Starting phenix.real_space_refine on Mon Feb 19 08:12:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xko_33258/02_2024/7xko_33258_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xko_33258/02_2024/7xko_33258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xko_33258/02_2024/7xko_33258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xko_33258/02_2024/7xko_33258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xko_33258/02_2024/7xko_33258_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xko_33258/02_2024/7xko_33258_updated.pdb" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 77 5.16 5 C 15217 2.51 5 N 4187 2.21 5 O 4593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 194": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24075 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" 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: "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: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} 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: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} 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: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {' PI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.92, per 1000 atoms: 0.54 Number of scatterers: 24075 At special positions: 0 Unit cell: (129.36, 132, 155.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 1 15.00 O 4593 8.00 N 4187 7.00 C 15217 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.52 Conformation dependent library (CDL) restraints added in 5.0 seconds 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 22 sheets defined 41.4% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 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 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.579A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.694A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 4.055A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) 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 397 removed outlier: 3.706A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.814A pdb=" N VAL A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.732A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.694A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.064A 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 300 removed outlier: 3.640A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.012A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 397 Processing helix chain 'B' and resid 405 through 420 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 4.908A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 459 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.810A pdb=" N LYS B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.560A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.580A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.364A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 395 removed outlier: 4.269A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.472A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 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 207 through 210 Processing helix chain 'D' and resid 222 through 241 removed outlier: 3.588A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.712A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.599A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 323 removed outlier: 3.674A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 4.239A pdb=" N LEU D 387 " --> pdb=" O ILE D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 410 removed outlier: 3.798A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.165A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 441 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.618A 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 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 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 5.152A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.585A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.530A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 361 through 387 removed outlier: 4.280A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.554A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.564A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.607A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 140 through 144 Processing helix chain 'F' and resid 164 through 178 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: 5.210A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.543A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.371A 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: 3.783A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 386 removed outlier: 4.296A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F 385 " --> pdb=" O GLN F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 410 Processing helix chain 'F' and resid 416 through 421 removed outlier: 3.544A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 441 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 Processing helix chain 'G' and resid 4 through 41 removed outlier: 3.944A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 53 Processing helix chain 'G' and resid 90 through 106 removed outlier: 3.944A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR G 100 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 removed outlier: 4.206A pdb=" N PHE G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE G 126 " --> pdb=" O GLY G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 removed outlier: 4.072A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 282 Proline residue: G 218 - end of helix removed outlier: 3.612A pdb=" N THR G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.644A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.281A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.786A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N HIS A 255 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE A 194 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A 257 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 196 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 259 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 198 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.924A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.569A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.752A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 340 through 344 removed outlier: 4.433A pdb=" N ASP B 170 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.673A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.520A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.295A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 340 through 343 Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.735A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.641A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (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: 8.633A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.787A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 330 removed outlier: 8.699A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.740A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.691A 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 94 through 96 removed outlier: 4.020A pdb=" N ARG F 94 " --> pdb=" O THR F 211 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU F 248 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA F 186 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE F 250 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL F 188 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA F 327 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N PHE F 157 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR F 329 " --> pdb=" O PHE F 157 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.868A pdb=" N ALA G 114 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU G 167 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU G 79 " --> pdb=" O GLU G 167 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N TYR G 169 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE G 81 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR G 171 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU G 189 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) 928 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: 8.12 Time building geometry restraints manager: 11.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8210 1.34 - 1.46: 3926 1.46 - 1.57: 12186 1.57 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 24476 Sorted by residual: bond pdb=" O4 PI D 501 " pdb=" P PI D 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" O3 PI D 501 " pdb=" P PI D 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" O1 PI D 501 " pdb=" P PI D 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" O2 PI D 501 " pdb=" P PI D 501 " ideal model delta sigma weight residual 1.562 1.525 0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" CG PRO E 342 " pdb=" CD PRO E 342 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.58e+00 ... (remaining 24471 not shown) Histogram of bond angle deviations from ideal: 98.25 - 104.92: 492 104.92 - 111.60: 11235 111.60 - 118.27: 7208 118.27 - 124.94: 14001 124.94 - 131.61: 218 Bond angle restraints: 33154 Sorted by residual: angle pdb=" N THR E 2 " pdb=" CA THR E 2 " pdb=" C THR E 2 " ideal model delta sigma weight residual 113.50 110.43 3.07 1.23e+00 6.61e-01 6.22e+00 angle pdb=" CA GLN B 172 " pdb=" CB GLN B 172 " pdb=" CG GLN B 172 " ideal model delta sigma weight residual 114.10 118.97 -4.87 2.00e+00 2.50e-01 5.93e+00 angle pdb=" N LEU G 87 " pdb=" CA LEU G 87 " pdb=" C LEU G 87 " ideal model delta sigma weight residual 108.58 112.74 -4.16 1.82e+00 3.02e-01 5.22e+00 angle pdb=" N LEU D 455 " pdb=" CA LEU D 455 " pdb=" C LEU D 455 " ideal model delta sigma weight residual 110.61 113.44 -2.83 1.25e+00 6.40e-01 5.12e+00 angle pdb=" CA ILE E 386 " pdb=" C ILE E 386 " pdb=" N LEU E 387 " ideal model delta sigma weight residual 116.60 119.81 -3.21 1.45e+00 4.76e-01 4.89e+00 ... (remaining 33149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 13689 17.82 - 35.63: 969 35.63 - 53.45: 178 53.45 - 71.27: 43 71.27 - 89.09: 25 Dihedral angle restraints: 14904 sinusoidal: 5985 harmonic: 8919 Sorted by residual: dihedral pdb=" CA TYR F 341 " pdb=" C TYR F 341 " pdb=" N PRO F 342 " pdb=" CA PRO F 342 " ideal model delta harmonic sigma weight residual 180.00 141.96 38.04 0 5.00e+00 4.00e-02 5.79e+01 dihedral pdb=" CA ARG B 354 " pdb=" C ARG B 354 " pdb=" N PRO B 355 " pdb=" CA PRO B 355 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA GLN F 217 " pdb=" C GLN F 217 " pdb=" N MET F 218 " pdb=" CA MET F 218 " ideal model delta harmonic sigma weight residual 180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 14901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2174 0.028 - 0.056: 984 0.056 - 0.084: 364 0.084 - 0.112: 244 0.112 - 0.140: 62 Chirality restraints: 3828 Sorted by residual: chirality pdb=" CB ILE D 386 " pdb=" CA ILE D 386 " pdb=" CG1 ILE D 386 " pdb=" CG2 ILE D 386 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE D 109 " pdb=" N ILE D 109 " pdb=" C ILE D 109 " pdb=" CB ILE D 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 357 " pdb=" N ILE B 357 " pdb=" C ILE B 357 " pdb=" CB ILE B 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 3825 not shown) Planarity restraints: 4355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO C 110 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 11 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO F 12 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 12 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 12 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO D 221 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.026 5.00e-02 4.00e+02 ... (remaining 4352 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 583 2.71 - 3.26: 24794 3.26 - 3.80: 37974 3.80 - 4.35: 48620 4.35 - 4.90: 82505 Nonbonded interactions: 194476 Sorted by model distance: nonbonded pdb=" O ILE G 103 " pdb=" ND1 HIS G 107 " model vdw 2.161 2.520 nonbonded pdb=" O THR F 137 " pdb=" ND2 ASN F 174 " model vdw 2.252 2.520 nonbonded pdb=" OE1 GLU E 136 " pdb=" OH TYR E 427 " model vdw 2.265 2.440 nonbonded pdb=" O ALA D 29 " pdb=" OG1 THR D 79 " model vdw 2.287 2.440 nonbonded pdb=" OH TYR C 195 " pdb=" OD1 ASP C 261 " model vdw 2.292 2.440 ... (remaining 194471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 0.030 Extract box with map and model: 12.460 Check model and map are aligned: 0.340 Set scattering table: 0.230 Process input model: 67.580 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.003 0.038 24476 Z= 0.199 Angle : 0.483 6.615 33154 Z= 0.263 Chirality : 0.043 0.140 3828 Planarity : 0.004 0.049 4355 Dihedral : 13.405 89.085 9196 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.15), residues: 3113 helix: 1.84 (0.15), residues: 1245 sheet: 0.70 (0.23), residues: 508 loop : 0.23 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.013 0.001 PHE D 322 TYR 0.012 0.001 TYR A 248 ARG 0.002 0.000 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.891 Fit side-chains REVERT: D 252 ASP cc_start: 0.7469 (p0) cc_final: 0.7183 (p0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3251 time to fit residues: 60.8270 Evaluate side-chains 93 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 80 optimal weight: 0.1980 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 overall best weight: 4.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN E 8 GLN E 401 HIS ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24476 Z= 0.376 Angle : 0.547 6.757 33154 Z= 0.287 Chirality : 0.046 0.140 3828 Planarity : 0.005 0.090 4355 Dihedral : 4.388 35.804 3397 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.55 % Allowed : 4.87 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3113 helix: 1.64 (0.15), residues: 1247 sheet: 0.47 (0.22), residues: 533 loop : 0.08 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.014 0.002 PHE A 463 TYR 0.016 0.001 TYR A 329 ARG 0.006 0.000 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 2.920 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 99 average time/residue: 0.3096 time to fit residues: 54.4348 Evaluate side-chains 97 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 chunk 304 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN E 8 GLN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24476 Z= 0.123 Angle : 0.437 6.206 33154 Z= 0.229 Chirality : 0.042 0.145 3828 Planarity : 0.004 0.072 4355 Dihedral : 3.990 34.533 3397 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.39 % Allowed : 6.94 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.15), residues: 3113 helix: 1.85 (0.15), residues: 1245 sheet: 0.66 (0.23), residues: 521 loop : 0.17 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.011 0.001 PHE C 463 TYR 0.010 0.001 TYR B 248 ARG 0.003 0.000 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 2.998 Fit side-chains REVERT: C 157 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8972 (m) outliers start: 10 outliers final: 6 residues processed: 104 average time/residue: 0.3057 time to fit residues: 56.0927 Evaluate side-chains 102 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 6 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 299 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN B 488 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 24476 Z= 0.509 Angle : 0.607 6.625 33154 Z= 0.317 Chirality : 0.048 0.156 3828 Planarity : 0.005 0.080 4355 Dihedral : 4.551 37.793 3397 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.29 % Allowed : 8.34 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.89 (0.15), residues: 3113 helix: 1.47 (0.15), residues: 1230 sheet: 0.38 (0.22), residues: 525 loop : -0.04 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 363 PHE 0.015 0.002 PHE E 255 TYR 0.017 0.002 TYR A 329 ARG 0.006 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 2.686 Fit side-chains REVERT: B 348 LEU cc_start: 0.5958 (mt) cc_final: 0.5734 (mt) REVERT: C 157 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.9017 (m) REVERT: C 375 MET cc_start: 0.8632 (tpt) cc_final: 0.8271 (tpp) outliers start: 33 outliers final: 21 residues processed: 117 average time/residue: 0.2839 time to fit residues: 58.8730 Evaluate side-chains 110 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 107 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 223 optimal weight: 0.0000 chunk 123 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24476 Z= 0.193 Angle : 0.464 6.533 33154 Z= 0.242 Chirality : 0.043 0.140 3828 Planarity : 0.004 0.072 4355 Dihedral : 4.201 35.884 3397 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.90 % Allowed : 9.55 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3113 helix: 1.71 (0.15), residues: 1235 sheet: 0.49 (0.22), residues: 529 loop : 0.00 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.011 0.001 PHE E 257 TYR 0.011 0.001 TYR B 248 ARG 0.003 0.000 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 3.012 Fit side-chains REVERT: C 157 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.9008 (m) outliers start: 23 outliers final: 15 residues processed: 111 average time/residue: 0.3012 time to fit residues: 59.6353 Evaluate side-chains 106 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 6 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 299 optimal weight: 20.0000 chunk 248 optimal weight: 0.0770 chunk 138 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 24476 Z= 0.459 Angle : 0.582 7.802 33154 Z= 0.302 Chirality : 0.047 0.148 3828 Planarity : 0.004 0.078 4355 Dihedral : 4.525 38.134 3397 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.33 % Allowed : 10.17 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3113 helix: 1.46 (0.15), residues: 1225 sheet: 0.25 (0.22), residues: 530 loop : -0.18 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 200 PHE 0.014 0.002 PHE E 257 TYR 0.013 0.002 TYR A 240 ARG 0.005 0.000 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 87 time to evaluate : 2.908 Fit side-chains outliers start: 34 outliers final: 28 residues processed: 118 average time/residue: 0.2977 time to fit residues: 62.4342 Evaluate side-chains 115 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 107 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 252 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 423 GLN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24476 Z= 0.338 Angle : 0.526 9.081 33154 Z= 0.273 Chirality : 0.045 0.197 3828 Planarity : 0.004 0.073 4355 Dihedral : 4.431 37.613 3397 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.44 % Allowed : 10.64 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3113 helix: 1.47 (0.15), residues: 1232 sheet: 0.29 (0.22), residues: 529 loop : -0.21 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 107 PHE 0.013 0.001 PHE E 257 TYR 0.020 0.001 TYR G 78 ARG 0.004 0.000 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 88 time to evaluate : 2.987 Fit side-chains REVERT: B 348 LEU cc_start: 0.6196 (mt) cc_final: 0.5947 (mt) outliers start: 37 outliers final: 34 residues processed: 121 average time/residue: 0.2985 time to fit residues: 64.4095 Evaluate side-chains 122 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 236 GLU 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: 7.9990 chunk 178 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 ASN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24476 Z= 0.416 Angle : 0.570 10.829 33154 Z= 0.294 Chirality : 0.046 0.187 3828 Planarity : 0.004 0.078 4355 Dihedral : 4.547 38.490 3397 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.71 % Allowed : 10.76 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.62 (0.15), residues: 3113 helix: 1.39 (0.15), residues: 1226 sheet: 0.19 (0.22), residues: 529 loop : -0.31 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.013 0.002 PHE E 257 TYR 0.021 0.001 TYR G 78 ARG 0.005 0.000 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 88 time to evaluate : 2.955 Fit side-chains REVERT: B 348 LEU cc_start: 0.6249 (mt) cc_final: 0.5975 (mt) REVERT: D 252 ASP cc_start: 0.7514 (p0) cc_final: 0.7244 (p0) REVERT: F 469 MET cc_start: 0.7842 (mtt) cc_final: 0.7137 (mtp) outliers start: 44 outliers final: 41 residues processed: 129 average time/residue: 0.2958 time to fit residues: 67.6838 Evaluate side-chains 129 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 88 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 236 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: 10.0000 chunk 261 optimal weight: 0.0980 chunk 278 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 263 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24476 Z= 0.195 Angle : 0.474 12.061 33154 Z= 0.245 Chirality : 0.043 0.169 3828 Planarity : 0.004 0.069 4355 Dihedral : 4.224 36.470 3397 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.21 % Allowed : 11.42 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.94 (0.15), residues: 3113 helix: 1.66 (0.15), residues: 1227 sheet: 0.37 (0.22), residues: 531 loop : -0.14 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.013 0.001 PHE E 257 TYR 0.017 0.001 TYR G 78 ARG 0.002 0.000 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 2.949 Fit side-chains REVERT: B 348 LEU cc_start: 0.6126 (mt) cc_final: 0.5867 (mt) REVERT: D 252 ASP cc_start: 0.7502 (p0) cc_final: 0.7245 (p0) REVERT: F 469 MET cc_start: 0.7798 (mtt) cc_final: 0.7097 (mtp) outliers start: 31 outliers final: 30 residues processed: 118 average time/residue: 0.2977 time to fit residues: 62.5230 Evaluate side-chains 120 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 236 GLU 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: 9.9990 chunk 179 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24476 Z= 0.427 Angle : 0.570 13.066 33154 Z= 0.294 Chirality : 0.046 0.171 3828 Planarity : 0.004 0.078 4355 Dihedral : 4.484 38.525 3397 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.21 % Allowed : 11.42 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3113 helix: 1.42 (0.15), residues: 1230 sheet: 0.23 (0.22), residues: 530 loop : -0.28 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.013 0.002 PHE E 453 TYR 0.020 0.001 TYR G 78 ARG 0.005 0.000 ARG F 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 3.190 Fit side-chains REVERT: B 348 LEU cc_start: 0.6234 (mt) cc_final: 0.5941 (mt) REVERT: D 252 ASP cc_start: 0.7566 (p0) cc_final: 0.7277 (p0) REVERT: F 469 MET cc_start: 0.7786 (mtt) cc_final: 0.7087 (mtp) outliers start: 31 outliers final: 31 residues processed: 117 average time/residue: 0.3070 time to fit residues: 64.0430 Evaluate side-chains 119 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 236 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 1.9990 chunk 261 optimal weight: 0.0170 chunk 75 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.043294 restraints weight = 87161.261| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.03 r_work: 0.2602 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24476 Z= 0.168 Angle : 0.466 13.026 33154 Z= 0.239 Chirality : 0.043 0.160 3828 Planarity : 0.004 0.068 4355 Dihedral : 4.142 35.742 3397 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.29 % Allowed : 11.54 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.99 (0.15), residues: 3113 helix: 1.71 (0.15), residues: 1227 sheet: 0.41 (0.23), residues: 519 loop : -0.14 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.013 0.001 PHE E 257 TYR 0.016 0.001 TYR G 78 ARG 0.003 0.000 ARG F 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.96 seconds wall clock time: 69 minutes 27.34 seconds (4167.34 seconds total)