Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 18:20:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vh7_21200/08_2023/6vh7_21200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vh7_21200/08_2023/6vh7_21200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vh7_21200/08_2023/6vh7_21200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vh7_21200/08_2023/6vh7_21200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vh7_21200/08_2023/6vh7_21200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vh7_21200/08_2023/6vh7_21200.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 12 5.16 5 C 3042 2.51 5 N 906 2.21 5 O 918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 345": "OD1" <-> "OD2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 345": "OD1" <-> "OD2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 4878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 2.77, per 1000 atoms: 0.57 Number of scatterers: 4878 At special positions: 0 Unit cell: (103.222, 193.718, 31.108, 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 12 16.00 O 918 8.00 N 906 7.00 C 3042 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: 2.03 Conformation dependent library (CDL) restraints added in 730.7 milliseconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 67.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 282 removed outlier: 6.993A pdb=" N GLN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 277 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 278 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN B 279 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS A 280 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 281 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 277 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 278 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C 279 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS B 280 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS C 281 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 299 removed outlier: 8.876A pdb=" N ASN A 286 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N SER B 289 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLN A 288 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N CYS B 291 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS A 290 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER B 293 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY A 292 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ASP B 295 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 294 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN A 296 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS B 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 298 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN B 286 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 287 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN B 288 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER C 289 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B 290 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER C 293 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 294 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 310 removed outlier: 6.740A pdb=" N GLY A 304 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLN B 307 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 304 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLN C 307 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 321 removed outlier: 6.272A pdb=" N ASP A 314 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LYS B 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 316 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR B 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 314 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS C 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER B 316 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.547A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 346 removed outlier: 6.801A pdb=" N VAL B 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU A 338 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 340 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER B 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 342 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS B 343 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU C 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP B 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE C 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 362 removed outlier: 6.433A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LYS B 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER A 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASN B 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP A 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER B 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU C 357 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 379 removed outlier: 6.034A pdb=" N LYS A 370 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU A 372 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS B 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N HIS A 374 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR B 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 376 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG B 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 378 " --> pdb=" O ARG B 379 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR C 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU B 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LYS C 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N HIS B 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR C 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU B 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG C 379 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 378 " --> pdb=" O ARG C 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 275 through 282 removed outlier: 6.993A pdb=" N GLN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE F 277 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 278 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN F 279 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS E 280 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS F 281 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE G 277 " --> pdb=" O GLN F 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE F 278 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN G 279 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS F 280 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS G 281 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 285 through 299 removed outlier: 8.876A pdb=" N ASN E 286 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N SER F 289 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLN E 288 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N CYS F 291 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS E 290 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER F 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY E 292 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASP F 295 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS E 294 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE F 297 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN E 296 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS F 299 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS E 298 " --> pdb=" O HIS F 299 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN F 286 " --> pdb=" O SER G 285 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL G 287 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN F 288 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER G 289 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS F 290 " --> pdb=" O SER G 289 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER G 293 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS F 294 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 303 through 310 removed outlier: 6.741A pdb=" N GLY E 304 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLN F 307 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL E 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL F 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY F 304 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLN G 307 " --> pdb=" O GLY F 304 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL F 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL G 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE F 308 " --> pdb=" O VAL G 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 313 through 321 removed outlier: 6.272A pdb=" N ASP E 314 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS F 317 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER E 316 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR F 319 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS F 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER E 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP F 314 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LYS G 317 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER F 316 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR G 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL F 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS G 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER F 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 327 through 330 removed outlier: 6.546A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE F 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 346 removed outlier: 6.800A pdb=" N VAL F 337 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU E 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL F 339 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS E 340 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER F 341 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU E 342 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS F 343 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU G 344 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP F 345 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE G 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 349 through 362 removed outlier: 6.432A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY F 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU F 357 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER E 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN F 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP E 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR F 361 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE E 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER F 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU G 357 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP F 358 " --> pdb=" O LEU G 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 369 through 379 removed outlier: 6.035A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR F 373 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU E 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS F 375 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR F 377 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU E 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG F 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE E 378 " --> pdb=" O ARG F 379 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS F 370 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 373 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU F 372 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS G 375 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS F 374 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR G 377 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 376 " --> pdb=" O THR G 377 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG G 379 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE F 378 " --> pdb=" O ARG G 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 58 hydrogen bonds defined for protein. 174 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: 1.12 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1626 1.34 - 1.46: 626 1.46 - 1.57: 2680 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 4944 Sorted by residual: bond pdb=" CA LYS G 353 " pdb=" CB LYS G 353 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.38e-02 5.25e+03 4.69e+00 bond pdb=" CA LYS C 353 " pdb=" CB LYS C 353 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.38e-02 5.25e+03 4.66e+00 bond pdb=" CA LYS E 353 " pdb=" CB LYS E 353 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.38e-02 5.25e+03 4.58e+00 bond pdb=" CA LYS A 353 " pdb=" CB LYS A 353 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.38e-02 5.25e+03 4.53e+00 bond pdb=" CA LYS F 353 " pdb=" CB LYS F 353 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.38e-02 5.25e+03 4.52e+00 ... (remaining 4939 not shown) Histogram of bond angle deviations from ideal: 102.01 - 107.87: 361 107.87 - 113.73: 2818 113.73 - 119.58: 1129 119.58 - 125.44: 2244 125.44 - 131.29: 54 Bond angle restraints: 6606 Sorted by residual: angle pdb=" C LYS E 347 " pdb=" N ASP E 348 " pdb=" CA ASP E 348 " ideal model delta sigma weight residual 122.17 115.25 6.92 1.54e+00 4.22e-01 2.02e+01 angle pdb=" C LYS G 347 " pdb=" N ASP G 348 " pdb=" CA ASP G 348 " ideal model delta sigma weight residual 122.17 115.28 6.89 1.54e+00 4.22e-01 2.00e+01 angle pdb=" C LYS B 347 " pdb=" N ASP B 348 " pdb=" CA ASP B 348 " ideal model delta sigma weight residual 122.17 115.28 6.89 1.54e+00 4.22e-01 2.00e+01 angle pdb=" C LYS F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta sigma weight residual 122.17 115.29 6.88 1.54e+00 4.22e-01 2.00e+01 angle pdb=" C LYS C 347 " pdb=" N ASP C 348 " pdb=" CA ASP C 348 " ideal model delta sigma weight residual 122.17 115.30 6.87 1.54e+00 4.22e-01 1.99e+01 ... (remaining 6601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 2654 16.26 - 32.52: 317 32.52 - 48.77: 53 48.77 - 65.03: 24 65.03 - 81.29: 6 Dihedral angle restraints: 3054 sinusoidal: 1284 harmonic: 1770 Sorted by residual: dihedral pdb=" CA VAL G 313 " pdb=" C VAL G 313 " pdb=" N ASP G 314 " pdb=" CA ASP G 314 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA VAL A 313 " pdb=" C VAL A 313 " pdb=" N ASP A 314 " pdb=" CA ASP A 314 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA VAL B 313 " pdb=" C VAL B 313 " pdb=" N ASP B 314 " pdb=" CA ASP B 314 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 3051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 394 0.036 - 0.073: 219 0.073 - 0.109: 92 0.109 - 0.145: 27 0.145 - 0.181: 12 Chirality restraints: 744 Sorted by residual: chirality pdb=" CB ILE B 277 " pdb=" CA ILE B 277 " pdb=" CG1 ILE B 277 " pdb=" CG2 ILE B 277 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CB ILE A 277 " pdb=" CA ILE A 277 " pdb=" CG1 ILE A 277 " pdb=" CG2 ILE A 277 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CB ILE C 277 " pdb=" CA ILE C 277 " pdb=" CG1 ILE C 277 " pdb=" CG2 ILE C 277 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 741 not shown) Planarity restraints: 846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 363 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO G 364 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 364 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 364 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 364 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 363 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO F 364 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 364 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 364 " 0.029 5.00e-02 4.00e+02 ... (remaining 843 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1567 2.83 - 3.35: 4573 3.35 - 3.87: 8817 3.87 - 4.38: 8741 4.38 - 4.90: 16812 Nonbonded interactions: 40510 Sorted by model distance: nonbonded pdb=" N GLU C 380 " pdb=" OE1 GLU C 380 " model vdw 2.318 2.520 nonbonded pdb=" N GLU E 380 " pdb=" OE1 GLU E 380 " model vdw 2.319 2.520 nonbonded pdb=" N GLU B 380 " pdb=" OE1 GLU B 380 " model vdw 2.319 2.520 nonbonded pdb=" N GLU A 380 " pdb=" OE1 GLU A 380 " model vdw 2.319 2.520 nonbonded pdb=" N GLU F 380 " pdb=" OE1 GLU F 380 " model vdw 2.319 2.520 ... (remaining 40505 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 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue 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: 0.820 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: 0.010 Extract box with map and model: 4.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.060 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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 0.039 4944 Z= 0.493 Angle : 1.025 6.915 6606 Z= 0.590 Chirality : 0.054 0.181 744 Planarity : 0.006 0.052 846 Dihedral : 15.142 81.287 1926 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 28.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer Outliers : 2.13 % 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: -4.78 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.18), residues: 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 174 average time/residue: 0.1858 time to fit residues: 39.7901 Evaluate side-chains 87 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0454 time to fit residues: 1.1157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS C 279 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS G 279 ASN G 362 HIS G 374 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4944 Z= 0.267 Angle : 0.790 7.750 6606 Z= 0.400 Chirality : 0.052 0.144 744 Planarity : 0.005 0.038 846 Dihedral : 7.085 18.392 654 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 3.37 % 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: -4.52 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.19), residues: 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.650 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 123 average time/residue: 0.1450 time to fit residues: 23.4305 Evaluate side-chains 92 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0497 time to fit residues: 1.5941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS A 330 HIS ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 HIS ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 4944 Z= 0.253 Angle : 0.723 6.861 6606 Z= 0.367 Chirality : 0.051 0.140 744 Planarity : 0.005 0.038 846 Dihedral : 6.589 21.853 654 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer Outliers : 3.19 % 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: -4.42 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.18), residues: 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.631 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 120 average time/residue: 0.1372 time to fit residues: 21.8558 Evaluate side-chains 103 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0461 time to fit residues: 1.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4944 Z= 0.267 Angle : 0.722 6.807 6606 Z= 0.366 Chirality : 0.052 0.148 744 Planarity : 0.005 0.036 846 Dihedral : 6.468 23.136 654 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer Outliers : 3.19 % 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: -4.44 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.18), residues: 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.800 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 113 average time/residue: 0.1504 time to fit residues: 22.3065 Evaluate side-chains 96 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0999 time to fit residues: 2.3928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4944 Z= 0.194 Angle : 0.677 7.625 6606 Z= 0.335 Chirality : 0.052 0.166 744 Planarity : 0.004 0.037 846 Dihedral : 6.019 21.126 654 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer Outliers : 1.77 % 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: -4.38 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.18), residues: 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.655 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 104 average time/residue: 0.1336 time to fit residues: 18.9920 Evaluate side-chains 93 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0466 time to fit residues: 1.2842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 HIS ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 HIS ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 HIS G 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 4944 Z= 0.387 Angle : 0.823 6.561 6606 Z= 0.420 Chirality : 0.054 0.171 744 Planarity : 0.005 0.039 846 Dihedral : 6.834 23.914 654 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 2.48 % 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: -4.62 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.17), residues: 630 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.641 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 0.1422 time to fit residues: 19.2445 Evaluate side-chains 96 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0579 time to fit residues: 1.5955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.0050 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.0030 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4944 Z= 0.171 Angle : 0.684 7.414 6606 Z= 0.337 Chirality : 0.053 0.220 744 Planarity : 0.004 0.042 846 Dihedral : 5.850 20.558 654 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 1.06 % 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: -4.47 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.18), residues: 630 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.572 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 108 average time/residue: 0.1690 time to fit residues: 23.0986 Evaluate side-chains 93 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0445 time to fit residues: 0.9366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 0.1980 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4944 Z= 0.178 Angle : 0.693 8.985 6606 Z= 0.338 Chirality : 0.053 0.293 744 Planarity : 0.004 0.043 846 Dihedral : 5.680 21.392 654 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 0.53 % 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: -4.38 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.18), residues: 630 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.618 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 95 average time/residue: 0.1396 time to fit residues: 17.7351 Evaluate side-chains 88 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0563 time to fit residues: 1.0077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.0570 chunk 53 optimal weight: 0.0040 chunk 35 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 39 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.0668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 4944 Z= 0.161 Angle : 0.669 9.019 6606 Z= 0.324 Chirality : 0.053 0.216 744 Planarity : 0.004 0.047 846 Dihedral : 5.152 19.578 654 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.00 % 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: -4.31 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.18), residues: 630 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.625 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1355 time to fit residues: 18.1565 Evaluate side-chains 88 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4944 Z= 0.184 Angle : 0.686 9.052 6606 Z= 0.335 Chirality : 0.053 0.234 744 Planarity : 0.005 0.047 846 Dihedral : 5.339 20.613 654 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 0.53 % 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: -4.29 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.18), residues: 630 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.644 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 92 average time/residue: 0.1429 time to fit residues: 17.5753 Evaluate side-chains 89 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0663 time to fit residues: 1.1149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.0870 chunk 41 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.0060 chunk 32 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.2492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.173547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.146152 restraints weight = 11437.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.146554 restraints weight = 8601.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.146505 restraints weight = 6448.598| |-----------------------------------------------------------------------------| r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 4944 Z= 0.159 Angle : 0.671 9.260 6606 Z= 0.324 Chirality : 0.053 0.212 744 Planarity : 0.005 0.046 846 Dihedral : 5.148 19.346 654 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.35 % 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: -4.23 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.19), residues: 630 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.76 seconds wall clock time: 26 minutes 33.25 seconds (1593.25 seconds total)