Starting phenix.real_space_refine on Fri Feb 14 17:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qk5_14038/02_2025/7qk5_14038.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qk5_14038/02_2025/7qk5_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/cci-nas-00/data/ceres_data/7qk5_14038/02_2025/7qk5_14038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qk5_14038/02_2025/7qk5_14038.map" model { file = "/net/cci-nas-00/data/ceres_data/7qk5_14038/02_2025/7qk5_14038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qk5_14038/02_2025/7qk5_14038.cif" } 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. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.09, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 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: 2.52 Conformation dependent library (CDL) restraints added in 664.3 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 54.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 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: 3.41 Time building geometry restraints manager: 3.02 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: 0.00 - 2.37: 15677 2.37 - 4.73: 2637 4.73 - 7.10: 806 7.10 - 9.47: 68 9.47 - 11.83: 9 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 2.450 nonbonded pdb=" OD2 ASP G 314 " pdb=" HZ1 LYS G 370 " model vdw 1.682 2.450 nonbonded pdb=" OD2 ASP H 314 " pdb=" HZ1 LYS H 370 " model vdw 1.684 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 2.920 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: 0.200 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.090 Find NCS groups from input model: 0.440 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: 0.000 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.902 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: 2.7415 time to fit residues: 736.3400 Evaluate side-chains 126 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 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: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 330 HIS K 336 GLN K 374 HIS B 336 GLN B 368 ASN B 374 HIS C 330 HIS C 336 GLN C 351 GLN C 374 HIS D 330 HIS D 336 GLN D 351 GLN 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 374 HIS H 336 GLN H 368 ASN H 374 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.147128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.130811 restraints weight = 15572.601| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 1.17 r_work: 0.4071 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5193 Z= 0.266 Angle : 0.700 6.561 6948 Z= 0.378 Chirality : 0.053 0.139 783 Planarity : 0.004 0.039 882 Dihedral : 6.287 17.120 684 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.93 % Allowed : 19.49 % 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: -1.35 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 374 PHE 0.017 0.003 PHE B 378 TYR 0.012 0.002 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7424 (tt0) cc_final: 0.7090 (tm-30) REVERT: A 342 GLU cc_start: 0.6657 (tt0) cc_final: 0.6276 (mm-30) REVERT: A 351 GLN cc_start: 0.7665 (mt0) cc_final: 0.7406 (mt0) REVERT: A 370 LYS cc_start: 0.8150 (tttp) cc_final: 0.7716 (tptt) REVERT: B 319 THR cc_start: 0.8349 (m) cc_final: 0.8141 (p) REVERT: B 370 LYS cc_start: 0.7990 (tttm) cc_final: 0.7722 (ttmt) REVERT: C 314 ASP cc_start: 0.7965 (t0) cc_final: 0.7708 (t70) REVERT: C 342 GLU cc_start: 0.6710 (tt0) cc_final: 0.6314 (tp30) REVERT: C 347 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7321 (pmtt) REVERT: D 317 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6546 (mtpp) REVERT: E 314 ASP cc_start: 0.7914 (t0) cc_final: 0.7663 (t70) REVERT: F 307 GLN cc_start: 0.7463 (tt0) cc_final: 0.7128 (tm-30) REVERT: F 342 GLU cc_start: 0.6588 (tt0) cc_final: 0.6267 (mm-30) REVERT: F 370 LYS cc_start: 0.8366 (tttm) cc_final: 0.8131 (ttmp) REVERT: F 377 THR cc_start: 0.8073 (m) cc_final: 0.7835 (m) REVERT: G 377 THR cc_start: 0.8185 (m) cc_final: 0.7948 (m) REVERT: H 353 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8143 (mtpp) REVERT: H 370 LYS cc_start: 0.8135 (tttm) cc_final: 0.7765 (ttmt) outliers start: 23 outliers final: 6 residues processed: 132 average time/residue: 2.7939 time to fit residues: 382.3597 Evaluate side-chains 110 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 353 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN C 351 GLN E 330 HIS E 351 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.148221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.132336 restraints weight = 15673.952| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.16 r_work: 0.4091 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5193 Z= 0.180 Angle : 0.584 5.620 6948 Z= 0.307 Chirality : 0.051 0.134 783 Planarity : 0.003 0.025 882 Dihedral : 5.505 16.198 684 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.39 % Allowed : 21.54 % Favored : 76.07 % 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 : -1.10 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 374 PHE 0.013 0.002 PHE H 378 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.899 Fit side-chains REVERT: A 307 GLN cc_start: 0.7450 (tt0) cc_final: 0.7117 (tm-30) REVERT: A 342 GLU cc_start: 0.6668 (tt0) cc_final: 0.6310 (mm-30) REVERT: A 351 GLN cc_start: 0.7625 (mt0) cc_final: 0.7388 (mt0) REVERT: B 369 LYS cc_start: 0.7710 (ptpp) cc_final: 0.7482 (mttt) REVERT: B 370 LYS cc_start: 0.8009 (tttm) cc_final: 0.7797 (ttmt) REVERT: C 342 GLU cc_start: 0.6721 (tt0) cc_final: 0.6394 (tp30) REVERT: C 347 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7219 (pmtt) REVERT: E 370 LYS cc_start: 0.8223 (tttm) cc_final: 0.8016 (tptm) REVERT: F 307 GLN cc_start: 0.7422 (tt0) cc_final: 0.7066 (tm-30) REVERT: F 314 ASP cc_start: 0.7561 (t0) cc_final: 0.7228 (t70) REVERT: F 342 GLU cc_start: 0.6571 (tt0) cc_final: 0.6274 (tp30) REVERT: F 345 ASP cc_start: 0.7319 (m-30) cc_final: 0.7117 (m-30) REVERT: F 370 LYS cc_start: 0.8279 (tttm) cc_final: 0.7999 (ttmp) REVERT: F 377 THR cc_start: 0.8133 (m) cc_final: 0.7906 (m) REVERT: H 370 LYS cc_start: 0.8113 (tttm) cc_final: 0.7812 (ttmt) outliers start: 14 outliers final: 7 residues processed: 111 average time/residue: 2.5620 time to fit residues: 296.0022 Evaluate side-chains 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL 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 348 ASP Chi-restraints excluded: chain G residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN K 368 ASN B 351 GLN D 351 GLN E 330 HIS E 351 GLN F 351 GLN G 368 ASN ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.143219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.127299 restraints weight = 15831.366| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.11 r_work: 0.4018 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5193 Z= 0.418 Angle : 0.777 5.988 6948 Z= 0.413 Chirality : 0.053 0.148 783 Planarity : 0.007 0.064 882 Dihedral : 5.977 17.580 684 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -1.69 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 374 PHE 0.017 0.004 PHE E 378 TYR 0.013 0.003 TYR A 310 ARG 0.004 0.001 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7412 (tt0) cc_final: 0.7111 (tm-30) REVERT: A 342 GLU cc_start: 0.6627 (tt0) cc_final: 0.6265 (mm-30) REVERT: A 351 GLN cc_start: 0.7582 (mt0) cc_final: 0.7294 (mt0) REVERT: C 342 GLU cc_start: 0.6656 (tt0) cc_final: 0.6349 (tp30) REVERT: C 347 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7364 (pmtt) REVERT: D 317 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6701 (mttm) REVERT: E 347 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6810 (pmtt) REVERT: F 307 GLN cc_start: 0.7415 (tt0) cc_final: 0.7119 (tm-30) REVERT: F 342 GLU cc_start: 0.6404 (tt0) cc_final: 0.6074 (mm-30) REVERT: F 345 ASP cc_start: 0.7394 (m-30) cc_final: 0.7105 (m-30) REVERT: F 351 GLN cc_start: 0.7437 (mt0) cc_final: 0.7232 (mt0) REVERT: H 370 LYS cc_start: 0.8188 (tttm) cc_final: 0.7894 (ttmt) outliers start: 25 outliers final: 13 residues processed: 101 average time/residue: 2.8246 time to fit residues: 295.9580 Evaluate side-chains 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL 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 315 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 317 LYS 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 315 LEU 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 40 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN E 330 HIS E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.148099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.132067 restraints weight = 15504.015| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 1.17 r_work: 0.4083 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.4016 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6232 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= 0.172 Angle : 0.564 4.673 6948 Z= 0.295 Chirality : 0.051 0.132 783 Planarity : 0.003 0.027 882 Dihedral : 5.455 17.537 684 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.56 % Allowed : 19.66 % Favored : 77.78 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 374 PHE 0.009 0.002 PHE E 378 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.931 Fit side-chains REVERT: A 307 GLN cc_start: 0.7453 (tt0) cc_final: 0.7151 (tm-30) REVERT: A 342 GLU cc_start: 0.6623 (tt0) cc_final: 0.6264 (mm-30) REVERT: A 351 GLN cc_start: 0.7648 (mt0) cc_final: 0.7416 (mt0) REVERT: B 369 LYS cc_start: 0.7782 (ptpp) cc_final: 0.7557 (mttt) REVERT: C 342 GLU cc_start: 0.6689 (tt0) cc_final: 0.6373 (tp30) REVERT: C 347 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7322 (pmtt) REVERT: E 347 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.6829 (pmtt) REVERT: F 307 GLN cc_start: 0.7361 (tt0) cc_final: 0.7000 (tm-30) REVERT: F 342 GLU cc_start: 0.6399 (tt0) cc_final: 0.6067 (mm-30) REVERT: F 345 ASP cc_start: 0.7317 (m-30) cc_final: 0.7083 (m-30) REVERT: H 370 LYS cc_start: 0.8113 (tttm) cc_final: 0.7839 (ttmt) outliers start: 15 outliers final: 10 residues processed: 99 average time/residue: 2.7219 time to fit residues: 280.1558 Evaluate side-chains 101 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 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 G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN E 330 HIS E 351 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.146228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.129983 restraints weight = 15634.711| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.17 r_work: 0.4060 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.6296 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 : 0.603 4.794 6948 Z= 0.316 Chirality : 0.051 0.138 783 Planarity : 0.005 0.042 882 Dihedral : 5.440 17.433 684 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.08 % Allowed : 19.32 % 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: -1.79 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (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 A 378 TYR 0.010 0.002 TYR F 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7458 (tt0) cc_final: 0.7160 (tm-30) REVERT: A 319 THR cc_start: 0.8536 (m) cc_final: 0.8301 (p) REVERT: A 342 GLU cc_start: 0.6625 (tt0) cc_final: 0.6278 (mm-30) REVERT: A 351 GLN cc_start: 0.7613 (mt0) cc_final: 0.7348 (mt0) REVERT: C 342 GLU cc_start: 0.6670 (tt0) cc_final: 0.6362 (tp30) REVERT: C 347 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7309 (pmtt) REVERT: E 347 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.6815 (pmtt) REVERT: F 307 GLN cc_start: 0.7348 (tt0) cc_final: 0.7038 (tm-30) REVERT: F 342 GLU cc_start: 0.6383 (tt0) cc_final: 0.6000 (mm-30) REVERT: F 345 ASP cc_start: 0.7306 (m-30) cc_final: 0.7016 (m-30) REVERT: H 370 LYS cc_start: 0.8104 (tttm) cc_final: 0.7842 (ttmt) outliers start: 18 outliers final: 11 residues processed: 99 average time/residue: 2.6092 time to fit residues: 268.6719 Evaluate side-chains 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 3 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.0020 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN D 351 GLN E 330 HIS E 351 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.146045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.130434 restraints weight = 16071.129| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.13 r_work: 0.4064 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5193 Z= 0.222 Angle : 0.591 4.764 6948 Z= 0.310 Chirality : 0.051 0.135 783 Planarity : 0.004 0.036 882 Dihedral : 5.415 17.703 684 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -1.88 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 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 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 112 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7461 (tt0) cc_final: 0.7176 (tm-30) REVERT: A 319 THR cc_start: 0.8511 (m) cc_final: 0.8309 (p) REVERT: A 342 GLU cc_start: 0.6612 (tt0) cc_final: 0.6271 (mm-30) REVERT: A 351 GLN cc_start: 0.7626 (mt0) cc_final: 0.7351 (mt0) REVERT: C 342 GLU cc_start: 0.6687 (tt0) cc_final: 0.6374 (tp30) REVERT: C 347 LYS cc_start: 0.7862 (mmmt) cc_final: 0.7291 (pmtt) REVERT: D 311 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8131 (ttpp) REVERT: E 347 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6808 (pmtt) REVERT: F 307 GLN cc_start: 0.7317 (tt0) cc_final: 0.7020 (tm-30) REVERT: F 342 GLU cc_start: 0.6365 (tt0) cc_final: 0.6050 (mm-30) REVERT: F 345 ASP cc_start: 0.7334 (m-30) cc_final: 0.7037 (m-30) REVERT: H 370 LYS cc_start: 0.8115 (tttm) cc_final: 0.7870 (ttmt) outliers start: 20 outliers final: 13 residues processed: 101 average time/residue: 2.6082 time to fit residues: 275.0837 Evaluate side-chains 108 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 306 VAL 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 D residue 370 LYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 GLN D 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.144716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.128870 restraints weight = 15903.210| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.13 r_work: 0.4045 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5193 Z= 0.301 Angle : 0.659 5.293 6948 Z= 0.348 Chirality : 0.051 0.143 783 Planarity : 0.006 0.050 882 Dihedral : 5.571 17.943 684 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.91 % Allowed : 19.49 % 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: -1.87 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 374 PHE 0.014 0.003 PHE E 378 TYR 0.012 0.003 TYR F 310 ARG 0.002 0.000 ARG K 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 110 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7468 (tt0) cc_final: 0.7177 (tm-30) REVERT: A 319 THR cc_start: 0.8527 (m) cc_final: 0.8324 (p) REVERT: A 342 GLU cc_start: 0.6646 (tt0) cc_final: 0.6299 (mm-30) REVERT: A 351 GLN cc_start: 0.7597 (mt0) cc_final: 0.7342 (mt0) REVERT: C 342 GLU cc_start: 0.6676 (tt0) cc_final: 0.6364 (tp30) REVERT: C 347 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7290 (pmtt) REVERT: F 307 GLN cc_start: 0.7341 (tt0) cc_final: 0.7053 (tm-30) REVERT: F 342 GLU cc_start: 0.6387 (tt0) cc_final: 0.6067 (mm-30) REVERT: F 345 ASP cc_start: 0.7343 (m-30) cc_final: 0.7045 (m-30) REVERT: H 370 LYS cc_start: 0.8166 (tttm) cc_final: 0.7927 (ttmt) outliers start: 17 outliers final: 16 residues processed: 99 average time/residue: 2.6084 time to fit residues: 268.8915 Evaluate side-chains 107 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 306 VAL 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 D residue 370 LYS 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 315 LEU Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 330 HIS E 351 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.147706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.131652 restraints weight = 15808.809| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.17 r_work: 0.4085 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5193 Z= 0.177 Angle : 0.559 5.995 6948 Z= 0.290 Chirality : 0.050 0.132 783 Planarity : 0.004 0.028 882 Dihedral : 5.294 17.686 684 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.91 % Allowed : 19.83 % 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: -1.91 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.008 0.002 PHE E 378 TYR 0.007 0.002 TYR F 310 ARG 0.001 0.000 ARG B 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 109 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7490 (tt0) cc_final: 0.7202 (tm-30) REVERT: A 342 GLU cc_start: 0.6615 (tt0) cc_final: 0.6269 (mm-30) REVERT: A 351 GLN cc_start: 0.7669 (mt0) cc_final: 0.7453 (mt0) REVERT: C 342 GLU cc_start: 0.6668 (tt0) cc_final: 0.6339 (tp30) REVERT: C 347 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7259 (pmtt) REVERT: D 311 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8056 (ttpp) REVERT: E 347 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6802 (pmtt) REVERT: F 307 GLN cc_start: 0.7300 (tt0) cc_final: 0.6987 (tm-30) REVERT: F 342 GLU cc_start: 0.6356 (tt0) cc_final: 0.6123 (tp30) REVERT: F 345 ASP cc_start: 0.7369 (m-30) cc_final: 0.7102 (m-30) REVERT: H 370 LYS cc_start: 0.8119 (tttm) cc_final: 0.7864 (ttmt) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 2.6413 time to fit residues: 272.3570 Evaluate side-chains 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL 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 311 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 370 LYS 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 315 LEU 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 61 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 330 HIS E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.147136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.131128 restraints weight = 15677.000| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.16 r_work: 0.4076 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6468 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= 0.194 Angle : 0.567 5.067 6948 Z= 0.296 Chirality : 0.050 0.132 783 Planarity : 0.004 0.037 882 Dihedral : 5.242 17.525 684 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -1.87 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.009 0.002 PHE A 378 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG H 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7480 (tt0) cc_final: 0.7191 (tm-30) REVERT: A 342 GLU cc_start: 0.6613 (tt0) cc_final: 0.6269 (mm-30) REVERT: A 351 GLN cc_start: 0.7626 (mt0) cc_final: 0.7390 (mt0) REVERT: C 342 GLU cc_start: 0.6684 (tt0) cc_final: 0.6363 (tp30) REVERT: C 347 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7250 (pmtt) REVERT: E 347 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6802 (pmtt) REVERT: F 307 GLN cc_start: 0.7300 (tt0) cc_final: 0.7008 (tm-30) REVERT: F 342 GLU cc_start: 0.6375 (tt0) cc_final: 0.6093 (tp30) REVERT: F 345 ASP cc_start: 0.7361 (m-30) cc_final: 0.7096 (m-30) REVERT: H 370 LYS cc_start: 0.8124 (tttm) cc_final: 0.7887 (ttmt) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 2.7196 time to fit residues: 277.1379 Evaluate side-chains 101 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL 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 315 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 370 LYS 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 315 LEU 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 61 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- 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 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.150768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.135056 restraints weight = 15621.401| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 1.17 r_work: 0.4129 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.4064 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5193 Z= 0.143 Angle : 0.510 6.441 6948 Z= 0.261 Chirality : 0.050 0.131 783 Planarity : 0.003 0.023 882 Dihedral : 4.937 17.173 684 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.37 % Allowed : 21.54 % 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: -1.92 (0.29), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.006 0.001 PHE H 378 TYR 0.006 0.001 TYR G 310 ARG 0.002 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10802.49 seconds wall clock time: 190 minutes 39.42 seconds (11439.42 seconds total)