Starting phenix.real_space_refine on Mon Feb 19 09:44:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh4_34751/02_2024/8hh4_34751_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh4_34751/02_2024/8hh4_34751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh4_34751/02_2024/8hh4_34751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh4_34751/02_2024/8hh4_34751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh4_34751/02_2024/8hh4_34751_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh4_34751/02_2024/8hh4_34751_updated.pdb" } resolution = 3.1 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= 0.002 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 18 5.49 5 Mg 6 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 206": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24277 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: {'PCIS': 1, 'PTRANS': 22, '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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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: 12.78, per 1000 atoms: 0.53 Number of scatterers: 24277 At special positions: 0 Unit cell: (126.72, 125.84, 154, 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 18 15.00 Mg 6 11.99 O 4670 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: 10.91 Conformation dependent library (CDL) restraints added in 5.0 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: 123 helices and 22 sheets defined 42.1% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' 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 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.840A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.973A 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 220 Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.732A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.156A 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 288 through 300 removed outlier: 4.318A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 293 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 299 " --> 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 351 Processing helix chain 'A' and resid 373 through 390 removed outlier: 4.563A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.519A pdb=" N GLN A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.546A pdb=" N ARG A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.718A pdb=" N ILE A 491 " --> pdb=" O LEU A 487 " (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 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.641A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.749A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (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 298 removed outlier: 3.723A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (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: 3.880A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.945A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 removed outlier: 4.121A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 454 through 467 removed outlier: 4.104A pdb=" N LYS B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' 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: 3.657A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 removed outlier: 3.627A pdb=" N HIS C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.746A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.750A 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 290 through 300 removed outlier: 4.451A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 395 removed outlier: 3.701A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'C' and resid 450 through 466 removed outlier: 3.947A pdb=" N VAL C 453 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 removed outlier: 3.636A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) 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 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 164 through 178 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 222 through 241 removed outlier: 5.018A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 281 through 290 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 321 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 386 removed outlier: 4.091A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.612A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 421 No H-bonds generated for 'chain 'D' and resid 418 through 421' Processing helix chain 'D' and resid 430 through 441 removed outlier: 4.018A pdb=" N ILE D 440 " --> pdb=" O GLY D 436 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 459 through 468 removed outlier: 3.613A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (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 144 Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 222 through 241 removed outlier: 4.836A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.192A 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 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.464A 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: 4.204A 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: 3.854A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 4.206A pdb=" N VAL E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 403 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG E 404 " --> 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 Processing helix chain 'E' and resid 460 through 466 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 144 Processing helix chain 'F' and resid 164 through 178 removed outlier: 5.094A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.394A 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 241 removed outlier: 5.064A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.519A pdb=" N SER F 265 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA F 266 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.672A 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 324 removed outlier: 4.718A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.692A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 387 removed outlier: 3.506A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 391 No H-bonds generated for 'chain 'F' and resid 389 through 391' Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.782A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.534A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) No H-bonds generated for '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: 3.546A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 39 removed outlier: 4.001A pdb=" N SER G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 removed outlier: 4.670A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 4.207A 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 150 through 161 removed outlier: 3.934A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 283 removed outlier: 4.729A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 4.461A pdb=" N LEU G 224 " --> pdb=" O TYR G 220 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ILE G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG G 264 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY G 280 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.536A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.360A 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 99 removed outlier: 4.088A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 106 through 109 removed outlier: 4.054A pdb=" N ARG A 106 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 223 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.544A 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: 6.948A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.104A 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: 6.378A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.414A 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 Processing sheet with id= G, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.694A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.715A 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: 6.551A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.532A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.073A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.572A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= M, first strand: chain 'D' and resid 5 through 9 removed outlier: 6.643A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.581A 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: 8.382A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 305 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 3 through 5 removed outlier: 5.888A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 44 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (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: 8.557A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E 216 " --> pdb=" O GLY E 187 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.527A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.669A 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: 7.948A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP F 252 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA F 186 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 113 through 118 removed outlier: 5.601A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU G 167 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU G 79 " --> pdb=" O GLU G 167 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR G 169 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ILE G 81 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR G 171 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2631 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: 8.86 Time building geometry restraints manager: 11.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4179 1.31 - 1.44: 5906 1.44 - 1.56: 14417 1.56 - 1.69: 28 1.69 - 1.81: 154 Bond restraints: 24684 Sorted by residual: bond pdb=" C LYS B 377 " pdb=" O LYS B 377 " ideal model delta sigma weight residual 1.236 1.388 -0.152 1.15e-02 7.56e+03 1.74e+02 bond pdb=" C LYS B 376 " pdb=" O LYS B 376 " ideal model delta sigma weight residual 1.236 1.319 -0.082 1.15e-02 7.56e+03 5.14e+01 bond pdb=" C ARG B 390 " pdb=" O ARG B 390 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.26e-02 6.30e+03 3.91e+01 bond pdb=" C ARG B 383 " pdb=" O ARG B 383 " ideal model delta sigma weight residual 1.236 1.304 -0.067 1.15e-02 7.56e+03 3.44e+01 bond pdb=" N LYS B 377 " pdb=" CA LYS B 377 " ideal model delta sigma weight residual 1.459 1.518 -0.059 1.19e-02 7.06e+03 2.47e+01 ... (remaining 24679 not shown) Histogram of bond angle deviations from ideal: 97.16 - 105.71: 667 105.71 - 114.26: 14680 114.26 - 122.81: 15954 122.81 - 131.36: 2160 131.36 - 139.91: 18 Bond angle restraints: 33479 Sorted by residual: angle pdb=" C GLY B 380 " pdb=" N THR B 381 " pdb=" CA THR B 381 " ideal model delta sigma weight residual 120.28 110.58 9.70 1.34e+00 5.57e-01 5.24e+01 angle pdb=" N ASP E 390 " pdb=" CA ASP E 390 " pdb=" C ASP E 390 " ideal model delta sigma weight residual 112.92 104.39 8.53 1.23e+00 6.61e-01 4.81e+01 angle pdb=" N GLY F 216 " pdb=" CA GLY F 216 " pdb=" C GLY F 216 " ideal model delta sigma weight residual 112.85 102.09 10.76 1.61e+00 3.86e-01 4.46e+01 angle pdb=" CA LYS B 376 " pdb=" C LYS B 376 " pdb=" N LYS B 377 " ideal model delta sigma weight residual 117.07 124.47 -7.40 1.14e+00 7.69e-01 4.21e+01 angle pdb=" CA MET E 271 " pdb=" C MET E 271 " pdb=" N PRO E 272 " ideal model delta sigma weight residual 117.67 124.04 -6.37 1.01e+00 9.80e-01 3.98e+01 ... (remaining 33474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.40: 14611 31.40 - 62.79: 432 62.79 - 94.19: 48 94.19 - 125.59: 0 125.59 - 156.99: 2 Dihedral angle restraints: 15093 sinusoidal: 6168 harmonic: 8925 Sorted by residual: dihedral pdb=" O2A ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PA ADP D 602 " pdb=" PB ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 96.99 -156.99 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' ADP D 602 " pdb=" O5' ADP D 602 " pdb=" PA ADP D 602 " pdb=" O2A ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 71.02 -131.02 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" C ASP E 394 " pdb=" N ASP E 394 " pdb=" CA ASP E 394 " pdb=" CB ASP E 394 " ideal model delta harmonic sigma weight residual -122.60 -136.01 13.41 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3522 0.092 - 0.183: 311 0.183 - 0.274: 16 0.274 - 0.366: 6 0.366 - 0.457: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA ASP E 394 " pdb=" N ASP E 394 " pdb=" C ASP E 394 " pdb=" CB ASP E 394 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA LEU B 402 " pdb=" N LEU B 402 " pdb=" C LEU B 402 " pdb=" CB LEU B 402 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LEU E 392 " pdb=" N LEU E 392 " pdb=" C LEU E 392 " pdb=" CB LEU E 392 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 374 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ALA B 374 " 0.075 2.00e-02 2.50e+03 pdb=" O ALA B 374 " -0.028 2.00e-02 2.50e+03 pdb=" N MET B 375 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 389 " -0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C TYR B 389 " 0.069 2.00e-02 2.50e+03 pdb=" O TYR B 389 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG B 390 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 384 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C LEU B 384 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU B 384 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP B 385 " -0.022 2.00e-02 2.50e+03 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 97 2.49 - 3.09: 17561 3.09 - 3.70: 35834 3.70 - 4.30: 53573 4.30 - 4.90: 89751 Nonbonded interactions: 196816 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.918 2.170 nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.919 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 603 " model vdw 1.929 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G ATP B 602 " model vdw 1.980 2.170 ... (remaining 196811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.320 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 67.170 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 24684 Z= 0.353 Angle : 0.757 10.756 33479 Z= 0.474 Chirality : 0.053 0.457 3856 Planarity : 0.005 0.046 4363 Dihedral : 14.804 156.985 9381 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 1.64 % Allowed : 0.90 % Favored : 97.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.38 % 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: 0.59 (0.15), residues: 3115 helix: 1.16 (0.15), residues: 1240 sheet: 0.35 (0.22), residues: 528 loop : -0.21 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 401 PHE 0.016 0.002 PHE A 494 TYR 0.017 0.001 TYR B 248 ARG 0.004 0.000 ARG B 455 *********************** 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 265 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8366 (ttp) cc_final: 0.8012 (ttt) REVERT: D 397 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8213 (mtmm) REVERT: E 393 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7685 (p) REVERT: E 394 ASP cc_start: 0.7486 (p0) cc_final: 0.7099 (p0) REVERT: F 220 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: G 67 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6475 (mmt) REVERT: G 193 ASP cc_start: 0.7263 (m-30) cc_final: 0.7020 (t70) REVERT: G 198 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5900 (ttpt) REVERT: G 241 MET cc_start: 0.8389 (ttp) cc_final: 0.7966 (ttp) outliers start: 42 outliers final: 11 residues processed: 258 average time/residue: 0.3891 time to fit residues: 154.8154 Evaluate side-chains 149 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.9990 chunk 234 optimal weight: 0.0770 chunk 130 optimal weight: 8.9990 chunk 80 optimal weight: 0.1980 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 0.0470 chunk 281 optimal weight: 10.0000 overall best weight: 1.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS D 253 ASN E 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24684 Z= 0.186 Angle : 0.533 8.558 33479 Z= 0.278 Chirality : 0.044 0.250 3856 Planarity : 0.004 0.057 4363 Dihedral : 9.013 164.463 3613 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.05 % Allowed : 5.30 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.85 (0.15), residues: 3115 helix: 1.39 (0.15), residues: 1237 sheet: 0.49 (0.22), residues: 525 loop : -0.08 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 200 PHE 0.020 0.001 PHE B 456 TYR 0.016 0.001 TYR B 248 ARG 0.005 0.000 ARG A 40 *********************** 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 168 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 56 ASP cc_start: 0.7570 (t0) cc_final: 0.7244 (t0) REVERT: E 396 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7280 (t70) REVERT: G 198 LYS cc_start: 0.6369 (OUTLIER) cc_final: 0.5821 (ttpt) REVERT: G 241 MET cc_start: 0.8263 (ttp) cc_final: 0.8047 (ttp) outliers start: 27 outliers final: 12 residues processed: 163 average time/residue: 0.3508 time to fit residues: 94.5173 Evaluate side-chains 134 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN C 215 HIS E 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 24684 Z= 0.523 Angle : 0.686 8.182 33479 Z= 0.358 Chirality : 0.050 0.292 3856 Planarity : 0.005 0.080 4363 Dihedral : 9.048 170.712 3593 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.48 % Allowed : 8.45 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.22 (0.15), residues: 3115 helix: 0.92 (0.15), residues: 1235 sheet: 0.23 (0.22), residues: 532 loop : -0.52 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 470 PHE 0.016 0.002 PHE A 494 TYR 0.026 0.002 TYR B 438 ARG 0.005 0.001 ARG C 127 *********************** 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 150 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 396 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7231 (t0) REVERT: G 198 LYS cc_start: 0.6367 (OUTLIER) cc_final: 0.5809 (ttpt) outliers start: 38 outliers final: 26 residues processed: 141 average time/residue: 0.3345 time to fit residues: 79.7168 Evaluate side-chains 138 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 148 ASP Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN B 433 GLN D 253 ASN F 324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24684 Z= 0.221 Angle : 0.525 7.884 33479 Z= 0.274 Chirality : 0.044 0.200 3856 Planarity : 0.004 0.067 4363 Dihedral : 8.457 170.985 3593 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.48 % Allowed : 9.50 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.57 (0.15), residues: 3115 helix: 1.24 (0.15), residues: 1234 sheet: 0.36 (0.22), residues: 517 loop : -0.32 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 200 PHE 0.013 0.001 PHE B 456 TYR 0.022 0.001 TYR B 438 ARG 0.004 0.000 ARG A 365 *********************** 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 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 2.843 Fit side-chains revert: symmetry clash REVERT: B 95 MET cc_start: 0.9361 (mmm) cc_final: 0.8773 (tpt) REVERT: B 393 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.5895 (pt0) REVERT: D 56 ASP cc_start: 0.7575 (t0) cc_final: 0.7104 (t0) REVERT: E 396 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7232 (t0) REVERT: E 441 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8624 (mt) REVERT: F 43 ASP cc_start: 0.8385 (m-30) cc_final: 0.8121 (m-30) REVERT: G 146 PHE cc_start: 0.6879 (t80) cc_final: 0.6625 (t80) REVERT: G 165 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7316 (m-10) REVERT: G 198 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.5884 (ttpt) outliers start: 38 outliers final: 20 residues processed: 152 average time/residue: 0.3242 time to fit residues: 82.8182 Evaluate side-chains 139 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 4 optimal weight: 0.0070 chunk 223 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN E 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24684 Z= 0.414 Angle : 0.608 7.813 33479 Z= 0.316 Chirality : 0.047 0.303 3856 Planarity : 0.005 0.062 4363 Dihedral : 8.437 172.780 3592 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.06 % Allowed : 11.02 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.33 (0.15), residues: 3115 helix: 1.06 (0.15), residues: 1230 sheet: 0.23 (0.22), residues: 523 loop : -0.49 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 200 PHE 0.016 0.002 PHE A 494 TYR 0.021 0.002 TYR B 248 ARG 0.004 0.000 ARG A 365 *********************** 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 168 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 115 time to evaluate : 2.749 Fit side-chains REVERT: B 393 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5958 (pt0) REVERT: D 56 ASP cc_start: 0.7627 (t0) cc_final: 0.7145 (t0) REVERT: E 441 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8688 (mt) REVERT: G 165 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: G 198 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5865 (ttpt) outliers start: 53 outliers final: 29 residues processed: 157 average time/residue: 0.3083 time to fit residues: 83.2550 Evaluate side-chains 142 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 148 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24684 Z= 0.178 Angle : 0.496 8.504 33479 Z= 0.258 Chirality : 0.043 0.241 3856 Planarity : 0.004 0.058 4363 Dihedral : 7.788 172.035 3592 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.91 % Allowed : 11.68 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.72 (0.15), residues: 3115 helix: 1.42 (0.15), residues: 1219 sheet: 0.48 (0.22), residues: 513 loop : -0.30 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.023 0.001 PHE G 126 TYR 0.019 0.001 TYR G 226 ARG 0.003 0.000 ARG A 40 *********************** 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 167 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 118 time to evaluate : 2.682 Fit side-chains REVERT: A 236 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8543 (t80) REVERT: B 357 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8927 (mp) REVERT: B 393 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6569 (pt0) REVERT: D 56 ASP cc_start: 0.7588 (t0) cc_final: 0.7181 (t0) REVERT: E 441 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8672 (mt) REVERT: G 146 PHE cc_start: 0.6884 (t80) cc_final: 0.6233 (m-80) REVERT: G 165 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7239 (m-80) REVERT: G 198 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.5942 (ttpt) outliers start: 49 outliers final: 28 residues processed: 156 average time/residue: 0.3244 time to fit residues: 86.1598 Evaluate side-chains 146 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 10.0000 chunk 33 optimal weight: 0.0470 chunk 170 optimal weight: 10.0000 chunk 219 optimal weight: 0.0370 chunk 169 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 overall best weight: 3.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN B 483 ASN G 65 HIS ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24684 Z= 0.267 Angle : 0.536 11.360 33479 Z= 0.276 Chirality : 0.044 0.308 3856 Planarity : 0.004 0.056 4363 Dihedral : 7.780 172.438 3591 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.02 % Allowed : 12.23 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.66 (0.15), residues: 3115 helix: 1.37 (0.15), residues: 1216 sheet: 0.41 (0.22), residues: 514 loop : -0.32 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 200 PHE 0.013 0.001 PHE A 494 TYR 0.016 0.001 TYR B 248 ARG 0.002 0.000 ARG A 365 *********************** 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 166 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 114 time to evaluate : 3.257 Fit side-chains REVERT: A 236 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8584 (t80) REVERT: B 357 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8910 (mp) REVERT: B 393 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6011 (pt0) REVERT: D 56 ASP cc_start: 0.7569 (t0) cc_final: 0.7154 (t0) REVERT: D 140 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: E 332 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7125 (tm-30) REVERT: E 441 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8669 (mt) REVERT: G 165 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: G 198 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5961 (ttpt) outliers start: 52 outliers final: 35 residues processed: 156 average time/residue: 0.3098 time to fit residues: 83.3071 Evaluate side-chains 150 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 148 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 ASN G 65 HIS ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24684 Z= 0.185 Angle : 0.498 10.012 33479 Z= 0.257 Chirality : 0.043 0.273 3856 Planarity : 0.004 0.089 4363 Dihedral : 7.567 171.752 3591 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.83 % Allowed : 12.58 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.83 (0.15), residues: 3115 helix: 1.51 (0.15), residues: 1213 sheet: 0.51 (0.22), residues: 516 loop : -0.21 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.012 0.001 PHE A 494 TYR 0.016 0.001 TYR B 438 ARG 0.002 0.000 ARG A 40 *********************** 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 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 115 time to evaluate : 2.745 Fit side-chains REVERT: A 236 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8528 (t80) REVERT: B 357 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8895 (mp) REVERT: B 393 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6036 (pt0) REVERT: D 56 ASP cc_start: 0.7530 (t0) cc_final: 0.7126 (t0) REVERT: E 441 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8664 (mt) REVERT: G 165 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: G 198 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.5982 (ttpt) outliers start: 47 outliers final: 33 residues processed: 152 average time/residue: 0.3234 time to fit residues: 83.8224 Evaluate side-chains 150 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 111 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 10.0000 chunk 286 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 251 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 chunk 277 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 ASN G 65 HIS ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24684 Z= 0.182 Angle : 0.494 9.351 33479 Z= 0.254 Chirality : 0.043 0.257 3856 Planarity : 0.004 0.082 4363 Dihedral : 7.427 171.203 3591 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.75 % Allowed : 12.73 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.56 (0.15), residues: 1212 sheet: 0.58 (0.22), residues: 522 loop : -0.17 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.014 0.001 PHE G 42 TYR 0.015 0.001 TYR B 438 ARG 0.002 0.000 ARG A 40 *********************** 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 163 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 3.302 Fit side-chains REVERT: A 236 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8519 (t80) REVERT: B 357 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8893 (mp) REVERT: B 393 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6077 (pt0) REVERT: D 56 ASP cc_start: 0.7533 (t0) cc_final: 0.7138 (t0) REVERT: D 140 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7984 (mttt) REVERT: E 332 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7193 (tm-30) REVERT: G 165 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: G 198 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5919 (ttpt) outliers start: 45 outliers final: 34 residues processed: 150 average time/residue: 0.3165 time to fit residues: 80.3943 Evaluate side-chains 150 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 110 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 ASN G 65 HIS ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24684 Z= 0.244 Angle : 0.522 10.086 33479 Z= 0.268 Chirality : 0.044 0.314 3856 Planarity : 0.004 0.077 4363 Dihedral : 7.500 172.389 3591 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.91 % Allowed : 12.77 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.85 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1210 sheet: 0.53 (0.22), residues: 522 loop : -0.22 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 200 PHE 0.015 0.001 PHE G 42 TYR 0.014 0.001 TYR B 248 ARG 0.003 0.000 ARG D 256 ********************** 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 160 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 111 time to evaluate : 2.846 Fit side-chains REVERT: A 236 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8532 (t80) REVERT: B 357 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8913 (mp) REVERT: B 393 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6106 (pt0) REVERT: D 56 ASP cc_start: 0.7554 (t0) cc_final: 0.7148 (t0) REVERT: D 140 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8033 (mttt) REVERT: E 332 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7232 (tm-30) REVERT: G 67 MET cc_start: 0.5286 (ppp) cc_final: 0.4192 (mtt) REVERT: G 165 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7047 (m-10) REVERT: G 198 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.5959 (ttpt) outliers start: 49 outliers final: 37 residues processed: 150 average time/residue: 0.3175 time to fit residues: 80.8020 Evaluate side-chains 151 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 108 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 ASN D 253 ASN G 65 HIS ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062056 restraints weight = 64548.176| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.63 r_work: 0.2908 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24684 Z= 0.322 Angle : 0.563 9.042 33479 Z= 0.290 Chirality : 0.045 0.297 3856 Planarity : 0.004 0.074 4363 Dihedral : 7.678 174.427 3591 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.71 % Allowed : 13.08 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.67 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1213 sheet: 0.43 (0.22), residues: 525 loop : -0.34 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 200 PHE 0.015 0.002 PHE A 494 TYR 0.017 0.001 TYR B 248 ARG 0.003 0.000 ARG D 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.64 seconds wall clock time: 74 minutes 44.75 seconds (4484.75 seconds total)