm) cc_final: 0.8070 (mt) REVERT: D 469 MET cc_start: 0.7690 (mtm) cc_final: 0.7283 (mmt) REVERT: E 59 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8976 (m) REVERT: G 67 MET cc_start: 0.7543 (mtp) cc_final: 0.6521 (mmt) REVERT: G 182 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8204 (mm-30) REVERT: G 191 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7769 (mt) REVERT: G 200 ARG cc_start: 0.6547 (mmm160) cc_final: 0.5742 (mmp-170) outliers start: 54 outliers final: 30 residues processed: 176 average time/residue: 1.4020 time to fit residues: 285.0099 Evaluate side-chains 163 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 197 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 294 optimal weight: 0.7980 chunk 276 optimal weight: 0.0870 chunk 131 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS E 304 GLN G 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.070098 restraints weight = 42880.019| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.06 r_work: 0.2740 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24688 Z= 0.110 Angle : 0.479 11.027 33486 Z= 0.254 Chirality : 0.043 0.177 3856 Planarity : 0.004 0.048 4363 Dihedral : 7.641 89.834 3606 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.83 % Allowed : 13.16 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3115 helix: 1.75 (0.15), residues: 1261 sheet: 0.76 (0.23), residues: 531 loop : 0.15 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.016 0.001 PHE A 398 TYR 0.040 0.001 TYR G 203 ARG 0.002 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1186) hydrogen bonds : angle 4.57692 ( 3372) covalent geometry : bond 0.00247 (24688) covalent geometry : angle 0.47854 (33486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8814 (tpt) cc_final: 0.8058 (tpt) REVERT: B 384 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7274 (tp) REVERT: C 376 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8616 (ttmm) REVERT: D 201 GLU cc_start: 0.8641 (tp30) cc_final: 0.8378 (tp30) REVERT: D 352 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8004 (mpt90) REVERT: D 386 ILE cc_start: 0.8385 (mm) cc_final: 0.8027 (mt) REVERT: D 469 MET cc_start: 0.7624 (mtm) cc_final: 0.7184 (mmt) REVERT: G 67 MET cc_start: 0.7560 (mtp) cc_final: 0.6510 (mmt) REVERT: G 191 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7794 (mt) REVERT: G 200 ARG cc_start: 0.6541 (mmm160) cc_final: 0.5734 (mmp-170) outliers start: 47 outliers final: 23 residues processed: 179 average time/residue: 1.4511 time to fit residues: 298.9946 Evaluate side-chains 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 148 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 249 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.087709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.067359 restraints weight = 43071.305| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.05 r_work: 0.2684 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24688 Z= 0.203 Angle : 0.553 10.661 33486 Z= 0.293 Chirality : 0.046 0.246 3856 Planarity : 0.005 0.049 4363 Dihedral : 8.050 87.838 3605 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.83 % Allowed : 13.59 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1261 sheet: 0.65 (0.23), residues: 528 loop : 0.08 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 363 PHE 0.017 0.002 PHE F 257 TYR 0.038 0.001 TYR G 203 ARG 0.005 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.05258 ( 1186) hydrogen bonds : angle 4.76795 ( 3372) covalent geometry : bond 0.00502 (24688) covalent geometry : angle 0.55341 (33486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 3.139 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8894 (tpt) cc_final: 0.8085 (tpt) REVERT: C 376 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8515 (ttmm) REVERT: D 201 GLU cc_start: 0.8678 (tp30) cc_final: 0.8413 (tp30) REVERT: D 352 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8050 (mpt90) REVERT: D 386 ILE cc_start: 0.8422 (mm) cc_final: 0.8061 (mt) REVERT: D 469 MET cc_start: 0.7691 (mtm) cc_final: 0.7259 (mmt) REVERT: G 67 MET cc_start: 0.7573 (mtp) cc_final: 0.6588 (mmt) REVERT: G 191 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7841 (mt) REVERT: G 200 ARG cc_start: 0.6409 (mmm160) cc_final: 0.5704 (mmp-170) outliers start: 47 outliers final: 25 residues processed: 164 average time/residue: 1.4356 time to fit residues: 274.6764 Evaluate side-chains 151 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 104 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 224 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 292 optimal weight: 0.2980 chunk 188 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN E 304 GLN G 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.089815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.069510 restraints weight = 42988.857| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.06 r_work: 0.2728 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24688 Z= 0.120 Angle : 0.491 11.409 33486 Z= 0.261 Chirality : 0.043 0.186 3856 Planarity : 0.004 0.053 4363 Dihedral : 7.685 88.791 3605 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.40 % Allowed : 13.98 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3115 helix: 1.72 (0.15), residues: 1260 sheet: 0.68 (0.23), residues: 528 loop : 0.13 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.012 0.001 PHE C 494 TYR 0.040 0.001 TYR G 203 ARG 0.003 0.000 ARG E 5 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 1186) hydrogen bonds : angle 4.59477 ( 3372) covalent geometry : bond 0.00279 (24688) covalent geometry : angle 0.49135 (33486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 2.887 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8862 (tpt) cc_final: 0.8093 (tpt) REVERT: B 384 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7261 (tp) REVERT: C 376 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8558 (ttmm) REVERT: D 201 GLU cc_start: 0.8667 (tp30) cc_final: 0.8415 (tp30) REVERT: D 352 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8008 (mpt90) REVERT: D 386 ILE cc_start: 0.8381 (mm) cc_final: 0.8025 (mt) REVERT: D 469 MET cc_start: 0.7629 (mtm) cc_final: 0.7200 (mmt) REVERT: G 67 MET cc_start: 0.7595 (mtp) cc_final: 0.6561 (mmt) REVERT: G 191 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7896 (mt) REVERT: G 200 ARG cc_start: 0.6348 (mmm160) cc_final: 0.5641 (mmp-170) outliers start: 36 outliers final: 22 residues processed: 160 average time/residue: 1.4113 time to fit residues: 260.9818 Evaluate side-chains 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 159 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.068910 restraints weight = 43047.039| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.06 r_work: 0.2714 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24688 Z= 0.140 Angle : 0.506 11.165 33486 Z= 0.268 Chirality : 0.044 0.200 3856 Planarity : 0.004 0.053 4363 Dihedral : 7.713 89.236 3605 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.32 % Allowed : 14.02 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3115 helix: 1.72 (0.15), residues: 1255 sheet: 0.68 (0.23), residues: 528 loop : 0.13 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.014 0.001 PHE C 494 TYR 0.035 0.001 TYR G 203 ARG 0.003 0.000 ARG E 5 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 1186) hydrogen bonds : angle 4.61695 ( 3372) covalent geometry : bond 0.00334 (24688) covalent geometry : angle 0.50561 (33486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 3.040 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8063 (tpt) REVERT: B 384 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7261 (tp) REVERT: C 376 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8567 (ttmm) REVERT: D 201 GLU cc_start: 0.8660 (tp30) cc_final: 0.8417 (tp30) REVERT: D 352 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8011 (mpt90) REVERT: D 386 ILE cc_start: 0.8388 (mm) cc_final: 0.8033 (mt) REVERT: D 469 MET cc_start: 0.7635 (mtm) cc_final: 0.7202 (mmt) REVERT: G 67 MET cc_start: 0.7578 (mtp) cc_final: 0.6547 (mmt) REVERT: G 191 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7938 (mt) REVERT: G 200 ARG cc_start: 0.6322 (mmm160) cc_final: 0.5610 (mmp-170) outliers start: 34 outliers final: 24 residues processed: 156 average time/residue: 1.4748 time to fit residues: 265.8915 Evaluate side-chains 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 244 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 302 optimal weight: 0.0010 chunk 128 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.087341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.066942 restraints weight = 42993.629| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.05 r_work: 0.2676 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24688 Z= 0.220 Angle : 0.567 11.066 33486 Z= 0.301 Chirality : 0.047 0.267 3856 Planarity : 0.005 0.054 4363 Dihedral : 8.127 88.842 3605 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.32 % Allowed : 14.06 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3115 helix: 1.48 (0.15), residues: 1259 sheet: 0.58 (0.23), residues: 529 loop : 0.00 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 363 PHE 0.017 0.002 PHE F 257 TYR 0.034 0.001 TYR G 203 ARG 0.004 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 1186) hydrogen bonds : angle 4.81199 ( 3372) covalent geometry : bond 0.00544 (24688) covalent geometry : angle 0.56692 (33486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13651.95 seconds wall clock time: 235 minutes 44.81 seconds (14144.81 seconds total)