Starting phenix.real_space_refine (version: dev) on Mon Apr 4 23:04:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/04_2022/6xwq_10635.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/04_2022/6xwq_10635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/04_2022/6xwq_10635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/04_2022/6xwq_10635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/04_2022/6xwq_10635.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/04_2022/6xwq_10635.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.020 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ASP 11": "OD1" <-> "OD2" Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ASP 11": "OD1" <-> "OD2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 409": "OD1" <-> "OD2" Residue "C ASP 424": "OD1" <-> "OD2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "C ASP 501": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9572 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "B" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3225 Chain: "C" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 265 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 265 " occ=0.50 Time building chain proxies: 7.23, per 1000 atoms: 0.76 Number of scatterers: 9572 At special positions: 0 Unit cell: (105.248, 108.284, 81.972, 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 48 16.00 O 1666 8.00 N 1549 7.00 C 6309 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 13 through 36 removed outlier: 3.644A pdb=" N ALA A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.722A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.532A pdb=" N VAL A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 110 removed outlier: 4.029A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 153 through 171 Processing helix chain 'A' and resid 175 through 223 removed outlier: 3.621A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Proline residue: A 208 - end of helix removed outlier: 3.869A pdb=" N ALA A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 257 removed outlier: 3.667A pdb=" N VAL A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 5.499A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.527A pdb=" N GLU A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.566A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.953A pdb=" N LEU A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.869A pdb=" N ILE A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 381 through 393 removed outlier: 3.978A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 419 removed outlier: 4.255A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 13 through 36 removed outlier: 3.670A pdb=" N LEU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.776A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 Processing helix chain 'B' and resid 76 through 110 removed outlier: 3.749A pdb=" N ARG B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 153 through 171 Processing helix chain 'B' and resid 175 through 223 removed outlier: 3.591A pdb=" N LYS B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Proline residue: B 208 - end of helix removed outlier: 3.563A pdb=" N ILE B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 257 removed outlier: 3.735A pdb=" N VAL B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 5.040A pdb=" N ASP B 269 " --> pdb=" O AARG B 265 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 304 through 313 removed outlier: 4.210A pdb=" N THR B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.747A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 354 removed outlier: 4.035A pdb=" N LEU B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.872A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 393 " --> pdb=" O MET B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 419 removed outlier: 3.640A pdb=" N LEU B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.693A pdb=" N ASP C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 36 removed outlier: 3.591A pdb=" N LEU C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.799A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 76 through 110 removed outlier: 3.950A pdb=" N TYR C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 153 through 171 Processing helix chain 'C' and resid 175 through 223 removed outlier: 3.881A pdb=" N SER C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Proline residue: C 208 - end of helix removed outlier: 3.529A pdb=" N ALA C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 216 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 257 removed outlier: 3.652A pdb=" N VAL C 233 " --> pdb=" O PRO C 229 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 278 removed outlier: 5.360A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 removed outlier: 3.597A pdb=" N GLU C 293 " --> pdb=" O ARG C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.567A pdb=" N PHE C 302 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 313 removed outlier: 4.315A pdb=" N THR C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.661A pdb=" N LEU C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 354 removed outlier: 3.965A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 365 removed outlier: 3.919A pdb=" N ILE C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 381 through 420 removed outlier: 4.054A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 393 " --> pdb=" O MET C 389 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 4.335A pdb=" N TRP C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2095 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: 2.77 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2976 1.34 - 1.46: 1339 1.46 - 1.57: 5336 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 9747 Sorted by residual: bond pdb=" CA VAL C 373 " pdb=" CB VAL C 373 " ideal model delta sigma weight residual 1.527 1.543 -0.017 1.31e-02 5.83e+03 1.61e+00 bond pdb=" CG1 ILE B 18 " pdb=" CD1 ILE B 18 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.08e-01 bond pdb=" CB VAL C 200 " pdb=" CG2 VAL C 200 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.41e-01 bond pdb=" CB VAL A 200 " pdb=" CG2 VAL A 200 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.11e-01 bond pdb=" N ARG C 278 " pdb=" CA ARG C 278 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.42e-02 4.96e+03 6.28e-01 ... (remaining 9742 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 278 106.76 - 113.58: 5615 113.58 - 120.40: 3895 120.40 - 127.21: 3400 127.21 - 134.03: 77 Bond angle restraints: 13265 Sorted by residual: angle pdb=" N VAL B 211 " pdb=" CA VAL B 211 " pdb=" C VAL B 211 " ideal model delta sigma weight residual 113.07 108.39 4.68 1.36e+00 5.41e-01 1.19e+01 angle pdb=" C LEU B 6 " pdb=" N ARG B 7 " pdb=" CA ARG B 7 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C LEU A 6 " pdb=" N ARG A 7 " pdb=" CA ARG A 7 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.31e+00 angle pdb=" C VAL C 246 " pdb=" N ILE C 247 " pdb=" CA ILE C 247 " ideal model delta sigma weight residual 121.84 118.82 3.02 1.13e+00 7.83e-01 7.12e+00 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 115.66 111.75 3.91 1.56e+00 4.11e-01 6.29e+00 ... (remaining 13260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5224 17.65 - 35.30: 437 35.30 - 52.95: 70 52.95 - 70.60: 7 70.60 - 88.25: 10 Dihedral angle restraints: 5748 sinusoidal: 2135 harmonic: 3613 Sorted by residual: dihedral pdb=" CA GLN A 128 " pdb=" C GLN A 128 " pdb=" N PRO A 129 " pdb=" CA PRO A 129 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLN B 128 " pdb=" C GLN B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLN C 128 " pdb=" C GLN C 128 " pdb=" N PRO C 129 " pdb=" CA PRO C 129 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 934 0.028 - 0.056: 495 0.056 - 0.085: 155 0.085 - 0.113: 55 0.113 - 0.141: 12 Chirality restraints: 1651 Sorted by residual: chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA LEU B 284 " pdb=" N LEU B 284 " pdb=" C LEU B 284 " pdb=" CB LEU B 284 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1648 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 207 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 208 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 207 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO C 208 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 207 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO B 208 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " -0.030 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 277 2.72 - 3.26: 10782 3.26 - 3.81: 15857 3.81 - 4.35: 18939 4.35 - 4.90: 32473 Nonbonded interactions: 78328 Sorted by model distance: nonbonded pdb=" OH TYR B 9 " pdb=" O GLN B 205 " model vdw 2.171 2.440 nonbonded pdb=" OG1 THR A 402 " pdb=" N ASP A 501 " model vdw 2.209 2.520 nonbonded pdb=" OG1 THR C 402 " pdb=" N ASP C 501 " model vdw 2.231 2.520 nonbonded pdb=" OG1 THR B 402 " pdb=" N ASP B 501 " model vdw 2.285 2.520 nonbonded pdb=" ND2 ASN A 313 " pdb=" OD1 ASP A 409 " model vdw 2.302 2.520 ... (remaining 78323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 264 or resid 266 through 430 or resid 501)) selection = (chain 'B' and (resid 5 through 264 or resid 266 through 430 or resid 501)) selection = (chain 'C' and (resid 5 through 264 or resid 266 through 430 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6309 2.51 5 N 1549 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 2.580 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 30.160 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.003 0.035 9747 Z= 0.206 Angle : 0.609 7.275 13265 Z= 0.346 Chirality : 0.039 0.141 1651 Planarity : 0.005 0.057 1632 Dihedral : 13.417 88.247 3454 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.54 % Favored : 96.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.21), residues: 1275 helix: -1.55 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : -2.27 (0.36), residues: 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1906 time to fit residues: 51.5646 Evaluate side-chains 126 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 138 ASN A 174 ASN A 321 GLN A 340 GLN B 110 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 340 GLN C 110 ASN C 138 ASN C 174 ASN C 340 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9747 Z= 0.219 Angle : 0.653 11.607 13265 Z= 0.317 Chirality : 0.040 0.199 1651 Planarity : 0.005 0.071 1632 Dihedral : 5.269 82.968 1368 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.69 % 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: -0.94 (0.23), residues: 1275 helix: -0.26 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : -1.62 (0.40), residues: 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.090 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 151 average time/residue: 0.1583 time to fit residues: 36.6979 Evaluate side-chains 137 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0848 time to fit residues: 3.0359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 39 optimal weight: 0.0870 chunk 91 optimal weight: 0.8980 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9747 Z= 0.238 Angle : 0.636 10.100 13265 Z= 0.310 Chirality : 0.040 0.197 1651 Planarity : 0.005 0.062 1632 Dihedral : 5.178 85.649 1368 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 1.29 % 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: 0.04 (0.24), residues: 1275 helix: 0.36 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -1.03 (0.43), residues: 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.096 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 147 average time/residue: 0.1606 time to fit residues: 36.6932 Evaluate side-chains 133 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0883 time to fit residues: 2.6034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 0.0980 chunk 12 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9747 Z= 0.219 Angle : 0.636 10.470 13265 Z= 0.306 Chirality : 0.040 0.191 1651 Planarity : 0.005 0.058 1632 Dihedral : 5.123 85.400 1368 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1275 helix: 0.61 (0.17), residues: 1047 sheet: None (None), residues: 0 loop : -0.93 (0.44), residues: 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.174 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 143 average time/residue: 0.1608 time to fit residues: 35.5207 Evaluate side-chains 134 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0975 time to fit residues: 2.5655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9747 Z= 0.180 Angle : 0.639 13.143 13265 Z= 0.300 Chirality : 0.040 0.185 1651 Planarity : 0.005 0.057 1632 Dihedral : 5.009 84.909 1368 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.59 % 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: 0.68 (0.25), residues: 1275 helix: 0.89 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.12 (0.42), residues: 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.215 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 158 average time/residue: 0.1609 time to fit residues: 39.4039 Evaluate side-chains 138 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0949 time to fit residues: 2.1871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9747 Z= 0.210 Angle : 0.664 11.686 13265 Z= 0.312 Chirality : 0.040 0.172 1651 Planarity : 0.005 0.054 1632 Dihedral : 4.981 82.792 1368 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.39 % 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: 0.82 (0.25), residues: 1275 helix: 0.98 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.085 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 148 average time/residue: 0.1600 time to fit residues: 36.7019 Evaluate side-chains 134 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0926 time to fit residues: 2.1400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9747 Z= 0.210 Angle : 0.674 10.443 13265 Z= 0.313 Chirality : 0.041 0.154 1651 Planarity : 0.005 0.052 1632 Dihedral : 4.926 80.505 1368 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.39 % 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: 0.96 (0.25), residues: 1275 helix: 1.08 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.00 (0.42), residues: 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.150 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 142 average time/residue: 0.1653 time to fit residues: 35.9685 Evaluate side-chains 132 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0930 time to fit residues: 2.1721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9747 Z= 0.187 Angle : 0.685 10.950 13265 Z= 0.314 Chirality : 0.040 0.155 1651 Planarity : 0.005 0.050 1632 Dihedral : 4.829 78.014 1368 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.60 % 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: 1.02 (0.25), residues: 1275 helix: 1.12 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.01 (0.42), residues: 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.216 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 142 average time/residue: 0.1662 time to fit residues: 36.6319 Evaluate side-chains 135 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0852 time to fit residues: 1.8251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9747 Z= 0.214 Angle : 0.690 10.354 13265 Z= 0.318 Chirality : 0.041 0.191 1651 Planarity : 0.005 0.049 1632 Dihedral : 4.772 76.080 1368 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1275 helix: 1.18 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 0.990 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 139 average time/residue: 0.1674 time to fit residues: 35.5247 Evaluate side-chains 134 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0844 time to fit residues: 1.6968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 chunk 125 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 138 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9747 Z= 0.166 Angle : 0.707 10.824 13265 Z= 0.318 Chirality : 0.040 0.226 1651 Planarity : 0.005 0.049 1632 Dihedral : 4.670 73.657 1368 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.60 % 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: 1.09 (0.25), residues: 1275 helix: 1.17 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 1.030 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 146 average time/residue: 0.1584 time to fit residues: 36.2839 Evaluate side-chains 139 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0959 time to fit residues: 2.3576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.075414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057823 restraints weight = 81039.518| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 6.52 r_work: 0.3065 rms_B_bonded: 6.22 restraints_weight: 2.0000 r_work: 0.3057 rms_B_bonded: 5.65 restraints_weight: 4.0000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9747 Z= 0.181 Angle : 0.718 15.960 13265 Z= 0.323 Chirality : 0.041 0.227 1651 Planarity : 0.005 0.049 1632 Dihedral : 4.595 72.325 1368 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1275 helix: 1.20 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 243 =============================================================================== Job complete usr+sys time: 1590.35 seconds wall clock time: 29 minutes 55.13 seconds (1795.13 seconds total)