Starting phenix.real_space_refine on Mon Feb 19 09:47:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh1_34748/02_2024/8hh1_34748_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh1_34748/02_2024/8hh1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh1_34748/02_2024/8hh1_34748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh1_34748/02_2024/8hh1_34748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh1_34748/02_2024/8hh1_34748_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh1_34748/02_2024/8hh1_34748_updated.pdb" } 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 Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.91, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.49 Conformation dependent library (CDL) restraints added in 5.1 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... running ksdssp... Secondary structure from input PDB file: 122 helices and 22 sheets defined 42.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.55 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.603A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 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 232 through 252 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 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 4.008A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 390 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 396 through 400 Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.959A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.647A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.674A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 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 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.855A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 290 through 300 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) removed outlier: 3.953A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 373 through 398 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 404 through 419 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 4.926A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 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 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.595A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 232 through 252 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) removed outlier: 3.656A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.532A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 293 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 404 through 419 removed outlier: 3.702A pdb=" N ALA C 411 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'C' and resid 450 through 467 removed outlier: 3.602A pdb=" N VAL C 453 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR C 461 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 467 " --> pdb=" O LEU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 477 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 242 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 255 through 268 removed outlier: 3.783A pdb=" N VAL D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.445A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.411A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 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 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.658A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 421 removed outlier: 3.586A pdb=" N GLU D 418 " --> pdb=" O HIS D 415 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 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 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 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 254 through 268 Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.187A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.631A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 386 removed outlier: 4.891A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.646A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 421 No H-bonds generated for 'chain 'E' and resid 418 through 421' Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 removed outlier: 3.572A pdb=" N PHE E 453 " --> pdb=" O GLU E 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 450 through 453' Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.616A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 179 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) Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 242 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) Processing helix chain 'F' and resid 255 through 268 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) Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.618A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 387 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 394 through 409 removed outlier: 3.669A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 468 removed outlier: 3.660A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 56 removed outlier: 3.920A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.954A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 161 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 201 through 204 removed outlier: 3.943A pdb=" N GLU G 204 " --> pdb=" O THR G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 201 through 204' Processing helix chain 'G' and resid 209 through 282 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= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.446A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.680A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.870A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.383A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, 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= G, first strand: chain 'B' and resid 341 through 344 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= H, first strand: chain 'B' and resid 221 through 226 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: 6.504A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 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: 6.812A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= J, 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= K, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.421A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.825A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 330 removed outlier: 7.794A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.602A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 330 removed outlier: 8.615A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA E 305 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.520A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.812A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (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: 6.777A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY F 216 " --> pdb=" O GLY F 187 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 189 removed outlier: 6.550A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N TYR G 175 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL G 117 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP G 136 " --> pdb=" O VAL G 117 " (cutoff:3.500A) 951 hydrogen bonds defined for protein. 2664 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: 8.28 Time building geometry restraints manager: 10.99 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: 99.19 - 107.31: 927 107.31 - 115.44: 15193 115.44 - 123.56: 16763 123.56 - 131.68: 585 131.68 - 139.80: 18 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: 174 2.61 - 3.37: 31627 3.37 - 4.14: 58471 4.14 - 4.90: 110136 Nonbonded interactions: 200412 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 200407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 2.320 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: 11.010 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 67.370 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.170 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:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.970 ------------------------------------------------------------------------------- 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= 0.242 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 *********************** 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 fitting. rotamer outliers: 26 poor density : 275 time to evaluate : 2.961 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: 1.6813 time to fit residues: 556.9207 Evaluate side-chains 160 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 2.820 ------------------------------------------------------------------------------- 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: 8.9990 chunk 234 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 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 E 372 GLN F 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 24688 Z= 0.664 Angle : 0.720 11.401 33486 Z= 0.380 Chirality : 0.055 0.421 3856 Planarity : 0.006 0.081 4363 Dihedral : 9.819 89.750 3634 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 8.72 % Favored : 88.90 % 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: 0.68 (0.15), residues: 3115 helix: 1.06 (0.15), residues: 1229 sheet: 0.87 (0.23), residues: 531 loop : -0.19 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS F 363 PHE 0.027 0.003 PHE C 456 TYR 0.041 0.002 TYR F 341 ARG 0.006 0.001 ARG E 270 *********************** 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 204 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 143 time to evaluate : 2.938 Fit side-chains revert: symmetry clash REVERT: A 278 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8395 (mtt90) REVERT: A 489 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8461 (mtpt) REVERT: B 451 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: C 409 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7872 (tmtt) REVERT: D 352 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7398 (mpt90) REVERT: G 58 LEU cc_start: 0.4819 (OUTLIER) cc_final: 0.4453 (tp) REVERT: G 200 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5233 (mmp-170) REVERT: G 219 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7441 (mt0) outliers start: 61 outliers final: 23 residues processed: 188 average time/residue: 1.6202 time to fit residues: 344.6176 Evaluate side-chains 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 489 LYS 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 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 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 19 GLU 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 200 ARG 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 156 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 282 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 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 : 0.003 0.036 24688 Z= 0.189 Angle : 0.499 9.154 33486 Z= 0.266 Chirality : 0.044 0.291 3856 Planarity : 0.004 0.041 4363 Dihedral : 8.807 89.786 3619 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.64 % Allowed : 11.06 % Favored : 87.31 % 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: 1.01 (0.15), residues: 3115 helix: 1.41 (0.15), residues: 1235 sheet: 0.96 (0.23), residues: 527 loop : -0.05 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.015 0.001 PHE C 456 TYR 0.026 0.001 TYR F 341 ARG 0.003 0.000 ARG D 240 *********************** 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 186 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 2.949 Fit side-chains REVERT: A 278 ARG cc_start: 0.8668 (mtp85) cc_final: 0.8351 (mtt90) REVERT: B 451 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: C 89 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7236 (ttp80) REVERT: D 177 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6916 (mp-120) REVERT: D 352 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7285 (mpt90) REVERT: D 469 MET cc_start: 0.7228 (mtm) cc_final: 0.6907 (mmt) REVERT: G 67 MET cc_start: 0.7202 (mtp) cc_final: 0.6320 (mmt) REVERT: G 200 ARG cc_start: 0.5928 (mmm160) cc_final: 0.5210 (mmp-170) outliers start: 42 outliers final: 16 residues processed: 177 average time/residue: 1.5032 time to fit residues: 304.4638 Evaluate side-chains 149 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 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 D residue 419 GLN 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 382 ASP Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 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 278 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 268 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 24688 Z= 0.460 Angle : 0.606 8.289 33486 Z= 0.318 Chirality : 0.049 0.337 3856 Planarity : 0.005 0.052 4363 Dihedral : 8.869 85.944 3610 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.88 % Allowed : 11.60 % Favored : 85.51 % 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: 0.77 (0.15), residues: 3115 helix: 1.20 (0.15), residues: 1228 sheet: 0.83 (0.23), residues: 533 loop : -0.17 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 363 PHE 0.019 0.002 PHE F 257 TYR 0.029 0.002 TYR F 341 ARG 0.004 0.000 ARG E 270 *********************** 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 204 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 130 time to evaluate : 2.979 Fit side-chains revert: symmetry clash REVERT: A 278 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8383 (mtt90) REVERT: B 451 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: D 177 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6970 (mp-120) REVERT: D 201 GLU cc_start: 0.7758 (tp30) cc_final: 0.7500 (tp30) REVERT: D 352 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7367 (mpt90) REVERT: D 469 MET cc_start: 0.7173 (mtm) cc_final: 0.6865 (mmt) REVERT: E 304 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: G 67 MET cc_start: 0.7329 (mtp) cc_final: 0.6508 (mmt) REVERT: G 191 LEU cc_start: 0.8246 (tm) cc_final: 0.7937 (mt) REVERT: G 200 ARG cc_start: 0.5817 (mmm160) cc_final: 0.5185 (mmp-170) outliers start: 74 outliers final: 33 residues processed: 194 average time/residue: 1.4161 time to fit residues: 316.4320 Evaluate side-chains 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 129 ILE 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 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 353 VAL Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 453 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 359 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 304 GLN 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 197 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 5.9990 chunk 170 optimal weight: 0.0000 chunk 4 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 153 optimal weight: 0.2980 chunk 268 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 324 HIS F 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1684 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= 0.189 Angle : 0.488 9.022 33486 Z= 0.258 Chirality : 0.043 0.242 3856 Planarity : 0.004 0.045 4363 Dihedral : 8.232 87.937 3608 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.06 % Allowed : 13.16 % Favored : 84.77 % 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: 1.47 (0.15), residues: 1233 sheet: 0.85 (0.22), residues: 547 loop : -0.10 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.013 0.001 PHE F 257 TYR 0.019 0.001 TYR F 341 ARG 0.002 0.000 ARG C 161 *********************** 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 191 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 138 time to evaluate : 2.740 Fit side-chains REVERT: A 278 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8346 (mtt90) REVERT: B 451 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: D 177 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6931 (mp-120) REVERT: D 352 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7311 (mpt90) REVERT: D 469 MET cc_start: 0.7184 (mtm) cc_final: 0.6846 (mmt) REVERT: E 304 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7526 (mp-120) REVERT: G 67 MET cc_start: 0.7370 (mtp) cc_final: 0.6522 (mmt) REVERT: G 116 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8225 (mm) REVERT: G 191 LEU cc_start: 0.8257 (tm) cc_final: 0.7952 (mt) REVERT: G 200 ARG cc_start: 0.5894 (mmm160) cc_final: 0.5287 (mmp-170) outliers start: 53 outliers final: 23 residues processed: 176 average time/residue: 1.4843 time to fit residues: 300.7290 Evaluate side-chains 155 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 173 THR 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 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 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 304 GLN 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 116 ILE Chi-restraints excluded: chain G residue 197 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 8.9990 chunk 269 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 299 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 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 0.044 24688 Z= 0.336 Angle : 0.542 8.358 33486 Z= 0.285 Chirality : 0.046 0.274 3856 Planarity : 0.004 0.047 4363 Dihedral : 8.357 84.211 3608 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.34 % Allowed : 13.71 % Favored : 83.96 % 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: 0.91 (0.15), residues: 3115 helix: 1.37 (0.15), residues: 1232 sheet: 0.82 (0.23), residues: 531 loop : -0.11 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 215 PHE 0.017 0.002 PHE F 257 TYR 0.017 0.001 TYR F 341 ARG 0.004 0.000 ARG C 161 *********************** 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 192 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 132 time to evaluate : 2.985 Fit side-chains revert: symmetry clash REVERT: A 278 ARG cc_start: 0.8669 (mtp85) cc_final: 0.8363 (mtt90) REVERT: B 451 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: C 376 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8265 (ttmm) REVERT: D 177 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6962 (mp-120) REVERT: D 352 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7334 (mpt90) REVERT: D 386 ILE cc_start: 0.8542 (mm) cc_final: 0.8317 (mt) REVERT: D 469 MET cc_start: 0.7196 (mtm) cc_final: 0.6864 (mmt) REVERT: E 304 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.7716 (mp-120) REVERT: E 469 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6885 (mtp) REVERT: G 67 MET cc_start: 0.7381 (mtp) cc_final: 0.6587 (mmt) REVERT: G 116 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8302 (mm) REVERT: G 191 LEU cc_start: 0.8224 (tm) cc_final: 0.7931 (mt) outliers start: 60 outliers final: 36 residues processed: 181 average time/residue: 1.4038 time to fit residues: 293.4631 Evaluate side-chains 170 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 THR 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 347 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain C residue 398 PHE 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 359 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 328 THR 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 116 ILE Chi-restraints excluded: chain G residue 183 VAL 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 289 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24688 Z= 0.193 Angle : 0.484 9.053 33486 Z= 0.256 Chirality : 0.043 0.213 3856 Planarity : 0.004 0.048 4363 Dihedral : 7.973 88.583 3608 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.84 % 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: 1.05 (0.15), residues: 3115 helix: 1.55 (0.15), residues: 1232 sheet: 0.82 (0.22), residues: 550 loop : -0.08 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.013 0.001 PHE F 257 TYR 0.017 0.001 TYR F 341 ARG 0.009 0.000 ARG A 455 *********************** 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 fitting. rotamer outliers: 52 poor density : 133 time to evaluate : 2.864 Fit side-chains revert: symmetry clash REVERT: A 278 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8322 (mtt90) REVERT: D 177 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7190 (mp-120) REVERT: D 352 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7289 (mpt90) REVERT: D 469 MET cc_start: 0.7164 (mtm) cc_final: 0.6818 (mmt) REVERT: E 304 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7544 (mp-120) REVERT: E 338 MET cc_start: 0.7912 (mtp) cc_final: 0.7710 (mtp) REVERT: G 67 MET cc_start: 0.7305 (mtp) cc_final: 0.6493 (mmt) REVERT: G 111 ASP cc_start: 0.7990 (m-30) cc_final: 0.7695 (p0) REVERT: G 116 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8225 (mm) REVERT: G 191 LEU cc_start: 0.8141 (tm) cc_final: 0.7927 (mt) REVERT: G 200 ARG cc_start: 0.6144 (mmm160) cc_final: 0.5326 (mmp-170) outliers start: 52 outliers final: 32 residues processed: 176 average time/residue: 1.4636 time to fit residues: 297.8284 Evaluate side-chains 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 173 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 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 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 359 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 304 GLN 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 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 116 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 234 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1761 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= 0.179 Angle : 0.474 8.826 33486 Z= 0.250 Chirality : 0.043 0.193 3856 Planarity : 0.004 0.049 4363 Dihedral : 7.770 88.128 3606 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.99 % Allowed : 14.29 % Favored : 83.72 % 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: 1.64 (0.15), residues: 1233 sheet: 0.84 (0.22), residues: 563 loop : -0.02 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.013 0.001 PHE F 257 TYR 0.012 0.001 TYR F 341 ARG 0.006 0.000 ARG A 455 *********************** 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 182 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 131 time to evaluate : 2.790 Fit side-chains REVERT: D 177 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7100 (mp-120) REVERT: D 352 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7267 (mpt90) REVERT: D 469 MET cc_start: 0.7100 (mtm) cc_final: 0.6851 (mmt) REVERT: E 304 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7559 (mp-120) REVERT: G 67 MET cc_start: 0.7297 (mtp) cc_final: 0.6466 (mmt) REVERT: G 111 ASP cc_start: 0.7946 (m-30) cc_final: 0.7692 (p0) REVERT: G 116 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8239 (mm) REVERT: G 191 LEU cc_start: 0.8130 (tm) cc_final: 0.7918 (mt) REVERT: G 200 ARG cc_start: 0.6283 (mmm160) cc_final: 0.5306 (mmp-170) outliers start: 51 outliers final: 32 residues processed: 175 average time/residue: 1.3299 time to fit residues: 270.6725 Evaluate side-chains 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 406 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 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 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 419 GLN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 304 GLN 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 328 THR 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 116 ILE Chi-restraints excluded: chain G residue 183 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 6.9990 chunk 286 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1780 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= 0.192 Angle : 0.484 8.958 33486 Z= 0.255 Chirality : 0.043 0.194 3856 Planarity : 0.004 0.050 4363 Dihedral : 7.719 86.971 3606 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.75 % Allowed : 14.64 % Favored : 83.61 % 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: 1.17 (0.15), residues: 3115 helix: 1.66 (0.15), residues: 1233 sheet: 0.85 (0.22), residues: 562 loop : -0.02 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.013 0.001 PHE F 257 TYR 0.012 0.001 TYR F 341 ARG 0.006 0.000 ARG A 455 *********************** 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 175 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 130 time to evaluate : 2.721 Fit side-chains revert: symmetry clash REVERT: D 177 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7088 (mp-120) REVERT: D 352 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7266 (mpt90) REVERT: D 469 MET cc_start: 0.7106 (mtm) cc_final: 0.6846 (mmt) REVERT: E 304 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7568 (mp-120) REVERT: G 67 MET cc_start: 0.7288 (mtp) cc_final: 0.6422 (mmt) REVERT: G 111 ASP cc_start: 0.7938 (m-30) cc_final: 0.7689 (p0) REVERT: G 116 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8215 (mm) REVERT: G 200 ARG cc_start: 0.6412 (mmm160) cc_final: 0.5331 (mmp-170) outliers start: 45 outliers final: 33 residues processed: 169 average time/residue: 1.4087 time to fit residues: 276.3502 Evaluate side-chains 164 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 173 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 353 VAL Chi-restraints excluded: chain C residue 398 PHE 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 419 GLN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 304 GLN 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 328 THR 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 116 ILE Chi-restraints excluded: chain G residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 25 optimal weight: 0.0770 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24688 Z= 0.350 Angle : 0.550 9.278 33486 Z= 0.290 Chirality : 0.046 0.261 3856 Planarity : 0.004 0.053 4363 Dihedral : 8.079 85.580 3606 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.71 % Allowed : 14.76 % Favored : 83.53 % 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: 0.97 (0.15), residues: 3115 helix: 1.45 (0.15), residues: 1225 sheet: 0.80 (0.22), residues: 556 loop : -0.10 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 200 PHE 0.025 0.002 PHE A 398 TYR 0.015 0.001 TYR F 341 ARG 0.005 0.000 ARG A 455 ********************** 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 169 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 2.929 Fit side-chains revert: symmetry clash REVERT: C 376 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: D 177 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7152 (mp-120) REVERT: D 201 GLU cc_start: 0.7596 (tp30) cc_final: 0.7337 (tp30) REVERT: D 352 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7322 (mpt90) REVERT: D 469 MET cc_start: 0.7068 (mtm) cc_final: 0.6811 (mmt) REVERT: E 304 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7828 (mp-120) REVERT: G 67 MET cc_start: 0.7316 (mtp) cc_final: 0.6534 (mmt) REVERT: G 116 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8247 (mm) REVERT: G 200 ARG cc_start: 0.6378 (mmm160) cc_final: 0.5317 (mmp-170) outliers start: 44 outliers final: 33 residues processed: 163 average time/residue: 1.3765 time to fit residues: 260.1750 Evaluate side-chains 160 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 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 353 VAL Chi-restraints excluded: chain C residue 376 LYS 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 419 GLN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 304 GLN 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 328 THR 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 116 ILE Chi-restraints excluded: chain G residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 246 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.087695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.067332 restraints weight = 43014.482| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.04 r_work: 0.2682 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1892 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= 0.292 Angle : 0.525 9.233 33486 Z= 0.277 Chirality : 0.045 0.248 3856 Planarity : 0.004 0.053 4363 Dihedral : 8.022 84.980 3606 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.83 % Allowed : 14.88 % Favored : 83.29 % 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: 0.96 (0.15), residues: 3115 helix: 1.46 (0.15), residues: 1230 sheet: 0.78 (0.22), residues: 556 loop : -0.12 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 215 PHE 0.015 0.001 PHE F 257 TYR 0.017 0.001 TYR F 341 ARG 0.005 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6470.49 seconds wall clock time: 117 minutes 16.50 seconds (7036.50 seconds total)