Starting phenix.real_space_refine on Fri Jan 19 05:15:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/01_2024/7qk5_14038.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/01_2024/7qk5_14038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/01_2024/7qk5_14038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/01_2024/7qk5_14038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/01_2024/7qk5_14038.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/01_2024/7qk5_14038.pdb" } resolution = 1.92 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= 0.003 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: 7 Type Number sf(0) Gaussians K 18 8.98 5 S 9 5.16 5 Cl 18 4.86 5 C 3213 2.51 5 N 945 2.21 5 O 945 1.98 5 H 5337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 338": "OE1" <-> "OE2" Residue "K GLU 342": "OE1" <-> "OE2" Residue "K PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 338": "OE1" <-> "OE2" Residue "G GLU 342": "OE1" <-> "OE2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 338": "OE1" <-> "OE2" Residue "H GLU 342": "OE1" <-> "OE2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10485 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "K" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "G" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "H" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 3, ' CL': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 2, ' CL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 2, ' CL': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 3, ' CL': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' K': 4, ' CL': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 3, ' CL': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.64, per 1000 atoms: 0.44 Number of scatterers: 10485 At special positions: 0 Unit cell: (144.2, 142.552, 44.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 18 19.00 Cl 18 17.00 S 9 16.00 O 945 8.00 N 945 7.00 C 3213 6.00 H 5337 1.00 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: 7.68 Conformation dependent library (CDL) restraints added in 978.8 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 54.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.574A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.785A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 330 removed outlier: 8.901A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASN C 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL F 318 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 319 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER F 320 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 321 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS F 322 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY A 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE F 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N HIS A 329 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS F 330 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 342 removed outlier: 6.473A pdb=" N VAL A 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS F 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU F 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.453A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.286A pdb=" N VAL A 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS F 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER A 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.447A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS F 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.626A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.589A pdb=" N GLN K 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR D 310 " --> pdb=" O GLN K 307 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL K 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.721A pdb=" N VAL K 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 330 removed outlier: 8.899A pdb=" N VAL K 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N LYS D 321 " --> pdb=" O VAL K 318 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N SER K 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N GLY D 323 " --> pdb=" O SER K 320 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N CYS K 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU D 325 " --> pdb=" O CYS K 322 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER K 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN D 327 " --> pdb=" O SER K 324 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N GLY K 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N HIS D 329 " --> pdb=" O GLY K 326 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ILE K 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL G 318 " --> pdb=" O LYS K 317 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR K 319 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER G 320 " --> pdb=" O THR K 319 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS K 321 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS G 322 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY K 323 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE G 328 " --> pdb=" O ASN K 327 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N HIS K 329 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS G 330 " --> pdb=" O HIS K 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 342 removed outlier: 6.400A pdb=" N GLN K 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL D 339 " --> pdb=" O GLN K 336 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU K 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER D 341 " --> pdb=" O GLU K 338 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS K 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.476A pdb=" N ASP K 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.282A pdb=" N VAL K 350 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LYS G 353 " --> pdb=" O VAL K 350 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER K 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.494A pdb=" N ILE K 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN K 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS G 362 " --> pdb=" O ASN K 359 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR K 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 378 removed outlier: 6.595A pdb=" N LYS K 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLU D 372 " --> pdb=" O LYS K 369 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE K 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N HIS D 374 " --> pdb=" O ILE K 371 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR K 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU D 376 " --> pdb=" O THR K 373 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS K 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N PHE D 378 " --> pdb=" O LYS K 375 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR K 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.511A pdb=" N GLN B 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR E 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.774A pdb=" N VAL B 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 317 through 330 removed outlier: 8.899A pdb=" N VAL B 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N LYS E 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N SER B 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N GLY E 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS B 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU E 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER B 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN E 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N GLY B 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N HIS E 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N ILE B 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL H 318 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR B 319 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER H 320 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS B 321 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS H 322 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 323 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE H 328 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS B 329 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS H 330 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 336 through 342 Processing sheet with id=AC3, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.465A pdb=" N ASP B 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.326A pdb=" N GLN B 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE E 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS B 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 359 through 362 removed outlier: 6.618A pdb=" N ASN B 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N HIS H 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR B 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 369 through 378 removed outlier: 6.623A pdb=" N LYS B 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLU E 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N HIS E 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR B 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU E 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS B 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE E 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR B 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 279 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: 3.36 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 5328 1.11 - 1.29: 846 1.29 - 1.47: 1683 1.47 - 1.64: 2664 1.64 - 1.82: 9 Bond restraints: 10530 Sorted by residual: bond pdb=" N ARG F 349 " pdb=" H ARG F 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH2 ARG F 349 " pdb="HH21 ARG F 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLN C 351 " pdb=" H GLN C 351 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU D 357 " pdb=" H LEU D 357 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN D 368 " pdb="HD21 ASN D 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 10525 not shown) Histogram of bond angle deviations from ideal: 97.17 - 103.58: 65 103.58 - 110.00: 9590 110.00 - 116.41: 4192 116.41 - 122.83: 4389 122.83 - 129.24: 961 Bond angle restraints: 19197 Sorted by residual: angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.21 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.00e+00 1.00e+00 2.92e+01 angle pdb=" OE1 GLN H 336 " pdb=" CD GLN H 336 " pdb=" NE2 GLN H 336 " ideal model delta sigma weight residual 122.60 117.27 5.33 1.00e+00 1.00e+00 2.84e+01 angle pdb=" CA ASP K 358 " pdb=" CB ASP K 358 " pdb=" CG ASP K 358 " ideal model delta sigma weight residual 112.60 117.80 -5.20 1.00e+00 1.00e+00 2.70e+01 ... (remaining 19192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.50: 4189 13.50 - 27.00: 256 27.00 - 40.50: 79 40.50 - 54.01: 31 54.01 - 67.51: 125 Dihedral angle restraints: 4680 sinusoidal: 2610 harmonic: 2070 Sorted by residual: dihedral pdb=" CA LYS D 375 " pdb=" C LYS D 375 " pdb=" N LEU D 376 " pdb=" CA LEU D 376 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LYS E 375 " pdb=" C LYS E 375 " pdb=" N LEU E 376 " pdb=" CA LEU E 376 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS A 375 " pdb=" C LYS A 375 " pdb=" N LEU A 376 " pdb=" CA LEU A 376 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 4677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 492 0.073 - 0.147: 219 0.147 - 0.220: 44 0.220 - 0.293: 8 0.293 - 0.366: 20 Chirality restraints: 783 Sorted by residual: chirality pdb=" CA LYS B 353 " pdb=" N LYS B 353 " pdb=" C LYS B 353 " pdb=" CB LYS B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA LYS B 369 " pdb=" N LYS B 369 " pdb=" C LYS B 369 " pdb=" CB LYS B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA LYS K 353 " pdb=" N LYS K 353 " pdb=" C LYS K 353 " pdb=" CB LYS K 353 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 780 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.075 2.00e-02 2.50e+03 3.32e-02 3.30e+01 pdb=" CG TYR B 310 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.067 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 359 " 0.053 2.00e-02 2.50e+03 4.67e-02 3.27e+01 pdb=" CG ASN K 359 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN K 359 " -0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN K 359 " -0.041 2.00e-02 2.50e+03 pdb="HD21 ASN K 359 " -0.034 2.00e-02 2.50e+03 pdb="HD22 ASN K 359 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 310 " 0.076 2.00e-02 2.50e+03 3.30e-02 3.26e+01 pdb=" CG TYR H 310 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR H 310 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 310 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR H 310 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR H 310 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 310 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 TYR H 310 " -0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR H 310 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR H 310 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 TYR H 310 " -0.009 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.23: 1094 2.23 - 2.95: 25177 2.95 - 3.68: 36170 3.68 - 4.41: 53007 4.41 - 5.14: 84797 Nonbonded interactions: 200245 Sorted by model distance: nonbonded pdb=" H GLY H 335 " pdb=" K K H1002 " model vdw 1.497 2.380 nonbonded pdb=" H GLY K 335 " pdb=" K K K 504 " model vdw 1.567 2.380 nonbonded pdb=" OD2 ASP F 314 " pdb=" HZ2 LYS F 370 " model vdw 1.680 1.850 nonbonded pdb=" OD2 ASP G 314 " pdb=" HZ1 LYS G 370 " model vdw 1.682 1.850 nonbonded pdb=" OD2 ASP H 314 " pdb=" HZ1 LYS H 370 " model vdw 1.684 1.850 ... (remaining 200240 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 306 through 379) selection = (chain 'B' and resid 306 through 379) selection = (chain 'C' and resid 306 through 379) selection = (chain 'D' and resid 306 through 379) selection = (chain 'E' and resid 306 through 379) selection = (chain 'F' and resid 306 through 379) selection = (chain 'G' and resid 306 through 379) selection = (chain 'H' and resid 306 through 379) selection = (chain 'K' and resid 306 through 379) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.160 Extract box with map and model: 11.960 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 35.530 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.011 0.034 5193 Z= 0.777 Angle : 1.888 8.537 6948 Z= 1.243 Chirality : 0.097 0.366 783 Planarity : 0.011 0.095 882 Dihedral : 10.956 62.849 1998 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS G 362 PHE 0.028 0.010 PHE F 378 TYR 0.068 0.023 TYR B 310 ARG 0.004 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7200 (tt0) cc_final: 0.6702 (tm-30) REVERT: A 314 ASP cc_start: 0.7630 (t0) cc_final: 0.7392 (t70) REVERT: A 342 GLU cc_start: 0.6272 (tt0) cc_final: 0.5826 (tp30) REVERT: A 351 GLN cc_start: 0.7380 (mt0) cc_final: 0.7116 (mt0) REVERT: A 369 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7606 (ptpp) REVERT: K 321 LYS cc_start: 0.7793 (tttt) cc_final: 0.7512 (ttmm) REVERT: K 369 LYS cc_start: 0.7815 (ptmt) cc_final: 0.7543 (mttt) REVERT: B 345 ASP cc_start: 0.6704 (m-30) cc_final: 0.6499 (m-30) REVERT: C 314 ASP cc_start: 0.7791 (t0) cc_final: 0.7465 (t70) REVERT: C 342 GLU cc_start: 0.6416 (tt0) cc_final: 0.5978 (tp30) REVERT: C 347 LYS cc_start: 0.7548 (mmmt) cc_final: 0.7274 (pmtt) REVERT: C 349 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6842 (mtt180) REVERT: D 342 GLU cc_start: 0.6608 (tt0) cc_final: 0.6196 (tp30) REVERT: D 349 ARG cc_start: 0.6716 (mtt180) cc_final: 0.6040 (pmt-80) REVERT: F 307 GLN cc_start: 0.7218 (tt0) cc_final: 0.6771 (tm-30) REVERT: F 319 THR cc_start: 0.8514 (m) cc_final: 0.7964 (t) REVERT: F 342 GLU cc_start: 0.6046 (tt0) cc_final: 0.5611 (tp30) REVERT: F 370 LYS cc_start: 0.8324 (tttm) cc_final: 0.7793 (ttmt) REVERT: F 377 THR cc_start: 0.7942 (m) cc_final: 0.7677 (m) REVERT: G 377 THR cc_start: 0.8210 (m) cc_final: 0.7958 (m) REVERT: H 369 LYS cc_start: 0.7613 (ptmt) cc_final: 0.6551 (tptp) REVERT: H 370 LYS cc_start: 0.8120 (tttm) cc_final: 0.7554 (ttmt) REVERT: H 377 THR cc_start: 0.7333 (m) cc_final: 0.6673 (p) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 2.6131 time to fit residues: 701.4288 Evaluate side-chains 126 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 368 ASN A 374 HIS K 336 GLN K 368 ASN K 374 HIS B 336 GLN B 368 ASN B 374 HIS C 336 GLN C 351 GLN C 374 HIS D 336 GLN D 351 GLN D 368 ASN D 374 HIS E 336 GLN E 351 GLN E 374 HIS F 336 GLN F 351 GLN F 368 ASN F 374 HIS G 336 GLN G 351 GLN G 368 ASN G 374 HIS H 336 GLN ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN H 374 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5193 Z= 0.319 Angle : 0.761 6.914 6948 Z= 0.410 Chirality : 0.053 0.142 783 Planarity : 0.005 0.047 882 Dihedral : 6.383 17.836 684 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.10 % Allowed : 18.63 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.28), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 374 PHE 0.019 0.003 PHE B 378 TYR 0.013 0.002 TYR A 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.880 Fit side-chains REVERT: A 307 GLN cc_start: 0.7292 (tt0) cc_final: 0.6653 (tm-30) REVERT: A 342 GLU cc_start: 0.6285 (tt0) cc_final: 0.5901 (mm-30) REVERT: A 351 GLN cc_start: 0.7461 (mt0) cc_final: 0.7182 (mt0) REVERT: A 370 LYS cc_start: 0.8016 (tttp) cc_final: 0.7616 (tptm) REVERT: K 369 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7435 (mttt) REVERT: C 314 ASP cc_start: 0.7924 (t0) cc_final: 0.7608 (t70) REVERT: C 342 GLU cc_start: 0.6343 (tt0) cc_final: 0.5939 (tp30) REVERT: C 347 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7381 (pmtt) REVERT: D 317 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6366 (mtpp) REVERT: E 314 ASP cc_start: 0.8007 (t0) cc_final: 0.7764 (t70) REVERT: F 307 GLN cc_start: 0.7242 (tt0) cc_final: 0.6692 (tm-30) REVERT: F 342 GLU cc_start: 0.6181 (tt0) cc_final: 0.5854 (mm-30) REVERT: F 370 LYS cc_start: 0.8398 (tttm) cc_final: 0.7956 (ttmp) REVERT: F 377 THR cc_start: 0.8063 (m) cc_final: 0.7831 (m) REVERT: H 370 LYS cc_start: 0.8098 (tttm) cc_final: 0.7516 (ttmt) REVERT: H 377 THR cc_start: 0.7369 (m) cc_final: 0.7061 (t) outliers start: 24 outliers final: 5 residues processed: 127 average time/residue: 2.8088 time to fit residues: 369.7468 Evaluate side-chains 101 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 345 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN C 351 GLN E 330 HIS E 351 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5193 Z= 0.167 Angle : 0.574 5.913 6948 Z= 0.301 Chirality : 0.051 0.135 783 Planarity : 0.003 0.022 882 Dihedral : 5.536 16.542 684 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.71 % Allowed : 22.39 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 374 PHE 0.010 0.002 PHE A 378 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.952 Fit side-chains REVERT: A 307 GLN cc_start: 0.7336 (tt0) cc_final: 0.6713 (tm-30) REVERT: A 338 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6702 (mt-10) REVERT: A 342 GLU cc_start: 0.6266 (tt0) cc_final: 0.5911 (mm-30) REVERT: C 342 GLU cc_start: 0.6337 (tt0) cc_final: 0.6008 (tp30) REVERT: C 347 LYS cc_start: 0.7676 (mmmt) cc_final: 0.7336 (pmtt) REVERT: E 369 LYS cc_start: 0.7973 (ptpp) cc_final: 0.7732 (mttt) REVERT: F 307 GLN cc_start: 0.7170 (tt0) cc_final: 0.6565 (tm-30) REVERT: F 308 ILE cc_start: 0.7844 (mt) cc_final: 0.7635 (mp) REVERT: F 342 GLU cc_start: 0.6230 (tt0) cc_final: 0.5916 (mm-30) REVERT: F 377 THR cc_start: 0.8021 (m) cc_final: 0.7799 (m) REVERT: G 369 LYS cc_start: 0.7901 (ptpp) cc_final: 0.7678 (ptpp) REVERT: H 319 THR cc_start: 0.8348 (m) cc_final: 0.7890 (p) REVERT: H 370 LYS cc_start: 0.8033 (tttm) cc_final: 0.7481 (ttmt) REVERT: H 377 THR cc_start: 0.7465 (m) cc_final: 0.7161 (t) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 2.4919 time to fit residues: 273.0510 Evaluate side-chains 102 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.0070 chunk 43 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 0.0010 chunk 54 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN K 351 GLN B 351 GLN D 351 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5193 Z= 0.242 Angle : 0.642 5.605 6948 Z= 0.339 Chirality : 0.051 0.136 783 Planarity : 0.005 0.043 882 Dihedral : 5.637 17.231 684 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.42 % Allowed : 19.49 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.013 0.002 PHE H 378 TYR 0.011 0.002 TYR A 310 ARG 0.002 0.000 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7301 (tt0) cc_final: 0.6714 (tm-30) REVERT: A 338 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: A 342 GLU cc_start: 0.6208 (tt0) cc_final: 0.5859 (mm-30) REVERT: A 351 GLN cc_start: 0.7307 (mt0) cc_final: 0.7018 (mt0) REVERT: K 369 LYS cc_start: 0.7962 (ptpp) cc_final: 0.7437 (ptmt) REVERT: C 342 GLU cc_start: 0.6375 (tt0) cc_final: 0.6053 (tp30) REVERT: C 347 LYS cc_start: 0.7678 (mmmt) cc_final: 0.7376 (pmtt) REVERT: E 347 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6833 (pmtt) REVERT: E 369 LYS cc_start: 0.8015 (ptpp) cc_final: 0.7764 (mttt) REVERT: F 307 GLN cc_start: 0.7128 (tt0) cc_final: 0.6518 (tm-30) REVERT: F 340 LYS cc_start: 0.7555 (mtpp) cc_final: 0.7291 (mttm) REVERT: F 342 GLU cc_start: 0.6062 (tt0) cc_final: 0.5676 (mm-30) REVERT: F 370 LYS cc_start: 0.8352 (tttm) cc_final: 0.7935 (ttmt) REVERT: H 319 THR cc_start: 0.8382 (m) cc_final: 0.7998 (p) REVERT: H 370 LYS cc_start: 0.8057 (tttm) cc_final: 0.7507 (ttmt) REVERT: H 377 THR cc_start: 0.7547 (m) cc_final: 0.7296 (t) outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 2.6113 time to fit residues: 279.5153 Evaluate side-chains 110 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN D 351 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5193 Z= 0.176 Angle : 0.557 4.776 6948 Z= 0.293 Chirality : 0.050 0.130 783 Planarity : 0.003 0.027 882 Dihedral : 5.328 17.492 684 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.76 % Allowed : 18.12 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 374 PHE 0.009 0.002 PHE E 378 TYR 0.008 0.002 TYR F 310 ARG 0.001 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.935 Fit side-chains REVERT: A 307 GLN cc_start: 0.7294 (tt0) cc_final: 0.6700 (tm-30) REVERT: A 338 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: A 342 GLU cc_start: 0.6197 (tt0) cc_final: 0.5857 (mm-30) REVERT: A 351 GLN cc_start: 0.7309 (mt0) cc_final: 0.7070 (mt0) REVERT: B 351 GLN cc_start: 0.7590 (mt0) cc_final: 0.7382 (mt0) REVERT: C 342 GLU cc_start: 0.6352 (tt0) cc_final: 0.6031 (tp30) REVERT: C 347 LYS cc_start: 0.7673 (mmmt) cc_final: 0.7325 (pmtt) REVERT: E 347 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6869 (pmtt) REVERT: F 307 GLN cc_start: 0.7080 (tt0) cc_final: 0.6513 (tm-30) REVERT: F 340 LYS cc_start: 0.7641 (mtpp) cc_final: 0.7356 (mttm) REVERT: F 342 GLU cc_start: 0.6077 (tt0) cc_final: 0.5688 (mm-30) REVERT: F 370 LYS cc_start: 0.8322 (tttm) cc_final: 0.7918 (ttmp) REVERT: H 319 THR cc_start: 0.8346 (m) cc_final: 0.8048 (p) REVERT: H 370 LYS cc_start: 0.8027 (tttm) cc_final: 0.7515 (ttmt) REVERT: H 377 THR cc_start: 0.7539 (m) cc_final: 0.7313 (t) outliers start: 22 outliers final: 13 residues processed: 107 average time/residue: 2.5914 time to fit residues: 288.5784 Evaluate side-chains 113 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN D 351 GLN E 351 GLN G 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5193 Z= 0.183 Angle : 0.561 4.643 6948 Z= 0.294 Chirality : 0.050 0.131 783 Planarity : 0.004 0.034 882 Dihedral : 5.257 17.225 684 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.59 % Allowed : 18.29 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.010 0.002 PHE H 378 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.029 Fit side-chains REVERT: A 307 GLN cc_start: 0.7311 (tt0) cc_final: 0.6724 (tm-30) REVERT: A 319 THR cc_start: 0.8436 (m) cc_final: 0.7972 (p) REVERT: A 338 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: A 342 GLU cc_start: 0.6231 (tt0) cc_final: 0.5888 (mm-30) REVERT: A 351 GLN cc_start: 0.7303 (mt0) cc_final: 0.7035 (mt0) REVERT: B 369 LYS cc_start: 0.7782 (ptpp) cc_final: 0.7456 (mttt) REVERT: C 342 GLU cc_start: 0.6341 (tt0) cc_final: 0.6033 (tp30) REVERT: C 347 LYS cc_start: 0.7669 (mmmt) cc_final: 0.7328 (pmtt) REVERT: E 347 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6870 (pmtt) REVERT: F 307 GLN cc_start: 0.7090 (tt0) cc_final: 0.6469 (tm-30) REVERT: F 340 LYS cc_start: 0.7659 (mtpp) cc_final: 0.7397 (mttm) REVERT: F 342 GLU cc_start: 0.6057 (tt0) cc_final: 0.5647 (mm-30) REVERT: F 370 LYS cc_start: 0.8320 (tttm) cc_final: 0.7949 (ttmp) REVERT: H 319 THR cc_start: 0.8365 (m) cc_final: 0.8130 (p) REVERT: H 370 LYS cc_start: 0.8052 (tttm) cc_final: 0.7568 (ttmt) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 2.7490 time to fit residues: 296.6151 Evaluate side-chains 112 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN C 351 GLN D 351 GLN E 351 GLN ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5193 Z= 0.291 Angle : 0.663 5.009 6948 Z= 0.350 Chirality : 0.051 0.140 783 Planarity : 0.006 0.054 882 Dihedral : 5.622 17.889 684 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.59 % Allowed : 18.80 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.68 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 374 PHE 0.014 0.003 PHE E 378 TYR 0.012 0.003 TYR F 310 ARG 0.003 0.000 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.830 Fit side-chains REVERT: A 307 GLN cc_start: 0.7316 (tt0) cc_final: 0.6699 (tm-30) REVERT: A 338 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: A 342 GLU cc_start: 0.6252 (tt0) cc_final: 0.5897 (mm-30) REVERT: A 351 GLN cc_start: 0.7397 (mt0) cc_final: 0.7124 (mt0) REVERT: K 369 LYS cc_start: 0.8007 (ptpp) cc_final: 0.7441 (ptmt) REVERT: B 369 LYS cc_start: 0.7849 (ptpp) cc_final: 0.7513 (mttt) REVERT: C 342 GLU cc_start: 0.6312 (tt0) cc_final: 0.6003 (tp30) REVERT: C 347 LYS cc_start: 0.7640 (mmmt) cc_final: 0.7357 (pmtt) REVERT: F 307 GLN cc_start: 0.7088 (tt0) cc_final: 0.6521 (tm-30) REVERT: F 340 LYS cc_start: 0.7650 (mtpp) cc_final: 0.7388 (mttm) REVERT: F 342 GLU cc_start: 0.6067 (tt0) cc_final: 0.5675 (mm-30) REVERT: H 370 LYS cc_start: 0.8087 (tttm) cc_final: 0.7622 (ttmt) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 2.6819 time to fit residues: 278.5272 Evaluate side-chains 108 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 347 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 0.0070 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN D 351 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5193 Z= 0.139 Angle : 0.514 4.597 6948 Z= 0.267 Chirality : 0.050 0.128 783 Planarity : 0.003 0.020 882 Dihedral : 5.104 17.383 684 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.56 % Allowed : 20.17 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.69 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 374 PHE 0.006 0.001 PHE A 378 TYR 0.006 0.001 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.891 Fit side-chains REVERT: A 307 GLN cc_start: 0.7331 (tt0) cc_final: 0.6727 (tm-30) REVERT: A 319 THR cc_start: 0.8432 (m) cc_final: 0.7963 (p) REVERT: A 338 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: A 342 GLU cc_start: 0.6235 (tt0) cc_final: 0.5882 (mm-30) REVERT: A 351 GLN cc_start: 0.7332 (mt0) cc_final: 0.7080 (mt0) REVERT: K 369 LYS cc_start: 0.7963 (ptpp) cc_final: 0.7422 (ptmt) REVERT: B 369 LYS cc_start: 0.7816 (ptpp) cc_final: 0.7444 (mttt) REVERT: C 342 GLU cc_start: 0.6293 (tt0) cc_final: 0.5971 (tp30) REVERT: C 347 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7282 (pmtt) REVERT: E 347 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.6858 (pmtt) REVERT: F 307 GLN cc_start: 0.7065 (tt0) cc_final: 0.6503 (tm-30) REVERT: F 308 ILE cc_start: 0.7877 (mt) cc_final: 0.7673 (mp) REVERT: F 340 LYS cc_start: 0.7651 (mtpp) cc_final: 0.7395 (mttm) REVERT: F 342 GLU cc_start: 0.6045 (tt0) cc_final: 0.5701 (mm-30) REVERT: H 370 LYS cc_start: 0.8035 (tttm) cc_final: 0.7570 (ttmt) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 2.6143 time to fit residues: 277.0932 Evaluate side-chains 108 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 56 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN D 351 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5193 Z= 0.153 Angle : 0.520 4.514 6948 Z= 0.271 Chirality : 0.050 0.130 783 Planarity : 0.004 0.033 882 Dihedral : 4.988 16.995 684 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.39 % Allowed : 20.34 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.65 (0.30), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.008 0.002 PHE A 378 TYR 0.007 0.002 TYR F 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.938 Fit side-chains REVERT: A 307 GLN cc_start: 0.7352 (tt0) cc_final: 0.6733 (tm-30) REVERT: A 319 THR cc_start: 0.8425 (m) cc_final: 0.8007 (p) REVERT: A 338 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6649 (mt-10) REVERT: A 342 GLU cc_start: 0.6218 (tt0) cc_final: 0.5893 (mm-30) REVERT: A 351 GLN cc_start: 0.7300 (mt0) cc_final: 0.7044 (mt0) REVERT: B 369 LYS cc_start: 0.7780 (ptpp) cc_final: 0.7373 (mttt) REVERT: C 342 GLU cc_start: 0.6306 (tt0) cc_final: 0.5984 (tp30) REVERT: C 347 LYS cc_start: 0.7589 (mmmt) cc_final: 0.7268 (pmtt) REVERT: E 311 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7933 (ptpp) REVERT: E 347 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6863 (pmtt) REVERT: F 307 GLN cc_start: 0.7050 (tt0) cc_final: 0.6464 (tm-30) REVERT: F 340 LYS cc_start: 0.7650 (mtpp) cc_final: 0.7395 (mttm) REVERT: F 342 GLU cc_start: 0.6060 (tt0) cc_final: 0.5633 (mm-30) REVERT: H 370 LYS cc_start: 0.8048 (tttm) cc_final: 0.7582 (ttmt) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 2.6507 time to fit residues: 278.1009 Evaluate side-chains 109 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN E 351 GLN ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5193 Z= 0.292 Angle : 0.651 4.988 6948 Z= 0.345 Chirality : 0.051 0.139 783 Planarity : 0.006 0.055 882 Dihedral : 5.518 17.677 684 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.56 % Allowed : 20.17 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS K 374 PHE 0.014 0.003 PHE E 378 TYR 0.013 0.003 TYR F 310 ARG 0.003 0.000 ARG G 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.858 Fit side-chains REVERT: A 307 GLN cc_start: 0.7383 (tt0) cc_final: 0.6769 (tm-30) REVERT: A 319 THR cc_start: 0.8442 (m) cc_final: 0.7984 (p) REVERT: A 338 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6663 (mt-10) REVERT: A 342 GLU cc_start: 0.6266 (tt0) cc_final: 0.5898 (mm-30) REVERT: A 351 GLN cc_start: 0.7384 (mt0) cc_final: 0.7100 (mt0) REVERT: K 369 LYS cc_start: 0.8001 (ptpp) cc_final: 0.7465 (ptmt) REVERT: B 369 LYS cc_start: 0.7874 (ptpp) cc_final: 0.7544 (mttt) REVERT: C 342 GLU cc_start: 0.6315 (tt0) cc_final: 0.6022 (tp30) REVERT: C 347 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7353 (pmtt) REVERT: F 307 GLN cc_start: 0.7067 (tt0) cc_final: 0.6506 (tm-30) REVERT: F 340 LYS cc_start: 0.7649 (mtpp) cc_final: 0.7390 (mttm) REVERT: F 342 GLU cc_start: 0.6062 (tt0) cc_final: 0.5655 (mm-30) REVERT: H 347 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6698 (mmtt) REVERT: H 370 LYS cc_start: 0.8079 (tttm) cc_final: 0.7557 (ttmt) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 2.7122 time to fit residues: 278.6817 Evaluate side-chains 107 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.146234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.129937 restraints weight = 15551.188| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.15 r_work: 0.4051 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3984 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5193 Z= 0.160 Angle : 0.533 4.608 6948 Z= 0.279 Chirality : 0.050 0.129 783 Planarity : 0.003 0.025 882 Dihedral : 5.157 17.443 684 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.05 % Allowed : 21.03 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 374 PHE 0.007 0.001 PHE E 378 TYR 0.007 0.002 TYR F 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6244.84 seconds wall clock time: 110 minutes 28.87 seconds (6628.87 seconds total)