Starting phenix.real_space_refine on Wed Feb 14 00:05:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p68_13221/02_2024/7p68_13221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p68_13221/02_2024/7p68_13221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p68_13221/02_2024/7p68_13221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p68_13221/02_2024/7p68_13221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p68_13221/02_2024/7p68_13221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p68_13221/02_2024/7p68_13221.pdb" } resolution = 2.9 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 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 GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 338": "OE1" <-> "OE2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 348": "OD1" <-> "OD2" Residue "J TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 338": "OE1" <-> "OE2" Residue "J PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 348": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: "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: "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: "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: "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: "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: "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: "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: 5.09, per 1000 atoms: 0.63 Number of scatterers: 8120 At special positions: 0 Unit cell: (140.3, 112.7, 55.2, 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: 2.50 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 22 sheets defined 0.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 280 removed outlier: 6.225A pdb=" N VAL C 275 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE E 278 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 277 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS E 280 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN C 279 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL A 275 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE I 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 277 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS I 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASN A 279 " --> pdb=" O LYS I 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 283 through 284 removed outlier: 6.182A pdb=" N ASP A 283 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP G 283 " --> pdb=" O LEU I 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.366A pdb=" N VAL C 287 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LYS E 290 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER C 289 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 287 " --> pdb=" O GLN I 288 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS I 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A 289 " --> pdb=" O LYS I 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.423A pdb=" N ILE C 297 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 297 " --> pdb=" O LYS I 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.697A pdb=" N ILE A 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE G 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.855A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.238A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS G 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER I 320 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR G 319 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N CYS I 322 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS G 321 " --> pdb=" O CYS I 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.636A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 345 removed outlier: 6.649A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU E 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER C 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU E 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LYS I 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLU I 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER A 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU I 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 350 removed outlier: 6.194A pdb=" N ARG C 349 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG A 349 " --> pdb=" O VAL I 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 354 through 362 removed outlier: 6.890A pdb=" N GLY E 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 360 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR E 361 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS C 362 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP E 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N LEU I 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER A 356 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASN I 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP A 358 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR I 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ILE A 360 " --> pdb=" O THR I 361 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP I 358 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU G 357 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE I 360 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASN G 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N HIS I 362 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N THR G 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.301A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS A 370 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS A 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLU I 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N HIS I 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU I 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS A 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS G 370 " --> pdb=" O LYS I 369 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 274 through 289 removed outlier: 6.715A pdb=" N LEU F 282 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP D 283 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU F 284 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER D 285 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN F 286 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 282 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 283 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU D 284 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER B 285 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN D 286 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS B 274 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE H 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 276 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN H 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 278 " --> pdb=" O ASN H 279 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LYS H 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LYS B 280 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASP H 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LEU B 282 " --> pdb=" O ASP H 283 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N SER H 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N LEU B 284 " --> pdb=" O SER H 285 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N VAL H 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 286 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N SER H 289 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN B 288 " --> pdb=" O SER H 289 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS H 274 " --> pdb=" O VAL J 275 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE J 277 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN H 276 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN J 279 " --> pdb=" O GLN H 276 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE H 278 " --> pdb=" O ASN J 279 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LYS J 281 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS H 280 " --> pdb=" O LYS J 281 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASP J 283 " --> pdb=" O LYS H 280 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LEU H 282 " --> pdb=" O ASP J 283 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N SER J 285 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU H 284 " --> pdb=" O SER J 285 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N VAL J 287 " --> pdb=" O LEU H 284 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN H 286 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER J 289 " --> pdb=" O ASN H 286 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN H 288 " --> pdb=" O SER J 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 297 through 298 removed outlier: 6.624A pdb=" N ILE D 297 " --> pdb=" O LYS F 298 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 297 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 306 through 310 removed outlier: 6.309A pdb=" N VAL B 306 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL H 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 308 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL H 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL J 309 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE H 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.806A pdb=" N VAL B 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL H 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 319 through 322 removed outlier: 5.984A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 328 through 330 removed outlier: 6.663A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 337 through 345 removed outlier: 6.412A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU F 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER D 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU F 344 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU D 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 348 through 350 removed outlier: 6.383A pdb=" N ARG D 349 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG B 349 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 354 through 362 removed outlier: 6.867A pdb=" N GLY F 355 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 360 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR F 361 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS D 362 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY D 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 360 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR D 361 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS B 362 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY B 355 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASP H 358 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 357 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE H 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN B 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N HIS H 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N THR B 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY H 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP J 358 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU H 357 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE J 360 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASN H 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N HIS J 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N THR H 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 369 through 377 removed outlier: 6.860A pdb=" N LYS F 370 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS D 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS B 370 " --> pdb=" O LYS H 369 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS H 370 " --> pdb=" O ILE J 371 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR J 373 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU H 372 " --> pdb=" O THR J 373 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS J 375 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS H 374 " --> pdb=" O LYS J 375 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR J 377 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 376 " --> pdb=" O THR J 377 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 513 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: 2.11 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2637 1.34 - 1.46: 877 1.46 - 1.57: 4696 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 8230 Sorted by residual: bond pdb=" N GLY H 273 " pdb=" CA GLY H 273 " ideal model delta sigma weight residual 1.444 1.477 -0.033 1.06e-02 8.90e+03 9.79e+00 bond pdb=" N GLY F 273 " pdb=" CA GLY F 273 " ideal model delta sigma weight residual 1.444 1.477 -0.032 1.06e-02 8.90e+03 9.40e+00 bond pdb=" N GLY B 273 " pdb=" CA GLY B 273 " ideal model delta sigma weight residual 1.444 1.477 -0.032 1.06e-02 8.90e+03 9.38e+00 bond pdb=" N GLY D 273 " pdb=" CA GLY D 273 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.06e-02 8.90e+03 9.29e+00 bond pdb=" N GLY J 273 " pdb=" CA GLY J 273 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.06e-02 8.90e+03 9.18e+00 ... (remaining 8225 not shown) Histogram of bond angle deviations from ideal: 102.61 - 108.38: 575 108.38 - 114.16: 4676 114.16 - 119.94: 2009 119.94 - 125.72: 3635 125.72 - 131.49: 95 Bond angle restraints: 10990 Sorted by residual: angle pdb=" CA HIS F 299 " pdb=" C HIS F 299 " pdb=" O HIS F 299 " ideal model delta sigma weight residual 122.44 117.94 4.50 1.32e+00 5.74e-01 1.16e+01 angle pdb=" CA HIS H 299 " pdb=" C HIS H 299 " pdb=" O HIS H 299 " ideal model delta sigma weight residual 122.44 117.96 4.48 1.32e+00 5.74e-01 1.15e+01 angle pdb=" CA HIS J 299 " pdb=" C HIS J 299 " pdb=" O HIS J 299 " ideal model delta sigma weight residual 122.44 117.98 4.46 1.32e+00 5.74e-01 1.14e+01 angle pdb=" CA HIS B 299 " pdb=" C HIS B 299 " pdb=" O HIS B 299 " ideal model delta sigma weight residual 122.44 117.99 4.45 1.32e+00 5.74e-01 1.14e+01 angle pdb=" CA ASN I 286 " pdb=" C ASN I 286 " pdb=" O ASN I 286 " ideal model delta sigma weight residual 122.14 117.96 4.18 1.24e+00 6.50e-01 1.14e+01 ... (remaining 10985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 4283 11.70 - 23.41: 507 23.41 - 35.11: 170 35.11 - 46.81: 55 46.81 - 58.52: 35 Dihedral angle restraints: 5050 sinusoidal: 2110 harmonic: 2940 Sorted by residual: dihedral pdb=" CA GLN J 351 " pdb=" C GLN J 351 " pdb=" N SER J 352 " pdb=" CA SER J 352 " ideal model delta harmonic sigma weight residual 180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLN D 351 " pdb=" C GLN D 351 " pdb=" N SER D 352 " pdb=" CA SER D 352 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLN F 351 " pdb=" C GLN F 351 " pdb=" N SER F 352 " pdb=" CA SER F 352 " ideal model delta harmonic sigma weight residual -180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 935 0.079 - 0.158: 266 0.158 - 0.236: 14 0.236 - 0.315: 5 0.315 - 0.394: 10 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CB THR D 377 " pdb=" CA THR D 377 " pdb=" OG1 THR D 377 " pdb=" CG2 THR D 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB THR F 377 " pdb=" CA THR F 377 " pdb=" OG1 THR F 377 " pdb=" CG2 THR F 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB THR H 377 " pdb=" CA THR H 377 " pdb=" OG1 THR H 377 " pdb=" CG2 THR H 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 1227 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " 0.039 2.00e-02 2.50e+03 3.58e-02 2.24e+01 pdb=" CG PHE F 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 346 " 0.040 2.00e-02 2.50e+03 3.57e-02 2.23e+01 pdb=" CG PHE D 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE D 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 346 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE D 346 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 346 " 0.040 2.00e-02 2.50e+03 3.56e-02 2.21e+01 pdb=" CG PHE H 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE H 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 346 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE H 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE H 346 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 346 " -0.000 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 3144 2.92 - 3.42: 6994 3.42 - 3.91: 14499 3.91 - 4.41: 15011 4.41 - 4.90: 30338 Nonbonded interactions: 69986 Sorted by model distance: nonbonded pdb=" NZ LYS B 340 " pdb=" OE2 GLU B 342 " model vdw 2.430 2.520 nonbonded pdb=" NZ LYS J 340 " pdb=" OE2 GLU J 342 " model vdw 2.430 2.520 nonbonded pdb=" NZ LYS D 340 " pdb=" OE2 GLU D 342 " model vdw 2.430 2.520 nonbonded pdb=" NZ LYS H 340 " pdb=" OE2 GLU H 342 " model vdw 2.430 2.520 nonbonded pdb=" NZ LYS F 340 " pdb=" OE2 GLU F 342 " model vdw 2.430 2.520 ... (remaining 69981 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: 3.290 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: 8.120 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 24.500 Find NCS groups from input model: 0.580 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.006 0.060 8230 Z= 0.362 Angle : 0.903 7.868 10990 Z= 0.487 Chirality : 0.071 0.394 1230 Planarity : 0.005 0.036 1410 Dihedral : 12.923 58.516 3190 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -3.06 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 329 PHE 0.080 0.009 PHE F 346 TYR 0.009 0.002 TYR H 310 ARG 0.003 0.001 ARG B 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 298 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 276 GLN cc_start: 0.8117 (mt0) cc_final: 0.7817 (mt0) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.9590 time to fit residues: 305.7089 Evaluate side-chains 217 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 327 ASN C 329 HIS C 351 GLN E 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN D 351 GLN F 276 GLN F 351 GLN H 327 ASN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 8230 Z= 0.511 Angle : 0.724 8.062 10990 Z= 0.365 Chirality : 0.052 0.141 1230 Planarity : 0.004 0.034 1410 Dihedral : 5.464 19.431 1100 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 6.99 % Allowed : 18.17 % Favored : 74.84 % 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: -3.16 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 362 PHE 0.018 0.002 PHE J 378 TYR 0.015 0.003 TYR E 310 ARG 0.004 0.001 ARG F 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 299 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 234 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 379 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6743 (tmm160) REVERT: C 342 GLU cc_start: 0.4742 (pm20) cc_final: 0.4163 (pm20) REVERT: C 379 ARG cc_start: 0.5371 (tpm170) cc_final: 0.5036 (tpm170) REVERT: E 379 ARG cc_start: 0.6305 (tpm170) cc_final: 0.5742 (tpm170) REVERT: D 276 GLN cc_start: 0.8151 (mt0) cc_final: 0.7909 (mt0) REVERT: D 342 GLU cc_start: 0.6461 (tm-30) cc_final: 0.6212 (tm-30) REVERT: F 349 ARG cc_start: 0.5723 (ppt90) cc_final: 0.5457 (pmt170) REVERT: F 379 ARG cc_start: 0.6348 (mmt90) cc_final: 0.5857 (ptp90) REVERT: H 345 ASP cc_start: 0.7803 (t0) cc_final: 0.7585 (t0) REVERT: H 379 ARG cc_start: 0.6721 (mmm-85) cc_final: 0.6513 (tmm160) outliers start: 65 outliers final: 45 residues processed: 274 average time/residue: 0.9738 time to fit residues: 287.1245 Evaluate side-chains 250 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 345 ASP Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 288 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN E 288 GLN E 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN F 276 GLN F 351 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8230 Z= 0.382 Angle : 0.664 7.032 10990 Z= 0.331 Chirality : 0.050 0.147 1230 Planarity : 0.004 0.033 1410 Dihedral : 5.298 19.879 1100 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 8.28 % Allowed : 20.75 % Favored : 70.97 % 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: -3.28 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.012 0.002 PHE D 346 TYR 0.009 0.002 TYR I 310 ARG 0.004 0.001 ARG E 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 297 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 220 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 379 ARG cc_start: 0.7055 (mmm-85) cc_final: 0.6774 (tmm160) REVERT: D 342 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6457 (tm-30) REVERT: F 311 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8363 (tppp) REVERT: F 379 ARG cc_start: 0.6563 (mmt90) cc_final: 0.6161 (ptp90) REVERT: J 343 LYS cc_start: 0.8381 (tptm) cc_final: 0.8118 (tptm) outliers start: 77 outliers final: 53 residues processed: 260 average time/residue: 0.9742 time to fit residues: 271.0796 Evaluate side-chains 262 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 208 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.0010 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN E 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN D 276 GLN F 351 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8230 Z= 0.316 Angle : 0.649 7.885 10990 Z= 0.320 Chirality : 0.050 0.143 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.159 20.255 1100 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 8.06 % Allowed : 22.26 % Favored : 69.68 % 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: -3.33 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 330 PHE 0.016 0.002 PHE J 378 TYR 0.013 0.002 TYR G 310 ARG 0.004 0.001 ARG H 379 *********************** 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 289 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 214 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.6376 (tm-30) cc_final: 0.5670 (tm-30) REVERT: B 344 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8129 (mm) REVERT: B 379 ARG cc_start: 0.7093 (mmm-85) cc_final: 0.6847 (tmm160) REVERT: G 349 ARG cc_start: 0.5673 (OUTLIER) cc_final: 0.4683 (pmt-80) REVERT: F 379 ARG cc_start: 0.6666 (mmt90) cc_final: 0.6198 (ptp90) REVERT: J 343 LYS cc_start: 0.8330 (tptm) cc_final: 0.8104 (tptm) outliers start: 75 outliers final: 49 residues processed: 254 average time/residue: 0.9244 time to fit residues: 251.7609 Evaluate side-chains 253 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 202 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 307 GLN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 288 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN C 351 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8230 Z= 0.384 Angle : 0.689 8.338 10990 Z= 0.342 Chirality : 0.050 0.144 1230 Planarity : 0.004 0.032 1410 Dihedral : 5.287 21.617 1100 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 8.92 % Allowed : 21.61 % Favored : 69.46 % 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 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.022 0.003 PHE H 346 TYR 0.012 0.002 TYR C 310 ARG 0.006 0.001 ARG A 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 299 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 216 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.6411 (tm-30) cc_final: 0.5852 (tm-30) REVERT: G 349 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.4629 (pmt-80) REVERT: G 353 LYS cc_start: 0.5735 (pmtt) cc_final: 0.3595 (pptt) REVERT: D 342 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6359 (tm-30) REVERT: F 349 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.4802 (ppt90) REVERT: F 379 ARG cc_start: 0.6749 (mmt90) cc_final: 0.6236 (ptp90) REVERT: J 342 GLU cc_start: 0.4942 (pm20) cc_final: 0.4630 (pm20) REVERT: J 343 LYS cc_start: 0.8367 (tptm) cc_final: 0.8159 (tptm) outliers start: 83 outliers final: 58 residues processed: 261 average time/residue: 0.9847 time to fit residues: 275.1271 Evaluate side-chains 268 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 208 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 44 optimal weight: 0.1980 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN C 279 ASN E 307 GLN G 307 GLN I 307 GLN I 351 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN J 276 GLN J 299 HIS J 351 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8230 Z= 0.187 Angle : 0.644 9.594 10990 Z= 0.311 Chirality : 0.050 0.146 1230 Planarity : 0.003 0.029 1410 Dihedral : 4.804 20.918 1100 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.59 % Allowed : 25.81 % Favored : 68.60 % 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: -3.26 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 362 PHE 0.018 0.002 PHE D 346 TYR 0.012 0.002 TYR C 310 ARG 0.006 0.001 ARG A 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 275 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 223 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 344 LEU cc_start: 0.8651 (mm) cc_final: 0.8269 (mp) REVERT: G 349 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.4420 (pmt-80) REVERT: G 360 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8343 (tp) REVERT: F 349 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.4922 (ppt90) REVERT: F 379 ARG cc_start: 0.6681 (mmt90) cc_final: 0.6281 (ptp-170) outliers start: 52 outliers final: 32 residues processed: 250 average time/residue: 1.0818 time to fit residues: 288.5920 Evaluate side-chains 241 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN F 351 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 ASN J 351 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8230 Z= 0.284 Angle : 0.691 8.648 10990 Z= 0.333 Chirality : 0.050 0.142 1230 Planarity : 0.003 0.037 1410 Dihedral : 4.977 20.599 1100 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 7.10 % Allowed : 24.73 % Favored : 68.17 % 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: -3.26 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.017 0.002 PHE I 346 TYR 0.014 0.002 TYR E 310 ARG 0.012 0.001 ARG E 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 278 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 212 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.6567 (tm-30) cc_final: 0.5526 (tm-30) REVERT: C 349 ARG cc_start: 0.5217 (mmm160) cc_final: 0.5017 (mmm160) REVERT: G 349 ARG cc_start: 0.5298 (OUTLIER) cc_final: 0.4269 (pmt-80) REVERT: G 379 ARG cc_start: 0.4916 (OUTLIER) cc_final: 0.3274 (ttp80) REVERT: F 349 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.4714 (ppt90) REVERT: F 379 ARG cc_start: 0.6680 (mmt90) cc_final: 0.6198 (ptp90) outliers start: 66 outliers final: 42 residues processed: 253 average time/residue: 0.9864 time to fit residues: 267.2712 Evaluate side-chains 247 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 202 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR 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: 0.6980 chunk 8 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN F 351 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN J 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8230 Z= 0.406 Angle : 0.768 10.261 10990 Z= 0.373 Chirality : 0.052 0.177 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.365 21.478 1100 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 6.56 % Allowed : 26.56 % Favored : 66.88 % 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: -3.33 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.023 0.003 PHE I 346 TYR 0.014 0.002 TYR G 310 ARG 0.005 0.001 ARG F 349 *********************** 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 269 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 208 time to evaluate : 0.976 Fit side-chains REVERT: G 349 ARG cc_start: 0.5497 (OUTLIER) cc_final: 0.4455 (pmt-80) REVERT: G 353 LYS cc_start: 0.5907 (pmtt) cc_final: 0.3564 (pptt) REVERT: G 379 ARG cc_start: 0.5034 (OUTLIER) cc_final: 0.3474 (ttp80) REVERT: F 342 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6675 (tm-30) REVERT: F 349 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.4605 (ppt90) REVERT: F 379 ARG cc_start: 0.6701 (mmt90) cc_final: 0.6199 (ptp90) outliers start: 61 outliers final: 50 residues processed: 245 average time/residue: 0.9529 time to fit residues: 250.3788 Evaluate side-chains 254 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 201 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN F 351 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8230 Z= 0.236 Angle : 0.728 10.407 10990 Z= 0.347 Chirality : 0.051 0.268 1230 Planarity : 0.003 0.032 1410 Dihedral : 4.976 20.545 1100 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.95 % Allowed : 28.28 % Favored : 66.77 % 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: -3.29 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 374 PHE 0.018 0.002 PHE I 346 TYR 0.011 0.001 TYR A 310 ARG 0.008 0.001 ARG A 349 *********************** 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 250 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7503 (t0) cc_final: 0.7291 (t0) REVERT: G 349 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.4364 (pmt-80) REVERT: G 379 ARG cc_start: 0.5010 (OUTLIER) cc_final: 0.3449 (ttp80) REVERT: F 349 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.4736 (ppt90) REVERT: F 379 ARG cc_start: 0.6664 (mmt90) cc_final: 0.6070 (ptp90) outliers start: 46 outliers final: 39 residues processed: 232 average time/residue: 0.9060 time to fit residues: 226.1347 Evaluate side-chains 238 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 196 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR 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: 7.9990 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 0.0070 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN D 276 GLN F 351 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8230 Z= 0.264 Angle : 0.731 9.023 10990 Z= 0.350 Chirality : 0.051 0.139 1230 Planarity : 0.003 0.031 1410 Dihedral : 4.951 20.173 1100 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.38 % Allowed : 27.53 % Favored : 67.10 % 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 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 374 PHE 0.025 0.003 PHE I 346 TYR 0.014 0.002 TYR E 310 ARG 0.008 0.001 ARG E 349 ********************** 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 253 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 349 ARG cc_start: 0.5351 (OUTLIER) cc_final: 0.4367 (pmt-80) REVERT: F 349 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.4706 (ppt90) REVERT: F 379 ARG cc_start: 0.6669 (mmt90) cc_final: 0.6067 (ptp90) outliers start: 50 outliers final: 40 residues processed: 232 average time/residue: 0.9570 time to fit residues: 238.0129 Evaluate side-chains 242 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 200 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR 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: 0.9980 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN F 351 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.121501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.102954 restraints weight = 12418.776| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.32 r_work: 0.3792 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8230 Z= 0.291 Angle : 0.756 10.351 10990 Z= 0.361 Chirality : 0.051 0.221 1230 Planarity : 0.003 0.029 1410 Dihedral : 5.038 19.371 1100 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.16 % Allowed : 28.17 % Favored : 66.67 % 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 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 374 PHE 0.023 0.003 PHE I 346 TYR 0.014 0.002 TYR E 310 ARG 0.008 0.001 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4197.14 seconds wall clock time: 75 minutes 29.11 seconds (4529.11 seconds total)