Starting phenix.real_space_refine on Wed Nov 15 03:26:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/11_2023/7qk5_14038.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/11_2023/7qk5_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_14038/11_2023/7qk5_14038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/11_2023/7qk5_14038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/11_2023/7qk5_14038.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk5_14038/11_2023/7qk5_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-1.21rc1-5144/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: 5.35, per 1000 atoms: 0.51 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: 7.93 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: 3.29 Time building geometry restraints manager: 8.08 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: 3625 13.50 - 27.00: 226 27.00 - 40.50: 52 40.50 - 54.01: 31 54.01 - 67.51: 125 Dihedral angle restraints: 4059 sinusoidal: 1989 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 4056 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: 5.430 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: 14.220 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.490 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.450 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.926 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 outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 2.5548 time to fit residues: 685.9289 Evaluate side-chains 117 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1712 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7783 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5193 Z= 0.346 Angle : 0.783 6.965 6948 Z= 0.421 Chirality : 0.053 0.143 783 Planarity : 0.005 0.050 882 Dihedral : 6.396 16.996 684 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.79 % Allowed : 20.34 % Favored : 74.87 % 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 (0.28), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.22), residues: 648 *********************** 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 136 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 0.880 Fit side-chains outliers start: 28 outliers final: 6 residues processed: 118 average time/residue: 2.7076 time to fit residues: 331.4436 Evaluate side-chains 98 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 1.7543 time to fit residues: 10.3204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 0.0030 chunk 51 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 330 HIS E 351 GLN F 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5193 Z= 0.146 Angle : 0.539 5.858 6948 Z= 0.281 Chirality : 0.051 0.142 783 Planarity : 0.003 0.022 882 Dihedral : 5.341 15.400 684 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.22 % Allowed : 23.08 % Favored : 74.70 % 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 *********************** 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 114 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.048 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 2.3433 time to fit residues: 254.5386 Evaluate side-chains 95 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.2331 time to fit residues: 2.4468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 C 351 GLN E 330 HIS E 351 GLN F 351 GLN ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5193 Z= 0.356 Angle : 0.733 5.964 6948 Z= 0.389 Chirality : 0.052 0.138 783 Planarity : 0.006 0.057 882 Dihedral : 5.754 16.647 684 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.79 % Allowed : 18.80 % 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: -1.60 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.22), residues: 648 *********************** 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: 28 poor density : 89 time to evaluate : 0.948 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 99 average time/residue: 2.6225 time to fit residues: 270.3975 Evaluate side-chains 105 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 9 average time/residue: 0.4989 time to fit residues: 6.3314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 351 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5193 Z= 0.153 Angle : 0.540 5.258 6948 Z= 0.283 Chirality : 0.050 0.133 783 Planarity : 0.003 0.021 882 Dihedral : 5.226 16.488 684 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.59 % Allowed : 19.83 % Favored : 76.58 % 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 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.22), residues: 648 *********************** 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 116 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 2.4365 time to fit residues: 256.4106 Evaluate side-chains 101 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 7 average time/residue: 0.2266 time to fit residues: 3.2911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.3782 ------------------------------------------------------------------------------- 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 C 351 GLN E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6493 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= 0.187 Angle : 0.565 4.868 6948 Z= 0.297 Chirality : 0.050 0.131 783 Planarity : 0.004 0.038 882 Dihedral : 5.172 15.974 684 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.91 % Allowed : 20.34 % Favored : 76.75 % 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 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 648 *********************** 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 108 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.873 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 2.4678 time to fit residues: 249.4704 Evaluate side-chains 102 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.5659 time to fit residues: 6.6047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN B 351 GLN E 351 GLN G 351 GLN H 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 5193 Z= 0.332 Angle : 0.702 5.260 6948 Z= 0.373 Chirality : 0.051 0.138 783 Planarity : 0.006 0.060 882 Dihedral : 5.635 16.908 684 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.59 % Allowed : 20.51 % 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: -1.78 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 648 *********************** 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 106 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.836 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 93 average time/residue: 2.4111 time to fit residues: 233.6624 Evaluate side-chains 100 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 8 average time/residue: 0.5068 time to fit residues: 5.8915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5193 Z= 0.150 Angle : 0.531 4.647 6948 Z= 0.278 Chirality : 0.050 0.129 783 Planarity : 0.003 0.022 882 Dihedral : 5.142 16.741 684 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.74 % Allowed : 21.54 % Favored : 75.73 % 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: -1.78 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 648 *********************** 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 105 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.871 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 2.3204 time to fit residues: 232.8004 Evaluate side-chains 98 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.6106 time to fit residues: 3.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 0.0770 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6643 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= 0.196 Angle : 0.572 4.715 6948 Z= 0.300 Chirality : 0.050 0.130 783 Planarity : 0.004 0.040 882 Dihedral : 5.189 16.600 684 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.56 % Allowed : 22.05 % Favored : 75.38 % 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: -1.77 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.22), residues: 648 *********************** 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 101 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.859 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 94 average time/residue: 2.3737 time to fit residues: 233.0484 Evaluate side-chains 101 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.2552 time to fit residues: 3.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.0980 chunk 39 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5193 Z= 0.130 Angle : 0.472 4.210 6948 Z= 0.242 Chirality : 0.050 0.127 783 Planarity : 0.002 0.021 882 Dihedral : 4.619 16.358 684 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.37 % Allowed : 23.42 % Favored : 75.21 % 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: -1.74 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 648 ********************** 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 103 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.010 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 2.3325 time to fit residues: 246.5674 Evaluate side-chains 90 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.1258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 20 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.148250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.133258 restraints weight = 15922.967| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.03 r_work: 0.4049 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5193 Z= 0.247 Angle : 0.604 4.842 6948 Z= 0.318 Chirality : 0.050 0.134 783 Planarity : 0.005 0.050 882 Dihedral : 5.109 16.124 684 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.71 % Allowed : 23.42 % Favored : 74.87 % 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 (0.30), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.23), residues: 648 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6055.18 seconds wall clock time: 106 minutes 42.11 seconds (6402.11 seconds total)