Starting phenix.real_space_refine on Mon Feb 19 09:51:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh5_34752/02_2024/8hh5_34752_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh5_34752/02_2024/8hh5_34752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh5_34752/02_2024/8hh5_34752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh5_34752/02_2024/8hh5_34752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh5_34752/02_2024/8hh5_34752_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh5_34752/02_2024/8hh5_34752_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 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 "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "F GLU 337": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 442": "OE1" <-> "OE2" Residue "G GLU 273": "OE1" <-> "OE2" Residue "G GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: {'PTRANS': 10, '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: 12.43, per 1000 atoms: 0.51 Number of scatterers: 24277 At special positions: 0 Unit cell: (125.84, 124.96, 152.24, 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: 9.49 Conformation dependent library (CDL) restraints added in 4.5 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 23 sheets defined 41.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.25 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 186 removed outlier: 3.579A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.617A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.022A 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: 4.574A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 391 removed outlier: 3.886A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.855A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.668A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.576A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.637A 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 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: 3.779A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 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 288 through 300 removed outlier: 4.353A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.843A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 413 through 420 Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.642A pdb=" N ILE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.675A pdb=" N VAL B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR B 461 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 486 through 497 removed outlier: 4.038A pdb=" N ALA B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 4.441A 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 220 removed outlier: 3.500A pdb=" N TYR C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) No H-bonds generated for '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: 3.683A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.661A 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: 4.225A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (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 392 removed outlier: 4.565A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 398 No H-bonds generated for 'chain 'C' and resid 396 through 398' 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: 3.526A pdb=" N VAL C 453 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 461 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 495 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 145 Processing helix chain 'D' and resid 164 through 179 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: 3.598A pdb=" N VAL D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.730A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.173A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 removed outlier: 3.536A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) 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 379 removed outlier: 3.768A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.627A 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: 3.947A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.897A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 removed outlier: 3.563A pdb=" N ARG D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.657A 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 145 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 225 No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 228 through 242 removed outlier: 3.842A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.507A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.539A 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: 3.576A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.179A 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 361 through 386 removed outlier: 4.051A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.695A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 421 No H-bonds generated for 'chain 'E' and resid 418 through 421' Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 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 145 Processing helix chain 'F' and resid 164 through 175 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 225 No H-bonds generated for 'chain 'F' and resid 222 through 225' Processing helix chain 'F' and resid 228 through 241 removed outlier: 3.543A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 4.189A pdb=" N ALA F 266 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 276 No H-bonds generated for 'chain 'F' and resid 274 through 276' Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.504A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.389A 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: 3.633A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.669A 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 387 removed outlier: 3.729A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.070A 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: 3.675A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.863A 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 441 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.539A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 56 removed outlier: 4.172A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 89 through 106 removed outlier: 4.123A pdb=" N ASN G 92 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL G 95 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU G 98 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN G 101 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR G 102 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLN G 104 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 105 " --> pdb=" O THR G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 126 removed outlier: 3.551A pdb=" N SER G 124 " --> pdb=" O ARG G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.995A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP G 162 " --> pdb=" O GLY G 158 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLY G 163 " --> pdb=" O LEU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 283 Proline residue: G 218 - end of helix removed outlier: 3.979A pdb=" N GLN G 267 " --> pdb=" O ASN G 263 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA G 269 " --> pdb=" O ALA G 265 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.522A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.074A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.765A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 8.886A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N HIS A 255 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE A 194 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 257 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL A 196 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 259 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE A 198 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.462A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.910A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.631A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.611A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.537A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.526A 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: 3.904A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.826A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 5 through 9 removed outlier: 6.497A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.535A 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: 3.637A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.625A 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: 6.597A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.581A 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: 8.613A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 5 removed outlier: 5.770A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (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: 7.730A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 114 through 118 removed outlier: 7.134A pdb=" N TYR G 169 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE G 81 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR G 171 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 172 through 175 removed outlier: 3.586A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2493 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: 8.42 Time building geometry restraints manager: 10.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8233 1.34 - 1.46: 3836 1.46 - 1.58: 12434 1.58 - 1.69: 27 1.69 - 1.81: 154 Bond restraints: 24684 Sorted by residual: bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.506 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.506 0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" CA VAL G 73 " pdb=" CB VAL G 73 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.18e+00 ... (remaining 24679 not shown) Histogram of bond angle deviations from ideal: 99.64 - 107.67: 948 107.67 - 115.70: 15368 115.70 - 123.73: 16659 123.73 - 131.76: 486 131.76 - 139.79: 18 Bond angle restraints: 33479 Sorted by residual: angle pdb=" N VAL C 366 " pdb=" CA VAL C 366 " pdb=" C VAL C 366 " ideal model delta sigma weight residual 111.91 106.58 5.33 8.90e-01 1.26e+00 3.59e+01 angle pdb=" C ASN E 97 " pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 121.97 132.10 -10.13 1.80e+00 3.09e-01 3.16e+01 angle pdb=" N VAL B 366 " pdb=" CA VAL B 366 " pdb=" C VAL B 366 " ideal model delta sigma weight residual 113.42 108.65 4.77 1.17e+00 7.31e-01 1.66e+01 angle pdb=" N VAL E 98 " pdb=" CA VAL E 98 " pdb=" CB VAL E 98 " ideal model delta sigma weight residual 111.23 116.95 -5.72 1.65e+00 3.67e-01 1.20e+01 angle pdb=" N ASP A 262 " pdb=" CA ASP A 262 " pdb=" C ASP A 262 " ideal model delta sigma weight residual 107.32 112.98 -5.66 1.65e+00 3.67e-01 1.18e+01 ... (remaining 33474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.41: 14710 33.41 - 66.82: 332 66.82 - 100.23: 49 100.23 - 133.64: 0 133.64 - 167.05: 2 Dihedral angle restraints: 15093 sinusoidal: 6168 harmonic: 8925 Sorted by residual: dihedral pdb=" O2A ADP D 603 " pdb=" O3A ADP D 603 " pdb=" PA ADP D 603 " pdb=" PB ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 107.05 -167.05 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual 300.00 133.97 166.03 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" CA LEU G 159 " pdb=" C LEU G 159 " pdb=" N PHE G 160 " pdb=" CA PHE G 160 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2279 0.031 - 0.063: 998 0.063 - 0.094: 341 0.094 - 0.126: 208 0.126 - 0.157: 30 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA VAL E 214 " pdb=" N VAL E 214 " pdb=" C VAL E 214 " pdb=" CB VAL E 214 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB THR F 301 " pdb=" CA THR F 301 " pdb=" OG1 THR F 301 " pdb=" CG2 THR F 301 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL E 456 " pdb=" N VAL E 456 " pdb=" C VAL E 456 " pdb=" CB VAL E 456 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 43 " 0.067 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO G 44 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO G 44 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO G 44 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 220 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO F 221 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO E 316 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.023 5.00e-02 4.00e+02 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 91 2.48 - 3.09: 17273 3.09 - 3.69: 35773 3.69 - 4.30: 54024 4.30 - 4.90: 90928 Nonbonded interactions: 198089 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O4 PO4 D 602 " model vdw 1.881 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.943 2.170 nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.984 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.005 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.008 2.170 ... (remaining 198084 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.200 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 64.660 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24684 Z= 0.233 Angle : 0.603 10.126 33479 Z= 0.346 Chirality : 0.045 0.157 3856 Planarity : 0.005 0.100 4363 Dihedral : 14.432 167.050 9381 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1277 sheet: 0.82 (0.22), residues: 511 loop : 0.03 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 363 PHE 0.011 0.001 PHE E 125 TYR 0.025 0.001 TYR G 175 ARG 0.014 0.000 ARG G 264 *********************** 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 201 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.812 Fit side-chains REVERT: B 418 GLU cc_start: 0.8319 (tp30) cc_final: 0.8068 (mp0) REVERT: D 56 ASP cc_start: 0.7984 (t0) cc_final: 0.7749 (t0) REVERT: D 311 ASP cc_start: 0.7999 (t70) cc_final: 0.7732 (t0) REVERT: D 469 MET cc_start: 0.8388 (mtm) cc_final: 0.8177 (mtp) REVERT: E 407 GLN cc_start: 0.8732 (tt0) cc_final: 0.8398 (tt0) REVERT: G 26 MET cc_start: 0.7575 (mmm) cc_final: 0.6866 (mmm) outliers start: 0 outliers final: 1 residues processed: 201 average time/residue: 1.3845 time to fit residues: 321.6130 Evaluate side-chains 143 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 80 optimal weight: 0.0770 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24684 Z= 0.404 Angle : 0.610 7.423 33479 Z= 0.320 Chirality : 0.048 0.188 3856 Planarity : 0.005 0.040 4363 Dihedral : 9.270 158.966 3582 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 1.32 % Allowed : 6.97 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3115 helix: 1.04 (0.15), residues: 1262 sheet: 0.54 (0.22), residues: 525 loop : -0.14 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 363 PHE 0.029 0.002 PHE B 350 TYR 0.018 0.002 TYR G 91 ARG 0.007 0.001 ARG G 264 *********************** 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 187 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 2.798 Fit side-chains REVERT: C 67 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: D 56 ASP cc_start: 0.8072 (t0) cc_final: 0.7831 (t0) REVERT: D 311 ASP cc_start: 0.8019 (t70) cc_final: 0.7609 (t0) REVERT: E 392 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8041 (mm) REVERT: E 407 GLN cc_start: 0.8734 (tt0) cc_final: 0.8445 (tt0) REVERT: G 26 MET cc_start: 0.7457 (mmm) cc_final: 0.6653 (mmm) REVERT: G 34 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.4635 (ttp80) REVERT: G 244 MET cc_start: 0.6207 (mmp) cc_final: 0.5978 (mmp) outliers start: 34 outliers final: 15 residues processed: 170 average time/residue: 1.3388 time to fit residues: 264.6393 Evaluate side-chains 163 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 282 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 chunk 251 optimal weight: 0.8980 chunk 279 optimal weight: 0.0670 chunk 96 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24684 Z= 0.211 Angle : 0.514 7.698 33479 Z= 0.267 Chirality : 0.044 0.147 3856 Planarity : 0.004 0.041 4363 Dihedral : 8.654 150.261 3580 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 1.32 % Allowed : 9.35 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3115 helix: 1.21 (0.15), residues: 1263 sheet: 0.61 (0.22), residues: 526 loop : -0.07 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 363 PHE 0.020 0.001 PHE B 350 TYR 0.015 0.001 TYR G 262 ARG 0.004 0.000 ARG E 333 *********************** 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 193 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 2.603 Fit side-chains REVERT: C 67 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: D 56 ASP cc_start: 0.8098 (t0) cc_final: 0.7861 (t0) REVERT: D 311 ASP cc_start: 0.8016 (t70) cc_final: 0.7575 (t0) REVERT: D 469 MET cc_start: 0.8311 (mtp) cc_final: 0.8045 (mtm) REVERT: E 333 ARG cc_start: 0.8501 (tpp80) cc_final: 0.7908 (tpp-160) REVERT: E 407 GLN cc_start: 0.8691 (tt0) cc_final: 0.8342 (tt0) REVERT: G 26 MET cc_start: 0.7419 (mmm) cc_final: 0.6576 (mmm) outliers start: 34 outliers final: 15 residues processed: 177 average time/residue: 1.2615 time to fit residues: 261.0652 Evaluate side-chains 165 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 249 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.1980 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN F 8 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24684 Z= 0.217 Angle : 0.510 7.094 33479 Z= 0.263 Chirality : 0.044 0.149 3856 Planarity : 0.004 0.040 4363 Dihedral : 8.430 147.461 3580 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 1.75 % Allowed : 10.63 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3115 helix: 1.23 (0.15), residues: 1268 sheet: 0.67 (0.23), residues: 524 loop : -0.07 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.025 0.001 PHE G 126 TYR 0.013 0.001 TYR G 91 ARG 0.003 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 3.092 Fit side-chains REVERT: B 191 MET cc_start: 0.8575 (ttp) cc_final: 0.8297 (ttp) REVERT: C 499 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8970 (m) REVERT: D 56 ASP cc_start: 0.8094 (t0) cc_final: 0.7851 (t0) REVERT: D 311 ASP cc_start: 0.7999 (t70) cc_final: 0.7541 (t0) REVERT: D 469 MET cc_start: 0.8356 (mtp) cc_final: 0.8114 (mtm) REVERT: E 2 THR cc_start: 0.6697 (OUTLIER) cc_final: 0.6253 (t) REVERT: E 333 ARG cc_start: 0.8529 (tpp80) cc_final: 0.7953 (tpp-160) REVERT: E 407 GLN cc_start: 0.8667 (tt0) cc_final: 0.8466 (tt0) REVERT: G 26 MET cc_start: 0.7401 (mmm) cc_final: 0.6579 (mmm) REVERT: G 87 LEU cc_start: 0.8594 (mt) cc_final: 0.8291 (mm) REVERT: G 175 TYR cc_start: 0.3754 (p90) cc_final: 0.3261 (p90) REVERT: G 200 ARG cc_start: 0.2574 (mpt180) cc_final: 0.1667 (tmt170) outliers start: 45 outliers final: 22 residues processed: 190 average time/residue: 1.1739 time to fit residues: 263.3590 Evaluate side-chains 172 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 249 ASP 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: 0.2980 chunk 4 optimal weight: 0.0070 chunk 223 optimal weight: 0.0020 chunk 123 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 207 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24684 Z= 0.135 Angle : 0.475 7.614 33479 Z= 0.243 Chirality : 0.042 0.141 3856 Planarity : 0.004 0.039 4363 Dihedral : 7.805 146.436 3580 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.71 % Allowed : 11.14 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3115 helix: 1.49 (0.15), residues: 1254 sheet: 0.78 (0.22), residues: 538 loop : 0.03 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.015 0.001 PHE B 350 TYR 0.011 0.001 TYR B 79 ARG 0.003 0.000 ARG E 333 *********************** 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 212 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 2.995 Fit side-chains REVERT: A 121 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8489 (p) REVERT: B 95 MET cc_start: 0.8737 (tpt) cc_final: 0.8510 (tpt) REVERT: B 191 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8220 (ttp) REVERT: C 262 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7753 (t0) REVERT: D 56 ASP cc_start: 0.8020 (t0) cc_final: 0.7802 (t0) REVERT: D 311 ASP cc_start: 0.7975 (t70) cc_final: 0.7485 (t0) REVERT: D 469 MET cc_start: 0.8361 (mtp) cc_final: 0.8120 (mtm) REVERT: E 2 THR cc_start: 0.6578 (OUTLIER) cc_final: 0.6143 (t) REVERT: E 333 ARG cc_start: 0.8520 (tpp80) cc_final: 0.7957 (tpp-160) REVERT: G 26 MET cc_start: 0.7367 (mmm) cc_final: 0.6549 (mmm) REVERT: G 44 PRO cc_start: 0.6412 (Cg_endo) cc_final: 0.6166 (Cg_exo) REVERT: G 167 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: G 175 TYR cc_start: 0.3795 (p90) cc_final: 0.3298 (p90) outliers start: 44 outliers final: 21 residues processed: 200 average time/residue: 1.1423 time to fit residues: 270.5403 Evaluate side-chains 172 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 299 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24684 Z= 0.255 Angle : 0.521 7.758 33479 Z= 0.267 Chirality : 0.045 0.153 3856 Planarity : 0.004 0.039 4363 Dihedral : 7.954 154.195 3580 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.99 % Allowed : 12.03 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 3115 helix: 1.39 (0.15), residues: 1254 sheet: 0.71 (0.22), residues: 533 loop : -0.02 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 363 PHE 0.014 0.001 PHE E 125 TYR 0.014 0.001 TYR G 91 ARG 0.002 0.000 ARG G 71 *********************** 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 196 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 2.825 Fit side-chains REVERT: B 191 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8274 (ttp) REVERT: C 499 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8970 (m) REVERT: D 56 ASP cc_start: 0.8065 (t0) cc_final: 0.7807 (t0) REVERT: D 311 ASP cc_start: 0.8021 (t70) cc_final: 0.7526 (t0) REVERT: E 2 THR cc_start: 0.6666 (OUTLIER) cc_final: 0.6241 (t) REVERT: E 333 ARG cc_start: 0.8536 (tpp80) cc_final: 0.7963 (tpp-160) REVERT: G 26 MET cc_start: 0.7359 (mmm) cc_final: 0.6548 (mmm) REVERT: G 126 PHE cc_start: 0.6065 (m-80) cc_final: 0.5705 (m-80) REVERT: G 167 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5975 (pp20) REVERT: G 175 TYR cc_start: 0.3854 (p90) cc_final: 0.3316 (p90) outliers start: 51 outliers final: 29 residues processed: 181 average time/residue: 1.1920 time to fit residues: 255.2626 Evaluate side-chains 171 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 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: 10.0000 chunk 170 optimal weight: 9.9990 chunk 219 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 186 optimal weight: 0.0870 chunk 182 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24684 Z= 0.152 Angle : 0.492 8.719 33479 Z= 0.250 Chirality : 0.043 0.141 3856 Planarity : 0.004 0.039 4363 Dihedral : 7.645 156.740 3580 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 1.67 % Allowed : 12.73 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3115 helix: 1.50 (0.15), residues: 1251 sheet: 0.78 (0.22), residues: 538 loop : 0.06 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.013 0.001 PHE B 350 TYR 0.012 0.001 TYR B 79 ARG 0.003 0.000 ARG E 333 *********************** 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 193 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 2.930 Fit side-chains REVERT: B 95 MET cc_start: 0.8756 (tpt) cc_final: 0.8525 (tpt) REVERT: B 191 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8181 (ttp) REVERT: D 56 ASP cc_start: 0.7985 (t0) cc_final: 0.7761 (t0) REVERT: D 311 ASP cc_start: 0.7980 (t70) cc_final: 0.7486 (t0) REVERT: D 469 MET cc_start: 0.8357 (mtp) cc_final: 0.8085 (mtm) REVERT: E 2 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.6172 (t) REVERT: E 333 ARG cc_start: 0.8525 (tpp80) cc_final: 0.7961 (tpp-160) REVERT: G 26 MET cc_start: 0.7355 (mmm) cc_final: 0.6541 (mmm) REVERT: G 126 PHE cc_start: 0.5846 (m-80) cc_final: 0.5592 (m-80) REVERT: G 167 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5939 (pp20) REVERT: G 175 TYR cc_start: 0.3818 (p90) cc_final: 0.3227 (p90) outliers start: 43 outliers final: 26 residues processed: 182 average time/residue: 1.2649 time to fit residues: 270.5508 Evaluate side-chains 168 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 189 optimal weight: 0.5980 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 ASN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24684 Z= 0.130 Angle : 0.486 12.803 33479 Z= 0.243 Chirality : 0.042 0.138 3856 Planarity : 0.003 0.039 4363 Dihedral : 7.177 157.446 3580 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 1.48 % Allowed : 13.24 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3115 helix: 1.61 (0.15), residues: 1250 sheet: 0.90 (0.22), residues: 557 loop : 0.13 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS D 363 PHE 0.011 0.001 PHE B 350 TYR 0.010 0.001 TYR B 79 ARG 0.003 0.000 ARG D 333 *********************** 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 199 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 3.256 Fit side-chains REVERT: A 121 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8489 (p) REVERT: B 95 MET cc_start: 0.8754 (tpt) cc_final: 0.8525 (tpt) REVERT: B 191 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8144 (ttp) REVERT: D 311 ASP cc_start: 0.7938 (t70) cc_final: 0.7481 (t0) REVERT: D 469 MET cc_start: 0.8367 (mtp) cc_final: 0.8111 (mtm) REVERT: E 2 THR cc_start: 0.6619 (OUTLIER) cc_final: 0.6194 (t) REVERT: E 271 MET cc_start: 0.8446 (mtp) cc_final: 0.8229 (ttt) REVERT: E 333 ARG cc_start: 0.8514 (tpp80) cc_final: 0.7947 (tpp-160) REVERT: G 26 MET cc_start: 0.7290 (mmm) cc_final: 0.6520 (mmm) REVERT: G 113 TYR cc_start: 0.4265 (p90) cc_final: 0.3857 (p90) REVERT: G 125 PHE cc_start: 0.6849 (t80) cc_final: 0.6579 (t80) REVERT: G 126 PHE cc_start: 0.5938 (m-80) cc_final: 0.5713 (m-80) REVERT: G 143 GLN cc_start: 0.5658 (pp30) cc_final: 0.5375 (pp30) REVERT: G 167 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5851 (pp20) REVERT: G 175 TYR cc_start: 0.4011 (p90) cc_final: 0.3357 (p90) outliers start: 38 outliers final: 24 residues processed: 189 average time/residue: 1.1765 time to fit residues: 262.7600 Evaluate side-chains 175 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 277 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24684 Z= 0.166 Angle : 0.515 15.416 33479 Z= 0.255 Chirality : 0.043 0.143 3856 Planarity : 0.004 0.038 4363 Dihedral : 7.194 157.547 3580 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 1.44 % Allowed : 14.06 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3115 helix: 1.61 (0.15), residues: 1250 sheet: 0.96 (0.22), residues: 538 loop : 0.07 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.011 0.001 PHE B 350 TYR 0.014 0.001 TYR B 461 ARG 0.004 0.000 ARG G 34 *********************** 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 187 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 2.674 Fit side-chains REVERT: A 121 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8485 (p) REVERT: B 95 MET cc_start: 0.8766 (tpt) cc_final: 0.8513 (tpt) REVERT: B 191 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8197 (ttp) REVERT: D 311 ASP cc_start: 0.7865 (t70) cc_final: 0.7408 (t0) REVERT: D 469 MET cc_start: 0.8374 (mtp) cc_final: 0.8108 (mtm) REVERT: E 2 THR cc_start: 0.6636 (OUTLIER) cc_final: 0.6217 (t) REVERT: E 197 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7615 (t0) REVERT: E 271 MET cc_start: 0.8484 (mtp) cc_final: 0.8265 (ttt) REVERT: E 333 ARG cc_start: 0.8514 (tpp80) cc_final: 0.7944 (tpp-160) REVERT: G 26 MET cc_start: 0.7270 (mmm) cc_final: 0.6520 (mmm) REVERT: G 113 TYR cc_start: 0.4138 (p90) cc_final: 0.3789 (p90) REVERT: G 125 PHE cc_start: 0.6878 (t80) cc_final: 0.6645 (t80) REVERT: G 126 PHE cc_start: 0.5860 (m-80) cc_final: 0.5596 (m-80) REVERT: G 143 GLN cc_start: 0.5564 (pp30) cc_final: 0.5349 (pp30) REVERT: G 167 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5865 (pp20) REVERT: G 175 TYR cc_start: 0.3831 (p90) cc_final: 0.3447 (p90) outliers start: 37 outliers final: 26 residues processed: 178 average time/residue: 1.1703 time to fit residues: 248.5376 Evaluate side-chains 176 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.6980 chunk 294 optimal weight: 0.3980 chunk 179 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 308 optimal weight: 0.5980 chunk 284 optimal weight: 9.9990 chunk 245 optimal weight: 0.0770 chunk 25 optimal weight: 0.0170 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24684 Z= 0.121 Angle : 0.500 14.955 33479 Z= 0.247 Chirality : 0.042 0.149 3856 Planarity : 0.003 0.039 4363 Dihedral : 6.861 154.229 3580 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 1.17 % Allowed : 14.33 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.15), residues: 3115 helix: 1.67 (0.15), residues: 1262 sheet: 1.26 (0.23), residues: 515 loop : 0.11 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 363 PHE 0.012 0.001 PHE G 146 TYR 0.011 0.001 TYR B 461 ARG 0.003 0.000 ARG E 333 ********************** 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 202 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 3.084 Fit side-chains REVERT: A 121 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8470 (p) REVERT: B 95 MET cc_start: 0.8748 (tpt) cc_final: 0.8521 (tpt) REVERT: B 191 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8081 (ttp) REVERT: D 311 ASP cc_start: 0.7803 (t70) cc_final: 0.7352 (t0) REVERT: D 469 MET cc_start: 0.8372 (mtp) cc_final: 0.8113 (mtm) REVERT: E 2 THR cc_start: 0.6637 (OUTLIER) cc_final: 0.6222 (t) REVERT: E 333 ARG cc_start: 0.8501 (tpp80) cc_final: 0.7932 (tpp-160) REVERT: G 26 MET cc_start: 0.7199 (mmm) cc_final: 0.6493 (mmm) REVERT: G 113 TYR cc_start: 0.4145 (p90) cc_final: 0.3792 (p90) REVERT: G 125 PHE cc_start: 0.6875 (t80) cc_final: 0.6586 (t80) REVERT: G 126 PHE cc_start: 0.5785 (m-80) cc_final: 0.5518 (m-80) REVERT: G 143 GLN cc_start: 0.5586 (pp30) cc_final: 0.5292 (pp30) REVERT: G 167 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5819 (pp20) REVERT: G 175 TYR cc_start: 0.3551 (p90) cc_final: 0.3113 (p90) REVERT: G 244 MET cc_start: 0.5990 (mmp) cc_final: 0.5715 (mmp) outliers start: 30 outliers final: 20 residues processed: 194 average time/residue: 1.2373 time to fit residues: 282.3257 Evaluate side-chains 175 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 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: 4.9990 chunk 226 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** G 107 HIS ** 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 = 0.3404 r_free = 0.3404 target = 0.097298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075062 restraints weight = 47311.276| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.46 r_work: 0.2924 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24684 Z= 0.371 Angle : 0.611 13.651 33479 Z= 0.309 Chirality : 0.047 0.155 3856 Planarity : 0.004 0.045 4363 Dihedral : 7.823 161.076 3580 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 1.44 % Allowed : 14.49 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1244 sheet: 0.87 (0.23), residues: 523 loop : -0.06 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 363 PHE 0.017 0.002 PHE E 125 TYR 0.014 0.002 TYR G 262 ARG 0.007 0.000 ARG G 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6275.94 seconds wall clock time: 113 minutes 40.83 seconds (6820.83 seconds total)