Starting phenix.real_space_refine on Thu Mar 14 19:28:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/03_2024/6xwq_10635.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/03_2024/6xwq_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_10635/03_2024/6xwq_10635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/03_2024/6xwq_10635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/03_2024/6xwq_10635.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwq_10635/03_2024/6xwq_10635.pdb" } resolution = 3.41 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= 0.003 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 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. 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-5265/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: 6.74, per 1000 atoms: 0.70 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: 3.44 Conformation dependent library (CDL) restraints added in 2.3 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: 0.96 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: 2.68 Time building geometry restraints manager: 3.71 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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 2.170 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.980 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 % Allowed : 5.27 % Favored : 94.73 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 428 HIS 0.001 0.000 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.013 0.001 TYR B 387 ARG 0.003 0.000 ARG C 278 *********************** 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 : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 LEU cc_start: 0.8706 (mt) cc_final: 0.8488 (mp) REVERT: C 271 MET cc_start: 0.7915 (mtp) cc_final: 0.7667 (mtp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1912 time to fit residues: 51.4336 Evaluate side-chains 126 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 0.9980 chunk 114 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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: 0.8163 moved from start: 0.1618 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= 0.206 Angle : 0.642 11.422 13265 Z= 0.312 Chirality : 0.040 0.194 1651 Planarity : 0.005 0.052 1632 Dihedral : 5.259 83.106 1368 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.69 % Allowed : 14.41 % Favored : 83.90 % 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: -0.89 (0.23), residues: 1275 helix: -0.23 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : -1.60 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 428 HIS 0.001 0.000 HIS C 334 PHE 0.012 0.001 PHE C 302 TYR 0.012 0.001 TYR B 387 ARG 0.006 0.000 ARG B 289 *********************** 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 : 1.079 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8467 (tpp) cc_final: 0.8217 (tpp) REVERT: B 109 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6469 (m-10) REVERT: C 109 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.5540 (m-10) outliers start: 17 outliers final: 10 residues processed: 151 average time/residue: 0.1627 time to fit residues: 37.6674 Evaluate side-chains 140 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 311 THR 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: 7.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8212 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9747 Z= 0.257 Angle : 0.634 9.690 13265 Z= 0.311 Chirality : 0.040 0.203 1651 Planarity : 0.005 0.050 1632 Dihedral : 5.187 86.064 1368 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.39 % Allowed : 16.60 % Favored : 81.01 % 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: 0.07 (0.24), residues: 1275 helix: 0.39 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -1.04 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 428 HIS 0.001 0.000 HIS C 334 PHE 0.013 0.001 PHE C 302 TYR 0.011 0.001 TYR B 387 ARG 0.004 0.000 ARG B 289 *********************** 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 161 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8483 (tpp) cc_final: 0.8199 (tpp) REVERT: B 109 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6568 (m-10) REVERT: C 109 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.5696 (m-10) outliers start: 24 outliers final: 16 residues processed: 151 average time/residue: 0.1567 time to fit residues: 36.5610 Evaluate side-chains 148 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 358 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8253 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9747 Z= 0.324 Angle : 0.666 9.099 13265 Z= 0.330 Chirality : 0.041 0.149 1651 Planarity : 0.005 0.049 1632 Dihedral : 5.280 87.291 1368 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.18 % Allowed : 19.58 % Favored : 77.24 % 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: 0.43 (0.25), residues: 1275 helix: 0.61 (0.17), residues: 1044 sheet: None (None), residues: 0 loop : -0.75 (0.45), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 428 HIS 0.001 0.000 HIS C 334 PHE 0.015 0.002 PHE C 302 TYR 0.015 0.002 TYR C 320 ARG 0.004 0.000 ARG B 289 *********************** 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 168 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8586 (tpp) cc_final: 0.8345 (tpp) REVERT: A 419 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 109 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6599 (m-10) REVERT: B 241 LEU cc_start: 0.9004 (mt) cc_final: 0.8773 (mp) REVERT: C 109 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.5806 (m-10) outliers start: 32 outliers final: 23 residues processed: 153 average time/residue: 0.1622 time to fit residues: 37.8136 Evaluate side-chains 152 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 358 VAL 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: 9.9990 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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: 0.8177 moved from start: 0.2651 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= 0.174 Angle : 0.629 9.824 13265 Z= 0.299 Chirality : 0.039 0.144 1651 Planarity : 0.004 0.050 1632 Dihedral : 5.163 89.765 1368 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.49 % Allowed : 21.37 % Favored : 76.14 % 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: 0.78 (0.25), residues: 1275 helix: 0.84 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -0.53 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 20 HIS 0.001 0.000 HIS C 334 PHE 0.015 0.001 PHE C 302 TYR 0.009 0.001 TYR B 90 ARG 0.004 0.000 ARG B 289 *********************** 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 171 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8554 (tpp) cc_final: 0.8261 (tpp) REVERT: B 241 LEU cc_start: 0.8987 (mt) cc_final: 0.8771 (mp) REVERT: B 403 MET cc_start: 0.8448 (tmm) cc_final: 0.8216 (tmm) REVERT: C 59 LEU cc_start: 0.8620 (tp) cc_final: 0.8231 (tt) REVERT: C 109 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.5924 (m-10) outliers start: 25 outliers final: 14 residues processed: 165 average time/residue: 0.1555 time to fit residues: 39.8051 Evaluate side-chains 150 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 224 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9747 Z= 0.259 Angle : 0.668 10.291 13265 Z= 0.321 Chirality : 0.041 0.171 1651 Planarity : 0.005 0.049 1632 Dihedral : 5.197 88.505 1368 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.18 % Allowed : 21.47 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1275 helix: 0.87 (0.17), residues: 1050 sheet: None (None), residues: 0 loop : -0.63 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 428 HIS 0.001 0.000 HIS C 334 PHE 0.014 0.001 PHE C 302 TYR 0.015 0.002 TYR B 197 ARG 0.004 0.000 ARG B 289 *********************** 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 167 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6497 (m-10) REVERT: A 365 MET cc_start: 0.8615 (tpp) cc_final: 0.8333 (tpp) REVERT: A 419 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8024 (p) REVERT: B 109 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6644 (m-10) REVERT: B 241 LEU cc_start: 0.9027 (mt) cc_final: 0.8820 (mp) REVERT: C 109 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.5980 (m-10) outliers start: 32 outliers final: 22 residues processed: 155 average time/residue: 0.1585 time to fit residues: 37.6048 Evaluate side-chains 152 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 358 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9747 Z= 0.232 Angle : 0.670 9.684 13265 Z= 0.316 Chirality : 0.041 0.158 1651 Planarity : 0.004 0.049 1632 Dihedral : 5.175 87.908 1368 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.98 % Allowed : 22.07 % Favored : 74.95 % 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: 1.01 (0.25), residues: 1275 helix: 1.00 (0.17), residues: 1053 sheet: None (None), residues: 0 loop : -0.56 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 428 HIS 0.001 0.000 HIS C 334 PHE 0.015 0.001 PHE C 302 TYR 0.014 0.001 TYR A 90 ARG 0.004 0.000 ARG B 289 *********************** 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 167 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: A 365 MET cc_start: 0.8650 (tpp) cc_final: 0.8377 (tpp) REVERT: A 419 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.8007 (p) REVERT: B 109 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6480 (m-10) REVERT: B 403 MET cc_start: 0.8463 (tmm) cc_final: 0.8235 (tmm) REVERT: C 59 LEU cc_start: 0.8547 (tp) cc_final: 0.8229 (tt) REVERT: C 109 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.5986 (m-10) outliers start: 30 outliers final: 18 residues processed: 159 average time/residue: 0.1535 time to fit residues: 37.9179 Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 0.0000 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 95 optimal weight: 0.0470 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.3082 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9747 Z= 0.163 Angle : 0.666 11.921 13265 Z= 0.309 Chirality : 0.040 0.150 1651 Planarity : 0.004 0.048 1632 Dihedral : 5.152 89.978 1368 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.58 % Allowed : 22.66 % Favored : 74.75 % 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: 1.03 (0.25), residues: 1275 helix: 1.13 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 20 HIS 0.000 0.000 HIS C 334 PHE 0.016 0.001 PHE B 242 TYR 0.012 0.001 TYR A 90 ARG 0.004 0.000 ARG B 289 *********************** 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 179 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6450 (m-10) REVERT: B 109 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6434 (m-10) REVERT: B 110 ASN cc_start: 0.8340 (t0) cc_final: 0.8109 (t0) REVERT: C 109 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.5947 (m-10) outliers start: 26 outliers final: 17 residues processed: 171 average time/residue: 0.1576 time to fit residues: 41.8348 Evaluate side-chains 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 403 MET 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: 5.9990 chunk 68 optimal weight: 7.9990 chunk 49 optimal weight: 0.0270 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9747 Z= 0.173 Angle : 0.703 17.943 13265 Z= 0.320 Chirality : 0.040 0.154 1651 Planarity : 0.004 0.048 1632 Dihedral : 5.038 87.295 1368 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.49 % Allowed : 23.96 % Favored : 73.56 % 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: 1.05 (0.25), residues: 1275 helix: 1.15 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.11 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 428 HIS 0.001 0.000 HIS C 334 PHE 0.013 0.001 PHE C 302 TYR 0.013 0.001 TYR A 90 ARG 0.004 0.000 ARG B 289 *********************** 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 169 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8363 (tp) cc_final: 0.8041 (tt) REVERT: A 109 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6466 (m-10) REVERT: B 109 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: B 110 ASN cc_start: 0.8318 (t0) cc_final: 0.8066 (t0) REVERT: B 272 ILE cc_start: 0.8835 (mm) cc_final: 0.8633 (mp) REVERT: C 109 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6066 (m-10) REVERT: C 272 ILE cc_start: 0.8600 (mm) cc_final: 0.8396 (mp) outliers start: 25 outliers final: 19 residues processed: 162 average time/residue: 0.1520 time to fit residues: 38.4606 Evaluate side-chains 160 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9747 Z= 0.199 Angle : 0.715 17.595 13265 Z= 0.326 Chirality : 0.041 0.156 1651 Planarity : 0.004 0.048 1632 Dihedral : 4.976 86.027 1368 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.19 % Allowed : 24.16 % Favored : 73.66 % 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: 1035 sheet: None (None), residues: 0 loop : -1.07 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 428 HIS 0.001 0.000 HIS C 34 PHE 0.014 0.001 PHE C 302 TYR 0.014 0.001 TYR A 90 ARG 0.004 0.000 ARG B 289 ********************** 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 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.094 Fit side-chains REVERT: A 59 LEU cc_start: 0.8495 (tp) cc_final: 0.8135 (tt) REVERT: A 109 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6531 (m-10) REVERT: B 109 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6450 (m-10) REVERT: B 110 ASN cc_start: 0.8315 (t0) cc_final: 0.8079 (t0) REVERT: C 109 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6010 (m-10) REVERT: C 272 ILE cc_start: 0.8609 (mm) cc_final: 0.8398 (mp) outliers start: 22 outliers final: 18 residues processed: 152 average time/residue: 0.1575 time to fit residues: 37.4058 Evaluate side-chains 154 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 0.0670 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.074888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057860 restraints weight = 81232.369| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 6.35 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9747 Z= 0.185 Angle : 0.725 17.456 13265 Z= 0.329 Chirality : 0.041 0.163 1651 Planarity : 0.004 0.048 1632 Dihedral : 4.945 84.643 1368 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.29 % Allowed : 24.35 % Favored : 73.36 % 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: 1.07 (0.25), residues: 1275 helix: 1.17 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.09 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 428 HIS 0.000 0.000 HIS C 334 PHE 0.015 0.001 PHE C 302 TYR 0.016 0.001 TYR B 197 ARG 0.004 0.000 ARG B 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.88 seconds wall clock time: 33 minutes 15.02 seconds (1995.02 seconds total)