Starting phenix.real_space_refine on Fri Mar 15 03:06:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/03_2024/7qk5_14038.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/03_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_14038/03_2024/7qk5_14038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/03_2024/7qk5_14038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/03_2024/7qk5_14038.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/03_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.13, per 1000 atoms: 0.49 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: 7.98 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.94 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: 3.24 Time building geometry restraints manager: 8.35 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: 4225 13.50 - 27.00: 276 27.00 - 40.50: 111 40.50 - 54.01: 84 54.01 - 67.51: 146 Dihedral angle restraints: 4842 sinusoidal: 2772 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 4839 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: 4.970 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: 0.150 Extract box with map and model: 12.670 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.580 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 68.310 ------------------------------------------------------------------------------- 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 : 0.769 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: 2.5166 time to fit residues: 675.7941 Evaluate side-chains 126 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5193 Z= 0.323 Angle : 0.761 6.904 6948 Z= 0.411 Chirality : 0.053 0.143 783 Planarity : 0.005 0.047 882 Dihedral : 6.376 17.870 684 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.27 % Allowed : 18.46 % 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: -1.43 (0.28), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 374 PHE 0.020 0.003 PHE B 378 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.000 ARG G 379 *********************** 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 143 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.933 Fit side-chains REVERT: A 307 GLN cc_start: 0.7291 (tt0) cc_final: 0.6653 (tm-30) REVERT: A 342 GLU cc_start: 0.6284 (tt0) cc_final: 0.5905 (mm-30) REVERT: A 351 GLN cc_start: 0.7461 (mt0) cc_final: 0.7158 (mt0) REVERT: A 370 LYS cc_start: 0.8021 (tttp) cc_final: 0.7616 (tptm) REVERT: K 369 LYS cc_start: 0.7833 (ptmt) cc_final: 0.7434 (mttt) REVERT: C 314 ASP cc_start: 0.7922 (t0) cc_final: 0.7606 (t70) REVERT: C 342 GLU cc_start: 0.6351 (tt0) cc_final: 0.5923 (tp30) REVERT: C 347 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7357 (pmtt) REVERT: D 317 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6350 (mtpp) REVERT: D 319 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8112 (p) REVERT: E 314 ASP cc_start: 0.8008 (t0) cc_final: 0.7762 (t70) REVERT: F 307 GLN cc_start: 0.7240 (tt0) cc_final: 0.6690 (tm-30) REVERT: F 342 GLU cc_start: 0.6158 (tt0) cc_final: 0.5840 (mm-30) REVERT: F 370 LYS cc_start: 0.8395 (tttm) cc_final: 0.7954 (ttmp) REVERT: F 377 THR cc_start: 0.8063 (m) cc_final: 0.7832 (m) REVERT: H 370 LYS cc_start: 0.8085 (tttm) cc_final: 0.7499 (ttmt) REVERT: H 377 THR cc_start: 0.7391 (m) cc_final: 0.7085 (t) outliers start: 25 outliers final: 5 residues processed: 128 average time/residue: 2.7083 time to fit residues: 359.2430 Evaluate side-chains 103 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR 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: 0.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN B 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: 0.7791 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5193 Z= 0.195 Angle : 0.603 5.935 6948 Z= 0.317 Chirality : 0.051 0.136 783 Planarity : 0.004 0.028 882 Dihedral : 5.601 17.104 684 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.74 % Allowed : 20.85 % Favored : 76.41 % 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: -1.47 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 374 PHE 0.011 0.002 PHE A 378 TYR 0.010 0.002 TYR F 310 ARG 0.002 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 117 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7304 (tt0) cc_final: 0.6652 (tm-30) REVERT: A 338 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: A 342 GLU cc_start: 0.6230 (tt0) cc_final: 0.5881 (mm-30) REVERT: C 342 GLU cc_start: 0.6379 (tt0) cc_final: 0.6050 (tp30) REVERT: C 347 LYS cc_start: 0.7640 (mmmt) cc_final: 0.7323 (pmtt) REVERT: E 347 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6820 (pmtt) REVERT: E 369 LYS cc_start: 0.7969 (ptpp) cc_final: 0.7731 (mttt) REVERT: F 307 GLN cc_start: 0.7161 (tt0) cc_final: 0.6530 (tm-30) REVERT: F 308 ILE cc_start: 0.7860 (mt) cc_final: 0.7649 (mp) REVERT: F 342 GLU cc_start: 0.6102 (tt0) cc_final: 0.5858 (tp30) REVERT: F 370 LYS cc_start: 0.8291 (tttm) cc_final: 0.7824 (ttmp) REVERT: H 319 THR cc_start: 0.8373 (m) cc_final: 0.7926 (p) REVERT: H 370 LYS cc_start: 0.8057 (tttm) cc_final: 0.7511 (ttmt) REVERT: H 377 THR cc_start: 0.7475 (m) cc_final: 0.7199 (t) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 2.4584 time to fit residues: 271.0955 Evaluate side-chains 108 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 338 GLU 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 315 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 29 optimal weight: 0.0170 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 overall best weight: 2.5424 ------------------------------------------------------------------------------- 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 D 351 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5972 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= 0.198 Angle : 0.588 5.311 6948 Z= 0.309 Chirality : 0.050 0.135 783 Planarity : 0.004 0.035 882 Dihedral : 5.445 17.061 684 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.74 % Allowed : 20.17 % 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: -1.48 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.011 0.002 PHE A 378 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG D 349 *********************** 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 115 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.909 Fit side-chains REVERT: A 307 GLN cc_start: 0.7319 (tt0) cc_final: 0.6734 (tm-30) REVERT: A 338 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6697 (mt-10) REVERT: A 342 GLU cc_start: 0.6204 (tt0) cc_final: 0.5857 (mm-30) REVERT: A 351 GLN cc_start: 0.7190 (mt0) cc_final: 0.6940 (mt0) REVERT: B 351 GLN cc_start: 0.7597 (mt0) cc_final: 0.7379 (mt0) REVERT: C 342 GLU cc_start: 0.6374 (tt0) cc_final: 0.6045 (tp30) REVERT: C 347 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7352 (pmtt) REVERT: E 347 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6834 (pmtt) REVERT: E 369 LYS cc_start: 0.7948 (ptpp) cc_final: 0.7741 (mttt) REVERT: F 307 GLN cc_start: 0.7108 (tt0) cc_final: 0.6496 (tm-30) REVERT: F 342 GLU cc_start: 0.6054 (tt0) cc_final: 0.5664 (mm-30) REVERT: F 370 LYS cc_start: 0.8328 (tttm) cc_final: 0.7922 (ttmp) REVERT: H 319 THR cc_start: 0.8368 (m) cc_final: 0.8019 (p) REVERT: H 342 GLU cc_start: 0.6063 (tt0) cc_final: 0.5857 (tt0) REVERT: H 370 LYS cc_start: 0.8029 (tttm) cc_final: 0.7501 (ttmt) REVERT: H 377 THR cc_start: 0.7542 (m) cc_final: 0.7268 (t) outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 2.5458 time to fit residues: 272.6070 Evaluate side-chains 110 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 345 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.6063 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= 0.204 Angle : 0.583 4.687 6948 Z= 0.307 Chirality : 0.050 0.133 783 Planarity : 0.004 0.037 882 Dihedral : 5.394 17.481 684 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.76 % Allowed : 18.29 % Favored : 77.95 % 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: -1.54 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 374 PHE 0.010 0.002 PHE E 378 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG G 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 121 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.893 Fit side-chains REVERT: A 307 GLN cc_start: 0.7307 (tt0) cc_final: 0.6724 (tm-30) REVERT: A 319 THR cc_start: 0.8438 (m) cc_final: 0.7963 (p) REVERT: A 338 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: A 342 GLU cc_start: 0.6223 (tt0) cc_final: 0.5884 (mm-30) REVERT: A 351 GLN cc_start: 0.7302 (mt0) cc_final: 0.7041 (mt0) REVERT: C 342 GLU cc_start: 0.6339 (tt0) cc_final: 0.6030 (tp30) REVERT: C 347 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7335 (pmtt) REVERT: D 317 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6268 (mtpp) REVERT: E 347 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6825 (pmtt) REVERT: F 307 GLN cc_start: 0.7091 (tt0) cc_final: 0.6526 (tm-30) REVERT: F 342 GLU cc_start: 0.6045 (tt0) cc_final: 0.5635 (mm-30) REVERT: F 370 LYS cc_start: 0.8322 (tttm) cc_final: 0.7936 (ttmt) REVERT: H 319 THR cc_start: 0.8322 (m) cc_final: 0.8079 (p) REVERT: H 342 GLU cc_start: 0.6060 (tt0) cc_final: 0.5848 (tt0) REVERT: H 370 LYS cc_start: 0.8018 (tttm) cc_final: 0.7533 (ttmt) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 2.6721 time to fit residues: 288.3979 Evaluate side-chains 114 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 311 LYS 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 317 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 G 351 GLN ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.6135 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= 0.229 Angle : 0.600 4.645 6948 Z= 0.317 Chirality : 0.050 0.133 783 Planarity : 0.005 0.041 882 Dihedral : 5.437 17.661 684 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.42 % Allowed : 18.97 % 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: -1.59 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.011 0.002 PHE A 378 TYR 0.011 0.002 TYR F 310 ARG 0.001 0.000 ARG G 379 *********************** 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 117 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.813 Fit side-chains REVERT: A 307 GLN cc_start: 0.7327 (tt0) cc_final: 0.6710 (tm-30) REVERT: A 319 THR cc_start: 0.8439 (m) cc_final: 0.7969 (p) REVERT: A 338 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: A 342 GLU cc_start: 0.6248 (tt0) cc_final: 0.5900 (mm-30) REVERT: A 351 GLN cc_start: 0.7424 (mt0) cc_final: 0.7143 (mt0) REVERT: B 369 LYS cc_start: 0.7832 (ptpp) cc_final: 0.7496 (mttt) REVERT: C 342 GLU cc_start: 0.6338 (tt0) cc_final: 0.6026 (tp30) REVERT: C 347 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7325 (pmtt) REVERT: E 347 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6830 (pmtt) REVERT: F 307 GLN cc_start: 0.7073 (tt0) cc_final: 0.6515 (tm-30) REVERT: F 342 GLU cc_start: 0.6065 (tt0) cc_final: 0.5660 (mm-30) REVERT: F 370 LYS cc_start: 0.8340 (tttm) cc_final: 0.7962 (ttmt) REVERT: H 319 THR cc_start: 0.8413 (m) cc_final: 0.8192 (p) REVERT: H 342 GLU cc_start: 0.6045 (tt0) cc_final: 0.5819 (tt0) REVERT: H 370 LYS cc_start: 0.8044 (tttm) cc_final: 0.7566 (ttmt) outliers start: 20 outliers final: 14 residues processed: 102 average time/residue: 2.6364 time to fit residues: 279.1940 Evaluate side-chains 112 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 315 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 ** 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: 0.7801 moved from start: 0.6168 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= 0.269 Angle : 0.634 4.959 6948 Z= 0.336 Chirality : 0.051 0.137 783 Planarity : 0.005 0.047 882 Dihedral : 5.548 17.738 684 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -1.66 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 374 PHE 0.013 0.003 PHE A 378 TYR 0.012 0.003 TYR F 310 ARG 0.002 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 119 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.942 Fit side-chains REVERT: A 307 GLN cc_start: 0.7337 (tt0) cc_final: 0.6734 (tm-30) REVERT: A 319 THR cc_start: 0.8447 (m) cc_final: 0.7972 (p) REVERT: A 338 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: A 342 GLU cc_start: 0.6243 (tt0) cc_final: 0.5890 (mm-30) REVERT: A 351 GLN cc_start: 0.7389 (mt0) cc_final: 0.7118 (mt0) REVERT: B 369 LYS cc_start: 0.7847 (ptpp) cc_final: 0.7518 (mttt) REVERT: C 342 GLU cc_start: 0.6304 (tt0) cc_final: 0.5985 (tp30) REVERT: C 347 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7361 (pmtt) REVERT: F 307 GLN cc_start: 0.7097 (tt0) cc_final: 0.6537 (tm-30) REVERT: F 342 GLU cc_start: 0.6036 (tt0) cc_final: 0.5699 (mm-30) REVERT: H 342 GLU cc_start: 0.6079 (tt0) cc_final: 0.5854 (tt0) REVERT: H 370 LYS cc_start: 0.8071 (tttm) cc_final: 0.7610 (ttmt) outliers start: 24 outliers final: 20 residues processed: 104 average time/residue: 2.5414 time to fit residues: 274.6844 Evaluate side-chains 114 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 C residue 369 LYS 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 306 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU 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: 6.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** 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: 0.7797 moved from start: 0.6216 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= 0.222 Angle : 0.594 4.790 6948 Z= 0.313 Chirality : 0.050 0.130 783 Planarity : 0.004 0.041 882 Dihedral : 5.441 17.539 684 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.25 % Allowed : 19.49 % 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: -1.73 (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 0.005 0.001 HIS K 374 PHE 0.011 0.002 PHE E 378 TYR 0.009 0.002 TYR F 310 ARG 0.002 0.000 ARG G 379 *********************** 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 111 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.721 Fit side-chains REVERT: A 307 GLN cc_start: 0.7348 (tt0) cc_final: 0.6747 (tm-30) REVERT: A 319 THR cc_start: 0.8431 (m) cc_final: 0.7970 (p) REVERT: A 338 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: A 342 GLU cc_start: 0.6236 (tt0) cc_final: 0.5882 (mm-30) REVERT: A 351 GLN cc_start: 0.7375 (mt0) cc_final: 0.7106 (mt0) REVERT: B 369 LYS cc_start: 0.7868 (ptpp) cc_final: 0.7517 (mttt) REVERT: C 342 GLU cc_start: 0.6317 (tt0) cc_final: 0.6001 (tp30) REVERT: C 347 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7329 (pmtt) REVERT: E 347 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6830 (pmtt) REVERT: F 307 GLN cc_start: 0.7112 (tt0) cc_final: 0.6552 (tm-30) REVERT: F 342 GLU cc_start: 0.5977 (tt0) cc_final: 0.5675 (tp30) REVERT: H 342 GLU cc_start: 0.6033 (tt0) cc_final: 0.5824 (tt0) REVERT: H 370 LYS cc_start: 0.8033 (tttm) cc_final: 0.7515 (ttmt) outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 2.5928 time to fit residues: 266.5570 Evaluate side-chains 108 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 315 LEU 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 315 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.0010 chunk 41 optimal weight: 10.0000 overall best weight: 2.9792 ------------------------------------------------------------------------------- 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 ** 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: 0.7798 moved from start: 0.6238 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= 0.214 Angle : 0.586 4.755 6948 Z= 0.309 Chirality : 0.050 0.131 783 Planarity : 0.004 0.039 882 Dihedral : 5.396 17.600 684 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.42 % Allowed : 19.32 % 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: -1.71 (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 0.005 0.001 HIS B 374 PHE 0.011 0.002 PHE H 378 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG G 379 *********************** 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 113 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.939 Fit side-chains REVERT: A 307 GLN cc_start: 0.7350 (tt0) cc_final: 0.6749 (tm-30) REVERT: A 319 THR cc_start: 0.8427 (m) cc_final: 0.7973 (p) REVERT: A 338 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: A 342 GLU cc_start: 0.6240 (tt0) cc_final: 0.5891 (mm-30) REVERT: A 351 GLN cc_start: 0.7363 (mt0) cc_final: 0.7088 (mt0) REVERT: B 369 LYS cc_start: 0.7831 (ptpp) cc_final: 0.7498 (mttt) REVERT: C 342 GLU cc_start: 0.6315 (tt0) cc_final: 0.5998 (tp30) REVERT: C 347 LYS cc_start: 0.7644 (mmmt) cc_final: 0.7318 (pmtt) REVERT: E 347 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6830 (pmtt) REVERT: F 307 GLN cc_start: 0.7110 (tt0) cc_final: 0.6544 (tm-30) REVERT: F 342 GLU cc_start: 0.5980 (tt0) cc_final: 0.5702 (tp30) REVERT: H 342 GLU cc_start: 0.6029 (tt0) cc_final: 0.5820 (tt0) REVERT: H 370 LYS cc_start: 0.8034 (tttm) cc_final: 0.7519 (ttmt) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 2.5630 time to fit residues: 263.6978 Evaluate side-chains 112 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain G residue 306 VAL 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 62 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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: 0.6274 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= 0.146 Angle : 0.510 4.474 6948 Z= 0.267 Chirality : 0.050 0.126 783 Planarity : 0.003 0.022 882 Dihedral : 5.052 17.229 684 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.39 % Allowed : 20.17 % Favored : 77.44 % 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 0.004 0.001 HIS F 374 PHE 0.008 0.001 PHE A 378 TYR 0.006 0.001 TYR F 310 ARG 0.001 0.000 ARG B 349 ********************** 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 111 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.883 Fit side-chains REVERT: A 307 GLN cc_start: 0.7369 (tt0) cc_final: 0.6772 (tm-30) REVERT: A 319 THR cc_start: 0.8397 (m) cc_final: 0.8031 (p) REVERT: A 338 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: A 342 GLU cc_start: 0.6232 (tt0) cc_final: 0.5886 (mm-30) REVERT: A 351 GLN cc_start: 0.7280 (mt0) cc_final: 0.7016 (mt0) REVERT: K 369 LYS cc_start: 0.7889 (ptmt) cc_final: 0.7503 (mtpt) REVERT: B 369 LYS cc_start: 0.7804 (ptpp) cc_final: 0.7480 (mttt) REVERT: C 342 GLU cc_start: 0.6308 (tt0) cc_final: 0.5979 (tp30) REVERT: C 347 LYS cc_start: 0.7613 (mmmt) cc_final: 0.7275 (pmtt) REVERT: D 311 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7911 (ttpp) REVERT: F 307 GLN cc_start: 0.7064 (tt0) cc_final: 0.6509 (tm-30) REVERT: F 342 GLU cc_start: 0.5984 (tt0) cc_final: 0.5688 (tp30) REVERT: H 370 LYS cc_start: 0.8023 (tttm) cc_final: 0.7574 (ttmt) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 2.5610 time to fit residues: 263.5337 Evaluate side-chains 105 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 311 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 345 ASP 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 13 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.144745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.128462 restraints weight = 15572.982| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.13 r_work: 0.4033 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5193 Z= 0.245 Angle : 0.606 4.676 6948 Z= 0.320 Chirality : 0.050 0.134 783 Planarity : 0.005 0.050 882 Dihedral : 5.376 17.473 684 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.39 % Allowed : 20.17 % Favored : 77.44 % 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 0.007 0.001 HIS B 374 PHE 0.013 0.002 PHE B 378 TYR 0.011 0.002 TYR F 310 ARG 0.002 0.000 ARG G 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6109.90 seconds wall clock time: 106 minutes 41.84 seconds (6401.84 seconds total)