Starting phenix.real_space_refine on Mon Mar 11 11:50:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p67_13220/03_2024/7p67_13220.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p67_13220/03_2024/7p67_13220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p67_13220/03_2024/7p67_13220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p67_13220/03_2024/7p67_13220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p67_13220/03_2024/7p67_13220.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p67_13220/03_2024/7p67_13220.pdb" } resolution = 3.1 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= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5060 2.51 5 N 1520 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "B" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "F" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "G" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "I" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "J" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 4.44, per 1000 atoms: 0.55 Number of scatterers: 8120 At special positions: 0 Unit cell: (120.75, 151.8, 51.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1520 8.00 N 1520 7.00 C 5060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 27 sheets defined 0.0% alpha, 47.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 284 removed outlier: 9.175A pdb=" N LYS B 274 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N ILE C 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N LYS A 274 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ILE B 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N GLN A 276 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ASN B 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ILE A 278 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N LYS B 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS A 280 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASP B 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 282 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 275 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN D 276 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 277 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE D 278 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A 279 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS D 280 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS A 281 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL D 275 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN E 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE D 277 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE E 278 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN D 279 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS E 280 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS D 281 " --> pdb=" O LYS E 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.750A pdb=" N GLN A 288 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN D 288 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.530A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 297 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.374A pdb=" N VAL A 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL D 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL D 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL E 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.794A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.488A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.700A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 341 removed outlier: 6.171A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU B 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER A 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU B 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER D 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS A 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER E 341 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS D 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 344 through 345 removed outlier: 7.839A pdb=" N LEU C 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS B 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU B 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER A 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU B 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP D 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 350 removed outlier: 6.823A pdb=" N ASP A 348 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASP D 348 " --> pdb=" O ARG E 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 353 through 357 removed outlier: 6.834A pdb=" N ILE B 354 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY C 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY B 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER D 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY A 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N LYS D 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N SER E 356 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY D 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.511A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.770A pdb=" N ILE C 371 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 371 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LYS D 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 374 through 378 removed outlier: 6.366A pdb=" N LYS B 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE C 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR B 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 274 through 284 removed outlier: 9.179A pdb=" N LYS G 274 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N ILE H 277 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N GLN G 276 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ASN H 279 " --> pdb=" O GLN G 276 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ILE G 278 " --> pdb=" O ASN H 279 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N LYS H 281 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS G 280 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASP H 283 " --> pdb=" O LYS G 280 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU G 282 " --> pdb=" O ASP H 283 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N LYS F 274 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ILE G 277 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N GLN F 276 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ASN G 279 " --> pdb=" O GLN F 276 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ILE F 278 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N LYS G 281 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS F 280 " --> pdb=" O LYS G 281 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ASP G 283 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU F 282 " --> pdb=" O ASP G 283 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL F 275 " --> pdb=" O LYS I 274 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN I 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE F 277 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE I 278 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASN F 279 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS I 280 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS F 281 " --> pdb=" O LYS I 280 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL I 275 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN J 276 " --> pdb=" O VAL I 275 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE I 277 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE J 278 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN I 279 " --> pdb=" O ILE J 278 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS J 280 " --> pdb=" O ASN I 279 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS I 281 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 287 through 290 removed outlier: 6.792A pdb=" N GLN F 288 " --> pdb=" O SER I 289 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN I 288 " --> pdb=" O SER J 289 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 297 through 298 removed outlier: 6.520A pdb=" N ILE G 297 " --> pdb=" O LYS H 298 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE F 297 " --> pdb=" O LYS G 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 306 through 310 removed outlier: 6.395A pdb=" N VAL F 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL I 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE F 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL I 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL J 309 " --> pdb=" O VAL I 306 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE I 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.819A pdb=" N VAL F 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL I 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 317 through 322 removed outlier: 6.504A pdb=" N VAL G 318 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS H 321 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER G 320 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LYS G 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER F 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 328 through 330 removed outlier: 6.716A pdb=" N ILE G 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE F 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 337 through 345 removed outlier: 6.146A pdb=" N VAL G 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LYS H 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL G 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU H 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER G 341 " --> pdb=" O GLU H 342 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU H 344 " --> pdb=" O SER G 341 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS G 343 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL F 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LYS G 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU G 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER F 341 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU G 344 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS F 343 " --> pdb=" O LEU G 344 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 348 through 350 removed outlier: 6.815A pdb=" N ASP F 348 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP I 348 " --> pdb=" O ARG J 349 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 353 through 357 removed outlier: 6.819A pdb=" N ILE G 354 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY H 355 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 354 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY G 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N LYS F 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER I 356 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY F 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LYS I 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N SER J 356 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY I 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 360 through 362 removed outlier: 6.502A pdb=" N THR G 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR F 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 369 through 371 removed outlier: 6.807A pdb=" N ILE H 371 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU G 372 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS F 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLU G 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE F 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS G 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR F 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU G 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS F 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N PHE G 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR F 377 " --> pdb=" O PHE G 378 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS F 370 " --> pdb=" O LYS I 369 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LYS I 369 " --> pdb=" O LYS J 370 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 374 through 378 removed outlier: 7.975A pdb=" N HIS H 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR G 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU H 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS G 375 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE H 378 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR G 377 " --> pdb=" O PHE H 378 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS F 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLU G 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE F 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS G 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR F 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU G 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS F 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N PHE G 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR F 377 " --> pdb=" O PHE G 378 " (cutoff:3.500A) 141 hydrogen bonds defined for protein. 423 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: 2.15 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2465 1.33 - 1.45: 844 1.45 - 1.57: 4891 1.57 - 1.69: 10 1.69 - 1.81: 20 Bond restraints: 8230 Sorted by residual: bond pdb=" N VAL J 313 " pdb=" CA VAL J 313 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.63e+00 bond pdb=" N VAL I 313 " pdb=" CA VAL I 313 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.50e+00 bond pdb=" N VAL E 313 " pdb=" CA VAL E 313 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.30e+00 bond pdb=" N VAL F 313 " pdb=" CA VAL F 313 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.24e-02 6.50e+03 8.25e+00 bond pdb=" N VAL D 313 " pdb=" CA VAL D 313 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.16e+00 ... (remaining 8225 not shown) Histogram of bond angle deviations from ideal: 102.59 - 108.34: 512 108.34 - 114.10: 4636 114.10 - 119.85: 2269 119.85 - 125.61: 3473 125.61 - 131.36: 100 Bond angle restraints: 10990 Sorted by residual: angle pdb=" CA ASN F 286 " pdb=" C ASN F 286 " pdb=" O ASN F 286 " ideal model delta sigma weight residual 122.14 117.56 4.58 1.24e+00 6.50e-01 1.36e+01 angle pdb=" CA ASN J 286 " pdb=" C ASN J 286 " pdb=" O ASN J 286 " ideal model delta sigma weight residual 122.14 117.57 4.57 1.24e+00 6.50e-01 1.36e+01 angle pdb=" CA ASN I 286 " pdb=" C ASN I 286 " pdb=" O ASN I 286 " ideal model delta sigma weight residual 122.14 117.59 4.55 1.24e+00 6.50e-01 1.35e+01 angle pdb=" CA ASN A 286 " pdb=" C ASN A 286 " pdb=" O ASN A 286 " ideal model delta sigma weight residual 122.14 117.60 4.54 1.24e+00 6.50e-01 1.34e+01 angle pdb=" CA ASN D 286 " pdb=" C ASN D 286 " pdb=" O ASN D 286 " ideal model delta sigma weight residual 122.14 117.62 4.52 1.24e+00 6.50e-01 1.33e+01 ... (remaining 10985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.66: 4206 9.66 - 19.33: 484 19.33 - 28.99: 200 28.99 - 38.66: 130 38.66 - 48.32: 30 Dihedral angle restraints: 5050 sinusoidal: 2110 harmonic: 2940 Sorted by residual: dihedral pdb=" CA ILE G 360 " pdb=" C ILE G 360 " pdb=" N THR G 361 " pdb=" CA THR G 361 " ideal model delta harmonic sigma weight residual 180.00 164.81 15.19 0 5.00e+00 4.00e-02 9.23e+00 dihedral pdb=" CA ILE D 360 " pdb=" C ILE D 360 " pdb=" N THR D 361 " pdb=" CA THR D 361 " ideal model delta harmonic sigma weight residual 180.00 164.83 15.17 0 5.00e+00 4.00e-02 9.20e+00 dihedral pdb=" CA ILE I 360 " pdb=" C ILE I 360 " pdb=" N THR I 361 " pdb=" CA THR I 361 " ideal model delta harmonic sigma weight residual 180.00 164.86 15.14 0 5.00e+00 4.00e-02 9.17e+00 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1093 0.117 - 0.235: 107 0.235 - 0.352: 20 0.352 - 0.470: 0 0.470 - 0.587: 10 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CB ILE G 360 " pdb=" CA ILE G 360 " pdb=" CG1 ILE G 360 " pdb=" CG2 ILE G 360 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.61e+00 chirality pdb=" CB ILE J 360 " pdb=" CA ILE J 360 " pdb=" CG1 ILE J 360 " pdb=" CG2 ILE J 360 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" CB ILE B 360 " pdb=" CA ILE B 360 " pdb=" CG1 ILE B 360 " pdb=" CG2 ILE B 360 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.58 2.00e-01 2.50e+01 8.51e+00 ... (remaining 1227 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 358 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASP C 358 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP C 358 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN C 359 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 358 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C ASP B 358 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP B 358 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 359 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 358 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ASP D 358 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP D 358 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN D 359 " 0.012 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2358 2.85 - 3.36: 7035 3.36 - 3.88: 13884 3.88 - 4.39: 15362 4.39 - 4.90: 30345 Nonbonded interactions: 68984 Sorted by model distance: nonbonded pdb=" OD2 ASP A 348 " pdb=" NZ LYS D 311 " model vdw 2.338 2.520 nonbonded pdb=" NZ LYS B 311 " pdb=" OD2 ASP C 348 " model vdw 2.342 2.520 nonbonded pdb=" NZ LYS G 311 " pdb=" OD2 ASP H 348 " model vdw 2.344 2.520 nonbonded pdb=" OD2 ASP D 348 " pdb=" NZ LYS E 311 " model vdw 2.348 2.520 nonbonded pdb=" OD2 ASP F 348 " pdb=" NZ LYS I 311 " model vdw 2.354 2.520 ... (remaining 68979 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.700 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: 0.000 Extract box with map and model: 8.190 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.420 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.007 0.048 8230 Z= 0.472 Angle : 1.057 8.269 10990 Z= 0.654 Chirality : 0.093 0.587 1230 Planarity : 0.005 0.027 1410 Dihedral : 11.976 48.319 3190 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 299 PHE 0.003 0.001 PHE G 346 TYR 0.007 0.002 TYR I 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.071 Fit side-chains REVERT: C 316 SER cc_start: 0.9184 (p) cc_final: 0.8978 (p) REVERT: C 349 ARG cc_start: 0.7451 (mtp180) cc_final: 0.6853 (pmt-80) REVERT: C 358 ASP cc_start: 0.8164 (p0) cc_final: 0.7863 (p0) REVERT: D 276 GLN cc_start: 0.7539 (tt0) cc_final: 0.7162 (tt0) REVERT: D 316 SER cc_start: 0.8989 (p) cc_final: 0.8693 (p) REVERT: E 359 ASN cc_start: 0.8018 (t0) cc_final: 0.7799 (t0) REVERT: F 316 SER cc_start: 0.9026 (p) cc_final: 0.8717 (p) REVERT: G 316 SER cc_start: 0.8892 (p) cc_final: 0.8687 (p) REVERT: I 357 LEU cc_start: 0.8655 (tp) cc_final: 0.8350 (tp) REVERT: J 316 SER cc_start: 0.9076 (p) cc_final: 0.8866 (p) REVERT: J 351 GLN cc_start: 0.8217 (pt0) cc_final: 0.7838 (mm-40) REVERT: J 357 LEU cc_start: 0.8725 (tp) cc_final: 0.8282 (tp) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1777 time to fit residues: 75.6335 Evaluate side-chains 261 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 279 ASN J 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8230 Z= 0.306 Angle : 0.547 6.067 10990 Z= 0.280 Chirality : 0.049 0.121 1230 Planarity : 0.003 0.021 1410 Dihedral : 5.279 15.827 1100 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.69 % Allowed : 10.00 % Favored : 87.31 % 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: -3.20 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 299 PHE 0.005 0.001 PHE B 346 TYR 0.011 0.002 TYR C 310 ARG 0.003 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 265 time to evaluate : 1.091 Fit side-chains REVERT: C 349 ARG cc_start: 0.7442 (mtp180) cc_final: 0.7064 (ppt170) REVERT: D 295 ASP cc_start: 0.8109 (m-30) cc_final: 0.7743 (m-30) REVERT: E 351 GLN cc_start: 0.4960 (mm110) cc_final: 0.4627 (tp-100) REVERT: F 295 ASP cc_start: 0.8141 (m-30) cc_final: 0.7770 (m-30) REVERT: F 314 ASP cc_start: 0.8296 (t0) cc_final: 0.8082 (t0) REVERT: F 359 ASN cc_start: 0.8272 (t0) cc_final: 0.7975 (t0) REVERT: G 295 ASP cc_start: 0.8146 (m-30) cc_final: 0.7879 (m-30) REVERT: H 358 ASP cc_start: 0.8213 (p0) cc_final: 0.7887 (p0) REVERT: I 359 ASN cc_start: 0.8509 (t0) cc_final: 0.8292 (t0) REVERT: J 351 GLN cc_start: 0.8373 (pt0) cc_final: 0.7553 (mm-40) outliers start: 25 outliers final: 18 residues processed: 279 average time/residue: 0.2075 time to fit residues: 78.9771 Evaluate side-chains 256 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 348 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN D 351 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.061 8230 Z= 0.656 Angle : 0.679 6.253 10990 Z= 0.357 Chirality : 0.053 0.130 1230 Planarity : 0.004 0.031 1410 Dihedral : 5.874 17.664 1100 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.55 % Allowed : 11.40 % Favored : 85.05 % 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: -3.28 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 299 PHE 0.011 0.001 PHE E 378 TYR 0.011 0.002 TYR C 310 ARG 0.004 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 0.962 Fit side-chains REVERT: C 349 ARG cc_start: 0.7568 (mtp180) cc_final: 0.7131 (ppt170) REVERT: E 342 GLU cc_start: 0.4697 (pm20) cc_final: 0.4066 (pm20) REVERT: E 351 GLN cc_start: 0.6170 (mm110) cc_final: 0.5309 (pt0) REVERT: F 295 ASP cc_start: 0.8201 (m-30) cc_final: 0.7919 (m-30) REVERT: I 349 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7663 (mtm-85) REVERT: J 351 GLN cc_start: 0.8410 (pt0) cc_final: 0.7461 (tp-100) outliers start: 33 outliers final: 28 residues processed: 269 average time/residue: 0.1919 time to fit residues: 69.6253 Evaluate side-chains 267 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8230 Z= 0.313 Angle : 0.569 5.936 10990 Z= 0.287 Chirality : 0.050 0.121 1230 Planarity : 0.003 0.029 1410 Dihedral : 5.330 14.941 1100 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.33 % Allowed : 12.58 % Favored : 84.09 % 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: -3.23 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 299 PHE 0.022 0.001 PHE G 378 TYR 0.013 0.002 TYR C 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 247 time to evaluate : 0.984 Fit side-chains REVERT: C 279 ASN cc_start: 0.8154 (m-40) cc_final: 0.7875 (m-40) REVERT: C 349 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7131 (ppt170) REVERT: D 351 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: D 358 ASP cc_start: 0.8432 (p0) cc_final: 0.8231 (p0) REVERT: E 342 GLU cc_start: 0.4230 (pm20) cc_final: 0.3692 (pm20) REVERT: E 349 ARG cc_start: 0.5945 (mmt-90) cc_final: 0.5553 (mmp80) REVERT: E 351 GLN cc_start: 0.6010 (mm110) cc_final: 0.5040 (pt0) REVERT: F 358 ASP cc_start: 0.8493 (p0) cc_final: 0.8275 (p0) REVERT: I 358 ASP cc_start: 0.8248 (p0) cc_final: 0.8024 (p0) REVERT: J 351 GLN cc_start: 0.8305 (pt0) cc_final: 0.7416 (tp-100) outliers start: 31 outliers final: 27 residues processed: 263 average time/residue: 0.1997 time to fit residues: 70.3761 Evaluate side-chains 264 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8230 Z= 0.413 Angle : 0.611 7.972 10990 Z= 0.307 Chirality : 0.051 0.124 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.474 15.446 1100 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.76 % Allowed : 12.90 % Favored : 83.33 % 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: -3.25 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 299 PHE 0.022 0.001 PHE G 378 TYR 0.005 0.001 TYR G 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 0.971 Fit side-chains REVERT: C 279 ASN cc_start: 0.8176 (m-40) cc_final: 0.7920 (m-40) REVERT: C 349 ARG cc_start: 0.7603 (mtp180) cc_final: 0.6937 (ppt170) REVERT: D 351 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: E 351 GLN cc_start: 0.6123 (mm110) cc_final: 0.4905 (pt0) REVERT: E 379 ARG cc_start: 0.4943 (tpp-160) cc_final: 0.4521 (mmm160) REVERT: F 358 ASP cc_start: 0.8544 (p0) cc_final: 0.8302 (p0) REVERT: I 288 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7355 (mm-40) REVERT: I 358 ASP cc_start: 0.8254 (p0) cc_final: 0.8015 (p0) REVERT: J 351 GLN cc_start: 0.8373 (pt0) cc_final: 0.7721 (tp-100) outliers start: 35 outliers final: 30 residues processed: 258 average time/residue: 0.1949 time to fit residues: 67.7138 Evaluate side-chains 268 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8230 Z= 0.346 Angle : 0.597 8.305 10990 Z= 0.296 Chirality : 0.050 0.122 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.322 15.017 1100 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.76 % Allowed : 13.12 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 299 PHE 0.018 0.002 PHE G 378 TYR 0.005 0.001 TYR G 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 1.080 Fit side-chains REVERT: C 279 ASN cc_start: 0.8149 (m-40) cc_final: 0.7899 (m-40) REVERT: C 349 ARG cc_start: 0.7586 (mtp180) cc_final: 0.6927 (ppt170) REVERT: D 351 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: D 358 ASP cc_start: 0.8214 (p0) cc_final: 0.7994 (p0) REVERT: E 351 GLN cc_start: 0.5707 (mm110) cc_final: 0.4485 (pt0) REVERT: F 358 ASP cc_start: 0.8502 (p0) cc_final: 0.8258 (p0) REVERT: I 288 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7282 (mm-40) REVERT: I 358 ASP cc_start: 0.8250 (p0) cc_final: 0.8015 (p0) REVERT: J 351 GLN cc_start: 0.8348 (pt0) cc_final: 0.7683 (tp-100) outliers start: 35 outliers final: 32 residues processed: 257 average time/residue: 0.2082 time to fit residues: 72.5916 Evaluate side-chains 267 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 233 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8230 Z= 0.349 Angle : 0.609 7.891 10990 Z= 0.300 Chirality : 0.050 0.122 1230 Planarity : 0.003 0.032 1410 Dihedral : 5.333 15.094 1100 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.76 % Allowed : 14.19 % Favored : 82.04 % 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: -3.31 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 299 PHE 0.017 0.002 PHE G 378 TYR 0.014 0.001 TYR C 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 234 time to evaluate : 1.058 Fit side-chains REVERT: C 279 ASN cc_start: 0.8162 (m-40) cc_final: 0.7952 (m110) REVERT: C 349 ARG cc_start: 0.7615 (mtp180) cc_final: 0.6929 (ppt170) REVERT: D 351 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: F 358 ASP cc_start: 0.8435 (p0) cc_final: 0.8199 (p0) REVERT: I 288 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7345 (mm-40) REVERT: I 358 ASP cc_start: 0.8197 (p0) cc_final: 0.7943 (p0) REVERT: J 351 GLN cc_start: 0.8377 (pt0) cc_final: 0.7730 (tp-100) outliers start: 35 outliers final: 30 residues processed: 252 average time/residue: 0.2141 time to fit residues: 73.2181 Evaluate side-chains 263 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8230 Z= 0.471 Angle : 0.654 7.669 10990 Z= 0.328 Chirality : 0.051 0.123 1230 Planarity : 0.003 0.036 1410 Dihedral : 5.551 16.000 1100 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.09 % Allowed : 14.41 % Favored : 81.51 % 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: -3.37 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 299 PHE 0.019 0.002 PHE G 378 TYR 0.006 0.001 TYR G 310 ARG 0.006 0.001 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 0.921 Fit side-chains REVERT: C 279 ASN cc_start: 0.8194 (m-40) cc_final: 0.7972 (m-40) REVERT: C 349 ARG cc_start: 0.7585 (mtp180) cc_final: 0.6904 (ppt170) REVERT: D 351 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: I 288 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7425 (mm-40) REVERT: I 358 ASP cc_start: 0.8242 (p0) cc_final: 0.7992 (p0) REVERT: J 351 GLN cc_start: 0.8371 (pt0) cc_final: 0.7731 (tp-100) outliers start: 38 outliers final: 34 residues processed: 252 average time/residue: 0.1877 time to fit residues: 63.9059 Evaluate side-chains 266 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8230 Z= 0.331 Angle : 0.616 8.115 10990 Z= 0.302 Chirality : 0.050 0.123 1230 Planarity : 0.003 0.031 1410 Dihedral : 5.306 15.223 1100 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.87 % Allowed : 14.73 % Favored : 81.40 % 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: -3.35 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 299 PHE 0.015 0.002 PHE G 378 TYR 0.005 0.001 TYR G 310 ARG 0.004 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.010 Fit side-chains REVERT: C 279 ASN cc_start: 0.8138 (m-40) cc_final: 0.7938 (m110) REVERT: C 349 ARG cc_start: 0.7572 (mtp180) cc_final: 0.6937 (ppt170) REVERT: D 349 ARG cc_start: 0.8107 (ttp-110) cc_final: 0.7856 (ttp-110) REVERT: D 351 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: G 288 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7777 (mm-40) REVERT: I 288 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7314 (mm-40) REVERT: J 351 GLN cc_start: 0.8329 (pt0) cc_final: 0.7782 (tp-100) outliers start: 36 outliers final: 30 residues processed: 256 average time/residue: 0.1931 time to fit residues: 67.7571 Evaluate side-chains 264 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8230 Z= 0.198 Angle : 0.596 8.461 10990 Z= 0.287 Chirality : 0.050 0.123 1230 Planarity : 0.003 0.027 1410 Dihedral : 4.961 14.750 1100 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.58 % Allowed : 16.45 % Favored : 80.97 % 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: -3.29 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 299 PHE 0.017 0.001 PHE G 378 TYR 0.015 0.001 TYR C 310 ARG 0.004 0.001 ARG D 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 1.034 Fit side-chains REVERT: C 349 ARG cc_start: 0.7602 (mtp180) cc_final: 0.6947 (ppt170) REVERT: D 351 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: G 288 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7737 (mm-40) REVERT: I 286 ASN cc_start: 0.8584 (t0) cc_final: 0.8321 (t0) REVERT: I 349 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7714 (ttp-170) REVERT: J 351 GLN cc_start: 0.8292 (pt0) cc_final: 0.7700 (tp-100) outliers start: 24 outliers final: 22 residues processed: 260 average time/residue: 0.1892 time to fit residues: 67.2953 Evaluate side-chains 268 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.119739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.102002 restraints weight = 12318.925| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.34 r_work: 0.3607 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8230 Z= 0.222 Angle : 0.606 8.680 10990 Z= 0.291 Chirality : 0.050 0.123 1230 Planarity : 0.003 0.025 1410 Dihedral : 4.972 14.604 1100 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.69 % Allowed : 16.99 % Favored : 80.32 % 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: -3.27 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 299 PHE 0.016 0.002 PHE G 378 TYR 0.005 0.001 TYR A 310 ARG 0.004 0.001 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.61 seconds wall clock time: 41 minutes 0.42 seconds (2460.42 seconds total)