Starting phenix.real_space_refine on Tue Aug 26 10:42:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yd0_39161/08_2025/8yd0_39161_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yd0_39161/08_2025/8yd0_39161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yd0_39161/08_2025/8yd0_39161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yd0_39161/08_2025/8yd0_39161.map" model { file = "/net/cci-nas-00/data/ceres_data/8yd0_39161/08_2025/8yd0_39161_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yd0_39161/08_2025/8yd0_39161_trim.cif" } resolution = 2.24 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 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= 0.002 sd= 0.015 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 2 5.21 5 S 166 5.16 5 B 14 2.79 5 C 22883 2.51 5 N 6119 2.21 5 O 6935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36135 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2623 Classifications: {'peptide': 341} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Chain: "B" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2694 Classifications: {'peptide': 349} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 331} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2624 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Chain: "D" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2611 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 16, 'TRANS': 321} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Chain: "E" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2630 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "F" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2535 Classifications: {'peptide': 329} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 312} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Chain: "H" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1427 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "L" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1473 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "M" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1479 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "O" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1454 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.94, per 1000 atoms: 0.22 Number of scatterers: 36135 At special positions: 0 Unit cell: (142, 140.58, 173.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 166 16.00 P 16 15.00 Mg 2 11.99 O 6935 8.00 N 6119 7.00 C 22883 6.00 B 14 5.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM35651 O3B ATP D 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM35650 O3A ATP D 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8588 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 55 sheets defined 51.0% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.719A pdb=" N GLY A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 101 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.539A pdb=" N LEU A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 219 removed outlier: 4.398A pdb=" N LYS A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.581A pdb=" N TYR A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 301 through 307 removed outlier: 3.505A pdb=" N ILE A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.704A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.995A pdb=" N GLN A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 365 " --> pdb=" O GLN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 380 removed outlier: 3.646A pdb=" N ALA A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.953A pdb=" N THR A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.550A pdb=" N GLY B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.511A pdb=" N LYS B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.684A pdb=" N LEU B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 180 Processing helix chain 'B' and resid 206 through 219 removed outlier: 4.552A pdb=" N LYS B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 4.044A pdb=" N HIS B 234 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN B 235 " --> pdb=" O HIS B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 235' Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.582A pdb=" N ILE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 291 through 297 removed outlier: 3.577A pdb=" N LEU B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.523A pdb=" N GLY B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.884A pdb=" N LYS B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.046A pdb=" N HIS B 364 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.953A pdb=" N ARG B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.553A pdb=" N GLU B 401 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 402' Processing helix chain 'C' and resid 63 through 72 Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 86 through 98 Processing helix chain 'C' and resid 127 through 136 removed outlier: 3.744A pdb=" N LYS C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 171 Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.549A pdb=" N LYS C 190 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 191 " --> pdb=" O VAL C 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'C' and resid 206 through 219 removed outlier: 3.551A pdb=" N GLN C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS C 215 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 4.019A pdb=" N ILE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.572A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 removed outlier: 3.589A pdb=" N ILE C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 306 " --> pdb=" O PRO C 302 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 307' Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.838A pdb=" N LYS C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.671A pdb=" N ILE C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.919A pdb=" N ARG C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.556A pdb=" N GLY D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 96 removed outlier: 4.016A pdb=" N VAL D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 136 removed outlier: 3.544A pdb=" N LYS D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 171 removed outlier: 3.535A pdb=" N LEU D 167 " --> pdb=" O ILE D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 207 through 219 removed outlier: 3.753A pdb=" N GLN D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS D 215 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.502A pdb=" N TYR D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.577A pdb=" N LEU D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.671A pdb=" N ILE D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 301 through 307' Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.805A pdb=" N LYS D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER D 327 " --> pdb=" O VAL D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 removed outlier: 3.719A pdb=" N LEU D 340 " --> pdb=" O GLN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.520A pdb=" N ILE D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS D 364 " --> pdb=" O ASP D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.962A pdb=" N ARG D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 387 removed outlier: 3.627A pdb=" N ASP D 386 " --> pdb=" O PRO D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 399 through 404 removed outlier: 3.904A pdb=" N GLN D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 78 through 98 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.505A pdb=" N ARG E 106 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 136 Processing helix chain 'E' and resid 161 through 169 removed outlier: 3.510A pdb=" N LEU E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 206 through 219 removed outlier: 3.610A pdb=" N LEU E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS E 215 " --> pdb=" O GLN E 211 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 removed outlier: 3.501A pdb=" N ILE E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.501A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 307 removed outlier: 3.544A pdb=" N ARG E 307 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.673A pdb=" N LYS E 324 " --> pdb=" O GLU E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 342 Processing helix chain 'E' and resid 351 through 365 Processing helix chain 'E' and resid 371 through 376 removed outlier: 3.915A pdb=" N MET E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'F' and resid 63 through 73 removed outlier: 3.669A pdb=" N GLY F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 98 removed outlier: 3.654A pdb=" N ILE F 96 " --> pdb=" O HIS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.739A pdb=" N LEU F 138 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 209 through 219 removed outlier: 4.243A pdb=" N LYS F 215 " --> pdb=" O GLN F 211 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.579A pdb=" N LYS F 231 " --> pdb=" O GLY F 228 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS F 232 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 263 removed outlier: 3.614A pdb=" N ARG F 263 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.794A pdb=" N LEU F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.503A pdb=" N GLY F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 327 removed outlier: 3.594A pdb=" N SER F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 342 Processing helix chain 'F' and resid 351 through 361 Processing helix chain 'F' and resid 367 through 370 Processing helix chain 'F' and resid 371 through 387 Proline residue: F 382 - end of helix Processing helix chain 'H' and resid 31 through 39 Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 82 through 96 Processing helix chain 'H' and resid 110 through 118 removed outlier: 3.778A pdb=" N VAL H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 173 Processing helix chain 'H' and resid 175 through 183 Processing helix chain 'H' and resid 190 through 198 Processing helix chain 'I' and resid 31 through 38 Processing helix chain 'I' and resid 49 through 67 removed outlier: 3.762A pdb=" N ASP I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 96 Processing helix chain 'I' and resid 110 through 118 Processing helix chain 'I' and resid 147 through 173 Processing helix chain 'I' and resid 175 through 183 Processing helix chain 'I' and resid 190 through 198 Processing helix chain 'K' and resid 31 through 39 Processing helix chain 'K' and resid 49 through 67 Processing helix chain 'K' and resid 82 through 96 Processing helix chain 'K' and resid 110 through 118 removed outlier: 3.508A pdb=" N VAL K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 173 Processing helix chain 'K' and resid 175 through 183 Processing helix chain 'K' and resid 190 through 198 Processing helix chain 'L' and resid 33 through 38 Processing helix chain 'L' and resid 49 through 67 Processing helix chain 'L' and resid 82 through 96 Processing helix chain 'L' and resid 110 through 118 removed outlier: 3.756A pdb=" N VAL L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 173 Processing helix chain 'L' and resid 175 through 183 Processing helix chain 'L' and resid 190 through 198 Processing helix chain 'M' and resid 31 through 39 Processing helix chain 'M' and resid 49 through 67 Processing helix chain 'M' and resid 82 through 96 Processing helix chain 'M' and resid 110 through 118 removed outlier: 3.584A pdb=" N VAL M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 173 Processing helix chain 'M' and resid 175 through 183 Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'N' and resid 31 through 39 removed outlier: 3.522A pdb=" N GLU N 39 " --> pdb=" O LYS N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 67 Processing helix chain 'N' and resid 82 through 96 Processing helix chain 'N' and resid 110 through 118 Processing helix chain 'N' and resid 147 through 173 removed outlier: 3.572A pdb=" N ILE N 152 " --> pdb=" O SER N 148 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY N 173 " --> pdb=" O ALA N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 183 Processing helix chain 'N' and resid 190 through 198 Processing helix chain 'O' and resid 16 through 27 Processing helix chain 'O' and resid 37 through 55 Processing helix chain 'O' and resid 70 through 84 Processing helix chain 'O' and resid 98 through 106 Processing helix chain 'O' and resid 133 through 159 Processing helix chain 'O' and resid 161 through 169 Processing helix chain 'O' and resid 176 through 184 Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 37 through 55 Processing helix chain 'P' and resid 70 through 84 Processing helix chain 'P' and resid 98 through 106 Processing helix chain 'P' and resid 133 through 159 Processing helix chain 'P' and resid 161 through 169 Processing helix chain 'P' and resid 176 through 184 Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 37 through 55 Processing helix chain 'Q' and resid 70 through 84 Processing helix chain 'Q' and resid 98 through 106 Processing helix chain 'Q' and resid 133 through 159 Processing helix chain 'Q' and resid 161 through 169 Processing helix chain 'Q' and resid 176 through 184 Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 37 through 55 Processing helix chain 'R' and resid 70 through 84 Processing helix chain 'R' and resid 98 through 106 Processing helix chain 'R' and resid 133 through 159 Processing helix chain 'R' and resid 161 through 169 Processing helix chain 'R' and resid 176 through 184 Processing helix chain 'S' and resid 16 through 27 Processing helix chain 'S' and resid 37 through 55 Processing helix chain 'S' and resid 70 through 84 Processing helix chain 'S' and resid 98 through 106 Processing helix chain 'S' and resid 133 through 159 Processing helix chain 'S' and resid 161 through 169 Processing helix chain 'S' and resid 176 through 184 Processing helix chain 'T' and resid 16 through 27 Processing helix chain 'T' and resid 37 through 55 Processing helix chain 'T' and resid 70 through 84 Processing helix chain 'T' and resid 98 through 106 Processing helix chain 'T' and resid 133 through 159 Processing helix chain 'T' and resid 161 through 169 Processing helix chain 'T' and resid 176 through 184 Processing helix chain 'U' and resid 16 through 27 Processing helix chain 'U' and resid 37 through 55 Processing helix chain 'U' and resid 70 through 84 Processing helix chain 'U' and resid 98 through 106 Processing helix chain 'U' and resid 133 through 159 Processing helix chain 'U' and resid 161 through 169 Processing helix chain 'U' and resid 176 through 184 Processing helix chain 'V' and resid 31 through 39 Processing helix chain 'V' and resid 49 through 67 Processing helix chain 'V' and resid 82 through 96 Processing helix chain 'V' and resid 110 through 118 removed outlier: 3.605A pdb=" N VAL V 114 " --> pdb=" O SER V 110 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 173 Processing helix chain 'V' and resid 175 through 183 Processing helix chain 'V' and resid 190 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 6.015A pdb=" N ALA A 143 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 224 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 146 removed outlier: 6.494A pdb=" N ALA B 143 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASP B 186 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 145 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B 117 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 224 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350 removed outlier: 6.842A pdb=" N GLU B 347 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 397 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU B 349 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 142 through 146 removed outlier: 6.063A pdb=" N ILE C 117 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY C 251 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET C 119 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 221 through 224 Processing sheet with id=AA9, first strand: chain 'D' and resid 142 through 146 removed outlier: 6.539A pdb=" N ALA D 143 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP D 186 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA D 145 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 221 through 223 Processing sheet with id=AB2, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AB3, first strand: chain 'E' and resid 142 through 146 removed outlier: 3.517A pdb=" N ASP E 186 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 221 through 224 Processing sheet with id=AB5, first strand: chain 'E' and resid 347 through 350 removed outlier: 6.308A pdb=" N GLU E 347 " --> pdb=" O LYS E 395 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL E 397 " --> pdb=" O GLU E 347 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU E 349 " --> pdb=" O VAL E 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 142 through 146 removed outlier: 5.846A pdb=" N ALA F 143 " --> pdb=" O TYR F 184 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP F 186 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA F 145 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 221 through 224 Processing sheet with id=AB8, first strand: chain 'F' and resid 347 through 350 removed outlier: 3.869A pdb=" N ALA F 394 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL F 412 " --> pdb=" O ALA F 394 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL F 396 " --> pdb=" O THR F 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 29 through 30 removed outlier: 3.661A pdb=" N PHE H 19 " --> pdb=" O SER H 30 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 41 through 44 removed outlier: 4.937A pdb=" N SER H 78 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN H 107 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG H 131 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY H 106 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU H 133 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 41 through 44 removed outlier: 4.937A pdb=" N SER H 78 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN H 107 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET H 125 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR H 102 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 138 through 146 removed outlier: 7.057A pdb=" N GLY H 141 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY R 131 " --> pdb=" O GLY H 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.567A pdb=" N ILE I 72 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL I 103 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N MET I 74 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU I 105 " --> pdb=" O MET I 74 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE I 76 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN I 107 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG I 131 " --> pdb=" O CYS I 104 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY I 106 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU I 133 " --> pdb=" O GLY I 106 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA I 108 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.567A pdb=" N ILE I 72 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL I 103 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N MET I 74 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU I 105 " --> pdb=" O MET I 74 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE I 76 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN I 107 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N MET I 125 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR I 102 " --> pdb=" O MET I 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 138 through 146 removed outlier: 7.414A pdb=" N GLY I 141 " --> pdb=" O GLY U 131 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY U 131 " --> pdb=" O GLY I 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 41 through 44 removed outlier: 5.190A pdb=" N SER K 78 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN K 107 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG K 131 " --> pdb=" O CYS K 104 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY K 106 " --> pdb=" O ARG K 131 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU K 133 " --> pdb=" O GLY K 106 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA K 108 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 41 through 44 removed outlier: 5.190A pdb=" N SER K 78 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN K 107 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N MET K 125 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR K 102 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 138 through 146 removed outlier: 7.154A pdb=" N GLY K 141 " --> pdb=" O GLY Q 131 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY Q 131 " --> pdb=" O GLY K 141 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 41 through 44 removed outlier: 5.145A pdb=" N SER L 78 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN L 107 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG L 131 " --> pdb=" O CYS L 104 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY L 106 " --> pdb=" O ARG L 131 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU L 133 " --> pdb=" O GLY L 106 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA L 108 " --> pdb=" O LEU L 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 41 through 44 removed outlier: 5.145A pdb=" N SER L 78 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN L 107 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N MET L 125 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR L 102 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 138 through 146 removed outlier: 7.071A pdb=" N GLY L 141 " --> pdb=" O GLY O 131 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY O 131 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 19 through 21 Processing sheet with id=AD5, first strand: chain 'M' and resid 41 through 44 removed outlier: 6.699A pdb=" N ILE M 72 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL M 103 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N MET M 74 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET M 125 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N THR M 102 " --> pdb=" O MET M 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 107 through 109 removed outlier: 6.301A pdb=" N ALA M 108 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 138 through 146 removed outlier: 6.924A pdb=" N GLY M 141 " --> pdb=" O GLY S 131 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY S 131 " --> pdb=" O GLY M 141 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 19 through 21 Processing sheet with id=AD9, first strand: chain 'N' and resid 41 through 44 removed outlier: 6.646A pdb=" N ILE N 72 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL N 103 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET N 74 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU N 105 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE N 76 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN N 107 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG N 131 " --> pdb=" O CYS N 104 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY N 106 " --> pdb=" O ARG N 131 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU N 133 " --> pdb=" O GLY N 106 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA N 108 " --> pdb=" O LEU N 133 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 41 through 44 removed outlier: 6.646A pdb=" N ILE N 72 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL N 103 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET N 74 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU N 105 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE N 76 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN N 107 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N MET N 125 " --> pdb=" O ILE N 100 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR N 102 " --> pdb=" O MET N 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 138 through 146 removed outlier: 6.989A pdb=" N GLY N 141 " --> pdb=" O GLY T 131 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY T 131 " --> pdb=" O GLY N 141 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.492A pdb=" N ILE O 30 " --> pdb=" O TYR O 63 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN O 65 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU O 32 " --> pdb=" O ASN O 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER O 66 " --> pdb=" O MET O 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET O 95 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.492A pdb=" N ILE O 30 " --> pdb=" O TYR O 63 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN O 65 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU O 32 " --> pdb=" O ASN O 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER O 66 " --> pdb=" O MET O 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET O 95 " --> pdb=" O SER O 66 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR O 113 " --> pdb=" O ILE O 88 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR O 90 " --> pdb=" O TYR O 113 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.490A pdb=" N ILE P 30 " --> pdb=" O TYR P 63 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN P 65 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU P 32 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER P 66 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET P 95 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.490A pdb=" N ILE P 30 " --> pdb=" O TYR P 63 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN P 65 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU P 32 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER P 66 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET P 95 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR P 113 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR P 90 " --> pdb=" O TYR P 113 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 126 through 132 removed outlier: 4.515A pdb=" N GLY P 131 " --> pdb=" O GLY V 141 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY V 141 " --> pdb=" O GLY P 131 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.490A pdb=" N ILE Q 30 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN Q 65 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU Q 32 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER Q 66 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET Q 95 " --> pdb=" O SER Q 66 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.490A pdb=" N ILE Q 30 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN Q 65 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU Q 32 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER Q 66 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET Q 95 " --> pdb=" O SER Q 66 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR Q 113 " --> pdb=" O ILE Q 88 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR Q 90 " --> pdb=" O TYR Q 113 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 29 through 32 removed outlier: 6.490A pdb=" N ILE R 30 " --> pdb=" O TYR R 63 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN R 65 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU R 32 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER R 66 " --> pdb=" O MET R 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET R 95 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 29 through 32 removed outlier: 6.490A pdb=" N ILE R 30 " --> pdb=" O TYR R 63 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN R 65 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU R 32 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER R 66 " --> pdb=" O MET R 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET R 95 " --> pdb=" O SER R 66 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR R 113 " --> pdb=" O ILE R 88 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR R 90 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 29 through 32 removed outlier: 6.490A pdb=" N ILE S 30 " --> pdb=" O TYR S 63 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN S 65 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU S 32 " --> pdb=" O ASN S 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER S 66 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET S 95 " --> pdb=" O SER S 66 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 29 through 32 removed outlier: 6.490A pdb=" N ILE S 30 " --> pdb=" O TYR S 63 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN S 65 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU S 32 " --> pdb=" O ASN S 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER S 66 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET S 95 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR S 113 " --> pdb=" O ILE S 88 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR S 90 " --> pdb=" O TYR S 113 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 29 through 32 removed outlier: 6.491A pdb=" N ILE T 30 " --> pdb=" O TYR T 63 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN T 65 " --> pdb=" O ILE T 30 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU T 32 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER T 66 " --> pdb=" O MET T 93 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N MET T 95 " --> pdb=" O SER T 66 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 29 through 32 removed outlier: 6.491A pdb=" N ILE T 30 " --> pdb=" O TYR T 63 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN T 65 " --> pdb=" O ILE T 30 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU T 32 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER T 66 " --> pdb=" O MET T 93 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N MET T 95 " --> pdb=" O SER T 66 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR T 113 " --> pdb=" O ILE T 88 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR T 90 " --> pdb=" O TYR T 113 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 29 through 32 removed outlier: 6.491A pdb=" N ILE U 30 " --> pdb=" O TYR U 63 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN U 65 " --> pdb=" O ILE U 30 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU U 32 " --> pdb=" O ASN U 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER U 66 " --> pdb=" O MET U 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET U 95 " --> pdb=" O SER U 66 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 29 through 32 removed outlier: 6.491A pdb=" N ILE U 30 " --> pdb=" O TYR U 63 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN U 65 " --> pdb=" O ILE U 30 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU U 32 " --> pdb=" O ASN U 65 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER U 66 " --> pdb=" O MET U 93 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N MET U 95 " --> pdb=" O SER U 66 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR U 113 " --> pdb=" O ILE U 88 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR U 90 " --> pdb=" O TYR U 113 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 41 through 44 removed outlier: 6.881A pdb=" N ILE V 42 " --> pdb=" O TYR V 75 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASN V 77 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU V 44 " --> pdb=" O ASN V 77 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE V 72 " --> pdb=" O GLN V 101 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL V 103 " --> pdb=" O ILE V 72 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET V 74 " --> pdb=" O VAL V 103 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU V 105 " --> pdb=" O MET V 74 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE V 76 " --> pdb=" O LEU V 105 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN V 107 " --> pdb=" O ILE V 76 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG V 131 " --> pdb=" O CYS V 104 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY V 106 " --> pdb=" O ARG V 131 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU V 133 " --> pdb=" O GLY V 106 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA V 108 " --> pdb=" O LEU V 133 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 41 through 44 removed outlier: 6.881A pdb=" N ILE V 42 " --> pdb=" O TYR V 75 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASN V 77 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU V 44 " --> pdb=" O ASN V 77 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE V 72 " --> pdb=" O GLN V 101 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL V 103 " --> pdb=" O ILE V 72 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET V 74 " --> pdb=" O VAL V 103 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU V 105 " --> pdb=" O MET V 74 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE V 76 " --> pdb=" O LEU V 105 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN V 107 " --> pdb=" O ILE V 76 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N MET V 125 " --> pdb=" O ILE V 100 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR V 102 " --> pdb=" O MET V 125 " (cutoff:3.500A) 1856 hydrogen bonds defined for protein. 5388 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: 6.81 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10549 1.33 - 1.45: 6274 1.45 - 1.57: 19517 1.57 - 1.69: 40 1.69 - 1.82: 300 Bond restraints: 36680 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C5 ATP D 502 " pdb=" C6 ATP D 502 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.94e+01 ... (remaining 36675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 49033 3.98 - 7.96: 516 7.96 - 11.94: 91 11.94 - 15.92: 1 15.92 - 19.90: 6 Bond angle restraints: 49647 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 119.97 19.90 1.00e+00 1.00e+00 3.96e+02 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 120.00 19.87 1.00e+00 1.00e+00 3.95e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 122.54 17.33 1.00e+00 1.00e+00 3.00e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.02 16.81 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA ATP D 502 " pdb=" O3A ATP D 502 " pdb=" PB ATP D 502 " ideal model delta sigma weight residual 136.83 125.69 11.14 1.00e+00 1.00e+00 1.24e+02 ... (remaining 49642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 21959 26.09 - 52.18: 469 52.18 - 78.28: 79 78.28 - 104.37: 3 104.37 - 130.46: 1 Dihedral angle restraints: 22511 sinusoidal: 9187 harmonic: 13324 Sorted by residual: dihedral pdb=" CA ASP B 172 " pdb=" C ASP B 172 " pdb=" N TYR B 173 " pdb=" CA TYR B 173 " ideal model delta harmonic sigma weight residual 180.00 141.62 38.38 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA MET C 137 " pdb=" C MET C 137 " pdb=" N LEU C 138 " pdb=" CA LEU C 138 " ideal model delta harmonic sigma weight residual -180.00 -142.78 -37.22 0 5.00e+00 4.00e-02 5.54e+01 dihedral pdb=" CA LEU C 61 " pdb=" C LEU C 61 " pdb=" N PRO C 62 " pdb=" CA PRO C 62 " ideal model delta harmonic sigma weight residual 180.00 -144.75 -35.25 0 5.00e+00 4.00e-02 4.97e+01 ... (remaining 22508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4883 0.081 - 0.161: 820 0.161 - 0.242: 51 0.242 - 0.323: 7 0.323 - 0.403: 9 Chirality restraints: 5770 Sorted by residual: chirality pdb=" CB ILE A 144 " pdb=" CA ILE A 144 " pdb=" CG1 ILE A 144 " pdb=" CG2 ILE A 144 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CB ILE E 144 " pdb=" CA ILE E 144 " pdb=" CG1 ILE E 144 " pdb=" CG2 ILE E 144 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CG LEU O 115 " pdb=" CB LEU O 115 " pdb=" CD1 LEU O 115 " pdb=" CD2 LEU O 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 5767 not shown) Planarity restraints: 6398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 M 301 " -0.182 2.00e-02 2.50e+03 2.62e-01 8.55e+02 pdb=" C18 BO2 M 301 " 0.084 2.00e-02 2.50e+03 pdb=" C21 BO2 M 301 " -0.309 2.00e-02 2.50e+03 pdb=" N20 BO2 M 301 " 0.452 2.00e-02 2.50e+03 pdb=" O19 BO2 M 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 H 301 " -0.180 2.00e-02 2.50e+03 2.35e-01 6.92e+02 pdb=" C18 BO2 H 301 " 0.078 2.00e-02 2.50e+03 pdb=" C21 BO2 H 301 " -0.280 2.00e-02 2.50e+03 pdb=" N20 BO2 H 301 " 0.399 2.00e-02 2.50e+03 pdb=" O19 BO2 H 301 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 R 201 " -0.171 2.00e-02 2.50e+03 2.16e-01 5.83e+02 pdb=" C18 BO2 R 201 " 0.063 2.00e-02 2.50e+03 pdb=" C21 BO2 R 201 " -0.258 2.00e-02 2.50e+03 pdb=" N20 BO2 R 201 " 0.365 2.00e-02 2.50e+03 pdb=" O19 BO2 R 201 " 0.002 2.00e-02 2.50e+03 ... (remaining 6395 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.58: 6 1.58 - 2.41: 84 2.41 - 3.24: 36845 3.24 - 4.07: 100962 4.07 - 4.90: 188444 Warning: very small nonbonded interaction distances. Nonbonded interactions: 326341 Sorted by model distance: nonbonded pdb=" OE2 GLU D 303 " pdb=" O2G ATP D 502 " model vdw 0.756 3.040 nonbonded pdb=" CD GLU D 303 " pdb=" O2G ATP D 502 " model vdw 0.969 3.270 nonbonded pdb=" O3B ADP E 501 " pdb="MG MG E 502 " model vdw 1.277 2.170 nonbonded pdb=" NH2 ARG F 370 " pdb=" PB ADP F 501 " model vdw 1.326 2.784 nonbonded pdb=" NZ LYS E 127 " pdb="MG MG E 502 " model vdw 1.511 2.250 ... (remaining 326336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 191 or (resid 192 and (name N or name CA or nam \ e C or name CB )) or resid 208 through 276 or (resid 277 and (name N or name CA \ or name C or name CB or name OG )) or resid 286 through 411 or (resid 412 and (n \ ame N or name CA or name C or name CB or name CG1 or name CG2)))) selection = (chain 'B' and (resid 60 through 100 or (resid 101 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name CE or name NZ )) or resid 109 throu \ gh 191 or (resid 192 and (name N or name CA or name C or name CB )) or resid 208 \ through 227 or (resid 228 and (name N or name CA or name C )) or resid 235 thro \ ugh 276 or (resid 277 and (name N or name CA or name C or name CB or name OG )) \ or resid 286 through 409 or (resid 410 and (name N or name CA or name C or name \ CB or name OG1 or name CG2)) or resid 411 or (resid 412 and (name N or name CA o \ r name C or name CB or name CG1 or name CG2)))) selection = (chain 'C' and (resid 60 through 101 or resid 109 through 191 or (resid 192 and \ (name N or name CA or name C or name CB )) or resid 208 through 227 or (resid 22 \ 8 and (name N or name CA or name C )) or resid 235 through 276 or (resid 277 and \ (name N or name CA or name C or name CB or name OG )) or resid 286 through 409 \ or (resid 410 and (name N or name CA or name C or name CB or name OG1 or name CG \ 2)) or resid 411 or (resid 412 and (name N or name CA or name C or name CB or na \ me CG1 or name CG2)))) selection = (chain 'D' and (resid 60 through 100 or (resid 101 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name CE or name NZ )) or resid 109 throu \ gh 191 or (resid 192 and (name N or name CA or name C or name CB )) or resid 208 \ through 227 or (resid 228 and (name N or name CA or name C )) or resid 235 thro \ ugh 409 or (resid 410 and (name N or name CA or name C or name CB or name OG1 or \ name CG2)) or resid 411 or (resid 412 and (name N or name CA or name C or name \ CB or name CG1 or name CG2)))) selection = (chain 'E' and (resid 60 through 100 or (resid 101 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name CE or name NZ )) or resid 109 throu \ gh 191 or (resid 192 and (name N or name CA or name C or name CB )) or resid 208 \ through 227 or (resid 228 and (name N or name CA or name C )) or resid 235 thro \ ugh 409 or (resid 410 and (name N or name CA or name C or name CB or name OG1 or \ name CG2)) or resid 411 through 412)) selection = (chain 'F' and (resid 60 through 100 or (resid 101 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name CE or name NZ )) or resid 109 throu \ gh 227 or (resid 228 and (name N or name CA or name C )) or resid 235 through 27 \ 7 or resid 286 through 409 or (resid 410 and (name N or name CA or name C or nam \ e CB or name OG1 or name CG2)) or resid 411 or (resid 412 and (name N or name CA \ or name C or name CB or name CG1 or name CG2)))) } ncs_group { reference = (chain 'H' and (resid 15 through 18 or (resid 19 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 31 through 301)) selection = (chain 'I' and (resid 15 through 18 or (resid 19 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 31 through 301)) selection = (chain 'K' and (resid 15 through 19 or resid 31 through 301)) selection = (chain 'L' and (resid 15 through 18 or (resid 19 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 31 through 301)) selection = (chain 'M' and (resid 15 through 18 or (resid 19 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 31 through 301)) selection = (chain 'N' and (resid 15 through 18 or (resid 19 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 31 through 301)) selection = (chain 'V' and (resid 15 through 18 or (resid 19 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 31 through 301)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.730 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: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.160 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.018 1.004 36708 Z= 1.400 Angle : 1.168 19.903 49647 Z= 0.662 Chirality : 0.060 0.403 5770 Planarity : 0.012 0.262 6398 Dihedral : 11.081 130.459 13923 Min Nonbonded Distance : 0.756 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Rotamer: Outliers : 0.26 % Allowed : 2.62 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.43 (0.09), residues: 4553 helix: -3.50 (0.06), residues: 2312 sheet: -1.89 (0.21), residues: 399 loop : -2.13 (0.12), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG I 40 TYR 0.040 0.004 TYR V 206 PHE 0.052 0.005 PHE M 25 TRP 0.004 0.002 TRP S 174 HIS 0.014 0.003 HIS P 117 Details of bonding type rmsd covalent geometry : bond 0.01195 (36680) covalent geometry : angle 1.16754 (49647) hydrogen bonds : bond 0.22136 ( 1780) hydrogen bonds : angle 8.72296 ( 5388) Misc. bond : bond 0.46839 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1127 time to evaluate : 1.200 Fit side-chains TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG E 193 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER N 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG S 192 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 156 VAL cc_start: 0.8817 (t) cc_final: 0.8524 (p) REVERT: A 320 GLU cc_start: 0.7639 (tp30) cc_final: 0.7380 (tp30) REVERT: A 353 ASP cc_start: 0.7953 (m-30) cc_final: 0.7655 (m-30) REVERT: A 356 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7453 (mp0) REVERT: C 401 GLU cc_start: 0.5483 (mt-10) cc_final: 0.4239 (tt0) REVERT: D 146 ASP cc_start: 0.7371 (p0) cc_final: 0.6917 (p0) REVERT: D 214 LEU cc_start: 0.7654 (pp) cc_final: 0.7008 (mt) REVERT: D 395 LYS cc_start: 0.6981 (tptp) cc_final: 0.6465 (tptm) REVERT: D 401 GLU cc_start: 0.5646 (mt-10) cc_final: 0.5313 (mt-10) REVERT: E 96 ILE cc_start: 0.8582 (mm) cc_final: 0.8277 (mm) REVERT: E 166 LYS cc_start: 0.8425 (mtmm) cc_final: 0.8212 (mtmp) REVERT: E 186 ASP cc_start: 0.6904 (p0) cc_final: 0.6687 (t0) REVERT: E 320 GLU cc_start: 0.7540 (pm20) cc_final: 0.7297 (pm20) REVERT: E 356 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6886 (mm-30) REVERT: E 386 ASP cc_start: 0.7738 (m-30) cc_final: 0.7515 (t0) REVERT: F 158 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6354 (mt-10) REVERT: F 218 GLU cc_start: 0.7220 (tt0) cc_final: 0.6823 (tp30) REVERT: F 319 LYS cc_start: 0.7775 (mtmp) cc_final: 0.7526 (mtpm) REVERT: F 395 LYS cc_start: 0.7684 (tppt) cc_final: 0.7474 (tptt) REVERT: I 165 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7497 (mt-10) REVERT: K 165 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7599 (mt-10) outliers start: 10 outliers final: 3 residues processed: 1134 average time/residue: 0.8211 time to fit residues: 1076.8700 Evaluate side-chains 672 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 669 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain I residue 27 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN A 210 GLN A 244 ASN B 91 ASN B 132 GLN B 210 GLN B 221 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN C 92 HIS C 162 ASN C 187 GLN C 210 GLN C 221 GLN D 162 ASN D 227 GLN D 232 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 132 GLN E 210 GLN E 316 ASN ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS F 221 GLN F 316 ASN F 406 ASN H 22 HIS H 31 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN K 129 ASN L 94 GLN L 101 GLN L 146 GLN M 94 GLN M 129 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 160 GLN P 117 HIS P 160 GLN Q 117 HIS Q 160 GLN R 160 GLN S 160 GLN T 117 HIS T 160 GLN U 117 HIS U 160 GLN ** V 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN V 101 GLN V 129 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089366 restraints weight = 54480.688| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.97 r_work: 0.3237 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 36708 Z= 0.189 Angle : 0.655 13.529 49647 Z= 0.332 Chirality : 0.045 0.356 5770 Planarity : 0.005 0.056 6398 Dihedral : 9.363 145.114 5413 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 2.81 % Allowed : 11.04 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.11), residues: 4553 helix: -0.93 (0.09), residues: 2349 sheet: -1.90 (0.21), residues: 447 loop : -1.95 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 370 TYR 0.018 0.002 TYR A 337 PHE 0.017 0.002 PHE H 19 TRP 0.002 0.000 TRP U 174 HIS 0.005 0.001 HIS O 117 Details of bonding type rmsd covalent geometry : bond 0.00423 (36680) covalent geometry : angle 0.65471 (49647) hydrogen bonds : bond 0.04152 ( 1780) hydrogen bonds : angle 4.92355 ( 5388) Misc. bond : bond 0.00389 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 778 time to evaluate : 1.485 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER N 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG S 192 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8415 (ttt-90) REVERT: A 137 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7994 (ttt) REVERT: A 156 VAL cc_start: 0.9009 (t) cc_final: 0.8704 (p) REVERT: A 361 GLN cc_start: 0.6597 (mt0) cc_final: 0.6317 (mt0) REVERT: B 97 GLN cc_start: 0.8121 (mm110) cc_final: 0.7878 (mt0) REVERT: B 320 GLU cc_start: 0.7980 (tp30) cc_final: 0.7570 (tp30) REVERT: B 324 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8387 (mtpp) REVERT: B 400 LYS cc_start: 0.8295 (mppt) cc_final: 0.8061 (mppt) REVERT: B 404 GLN cc_start: 0.6566 (mt0) cc_final: 0.6323 (mp10) REVERT: C 158 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7058 (mm-30) REVERT: C 207 GLU cc_start: 0.6364 (pt0) cc_final: 0.5564 (mm-30) REVERT: C 377 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 401 GLU cc_start: 0.5708 (mt-10) cc_final: 0.4160 (tt0) REVERT: D 146 ASP cc_start: 0.7448 (p0) cc_final: 0.7020 (p0) REVERT: D 214 LEU cc_start: 0.6983 (pp) cc_final: 0.6716 (mt) REVERT: D 347 GLU cc_start: 0.8572 (tt0) cc_final: 0.8200 (pp20) REVERT: E 186 ASP cc_start: 0.6804 (p0) cc_final: 0.6569 (t0) REVERT: E 227 GLN cc_start: 0.8427 (tp40) cc_final: 0.8202 (tt0) REVERT: E 320 GLU cc_start: 0.8006 (pm20) cc_final: 0.7441 (pm20) REVERT: E 356 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7011 (mm-30) REVERT: E 386 ASP cc_start: 0.7928 (m-30) cc_final: 0.7570 (t0) REVERT: F 218 GLU cc_start: 0.6901 (tt0) cc_final: 0.6485 (tp30) REVERT: F 319 LYS cc_start: 0.7024 (mtmp) cc_final: 0.6796 (mppt) REVERT: L 144 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: M 20 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8911 (mm) REVERT: M 27 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7576 (t) REVERT: P 35 GLU cc_start: 0.8446 (tt0) cc_final: 0.8202 (tt0) REVERT: P 166 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: R 22 GLU cc_start: 0.8438 (tt0) cc_final: 0.7932 (tm-30) REVERT: S 18 ASP cc_start: 0.8784 (m-30) cc_final: 0.8564 (m-30) REVERT: U 35 GLU cc_start: 0.8409 (pt0) cc_final: 0.8193 (tt0) REVERT: U 39 GLU cc_start: 0.8712 (tt0) cc_final: 0.8436 (mp0) REVERT: U 43 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8204 (tmm160) outliers start: 106 outliers final: 23 residues processed: 840 average time/residue: 0.7113 time to fit residues: 704.3139 Evaluate side-chains 694 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 665 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain T residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 162 optimal weight: 0.0060 chunk 276 optimal weight: 0.6980 chunk 211 optimal weight: 0.0030 chunk 89 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 450 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 411 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 407 optimal weight: 0.5980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN A 244 ASN A 406 ASN B 221 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN B 361 GLN C 361 GLN C 364 HIS D 91 ASN D 336 GLN E 404 GLN ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN L 101 GLN L 153 GLN M 136 GLN M 144 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 160 GLN P 42 ASN U 139 GLN V 136 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090571 restraints weight = 54602.340| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.04 r_work: 0.3263 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36708 Z= 0.136 Angle : 0.576 14.600 49647 Z= 0.290 Chirality : 0.043 0.293 5770 Planarity : 0.004 0.067 6398 Dihedral : 8.539 131.279 5409 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 2.30 % Allowed : 12.79 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.12), residues: 4553 helix: 0.35 (0.10), residues: 2355 sheet: -1.86 (0.21), residues: 459 loop : -1.75 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 276 TYR 0.018 0.001 TYR A 337 PHE 0.015 0.001 PHE H 19 TRP 0.001 0.000 TRP S 174 HIS 0.005 0.001 HIS L 171 Details of bonding type rmsd covalent geometry : bond 0.00298 (36680) covalent geometry : angle 0.57616 (49647) hydrogen bonds : bond 0.03485 ( 1780) hydrogen bonds : angle 4.40863 ( 5388) Misc. bond : bond 0.00250 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 753 time to evaluate : 1.522 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG S 192 " (corrupted residue). Skipping it. REVERT: A 137 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7998 (ttt) REVERT: A 175 VAL cc_start: 0.8474 (t) cc_final: 0.8253 (p) REVERT: A 177 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8233 (ttp80) REVERT: A 218 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 320 GLU cc_start: 0.7122 (mp0) cc_final: 0.6724 (mp0) REVERT: B 97 GLN cc_start: 0.8114 (mm110) cc_final: 0.7889 (mt0) REVERT: B 320 GLU cc_start: 0.8000 (tp30) cc_final: 0.7538 (tp30) REVERT: B 324 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8362 (mtpp) REVERT: B 400 LYS cc_start: 0.8187 (mppt) cc_final: 0.7931 (mppt) REVERT: B 404 GLN cc_start: 0.6570 (mt0) cc_final: 0.6319 (mp10) REVERT: C 158 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7002 (mm-30) REVERT: C 207 GLU cc_start: 0.6296 (pt0) cc_final: 0.5587 (mm-30) REVERT: C 377 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 378 GLU cc_start: 0.8509 (tt0) cc_final: 0.7892 (mp0) REVERT: C 401 GLU cc_start: 0.5721 (mt-10) cc_final: 0.4021 (tt0) REVERT: D 146 ASP cc_start: 0.7320 (p0) cc_final: 0.6889 (p0) REVERT: D 347 GLU cc_start: 0.8583 (tt0) cc_final: 0.8176 (pp20) REVERT: D 395 LYS cc_start: 0.7400 (tptt) cc_final: 0.6488 (tppt) REVERT: E 186 ASP cc_start: 0.6747 (p0) cc_final: 0.6484 (t0) REVERT: E 263 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8356 (ttp-110) REVERT: E 291 MET cc_start: 0.6818 (tpp) cc_final: 0.6524 (mmm) REVERT: E 319 LYS cc_start: 0.8082 (tttt) cc_final: 0.7766 (tttt) REVERT: E 320 GLU cc_start: 0.8017 (pm20) cc_final: 0.7807 (pm20) REVERT: E 353 ASP cc_start: 0.8345 (m-30) cc_final: 0.8126 (m-30) REVERT: E 356 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6969 (mm-30) REVERT: E 384 MET cc_start: 0.8446 (mtt) cc_final: 0.7928 (mtt) REVERT: E 386 ASP cc_start: 0.7863 (m-30) cc_final: 0.7492 (t0) REVERT: F 218 GLU cc_start: 0.6854 (tt0) cc_final: 0.6611 (tp30) REVERT: F 361 GLN cc_start: 0.6102 (mm-40) cc_final: 0.5748 (mm-40) REVERT: F 395 LYS cc_start: 0.7981 (tppt) cc_final: 0.7305 (tptt) REVERT: H 38 GLU cc_start: 0.8263 (tp30) cc_final: 0.7958 (mp0) REVERT: L 144 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: M 20 ILE cc_start: 0.9201 (mt) cc_final: 0.8875 (mm) REVERT: M 30 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8231 (p) REVERT: P 35 GLU cc_start: 0.8389 (tt0) cc_final: 0.8165 (tm-30) REVERT: P 39 GLU cc_start: 0.8854 (tt0) cc_final: 0.8642 (tt0) REVERT: Q 35 GLU cc_start: 0.8459 (tt0) cc_final: 0.8241 (tp30) REVERT: R 22 GLU cc_start: 0.8420 (tt0) cc_final: 0.8045 (tm-30) REVERT: S 40 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8748 (mp) REVERT: S 164 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8700 (tpt90) REVERT: U 35 GLU cc_start: 0.8416 (pt0) cc_final: 0.8198 (tt0) REVERT: U 55 ASP cc_start: 0.8669 (t0) cc_final: 0.8428 (t0) REVERT: V 144 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8035 (mp10) outliers start: 87 outliers final: 23 residues processed: 798 average time/residue: 0.8158 time to fit residues: 765.5943 Evaluate side-chains 706 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 676 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain S residue 35 GLU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 164 ARG Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 ASP Chi-restraints excluded: chain V residue 144 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 353 optimal weight: 0.7980 chunk 258 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 433 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 385 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 244 ASN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 232 HIS ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN K 136 GLN L 101 GLN L 136 GLN M 144 GLN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 160 GLN Q 42 ASN R 160 GLN S 42 ASN S 117 HIS U 124 GLN U 160 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.112283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087058 restraints weight = 54318.052| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.97 r_work: 0.3203 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 36708 Z= 0.203 Angle : 0.595 14.664 49647 Z= 0.299 Chirality : 0.044 0.270 5770 Planarity : 0.004 0.063 6398 Dihedral : 8.402 117.361 5409 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 2.70 % Allowed : 13.61 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.12), residues: 4553 helix: 0.82 (0.11), residues: 2358 sheet: -1.68 (0.21), residues: 468 loop : -1.61 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 276 TYR 0.015 0.001 TYR A 337 PHE 0.021 0.001 PHE K 43 TRP 0.002 0.000 TRP P 174 HIS 0.005 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00464 (36680) covalent geometry : angle 0.59547 (49647) hydrogen bonds : bond 0.03696 ( 1780) hydrogen bonds : angle 4.32086 ( 5388) Misc. bond : bond 0.00272 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 678 time to evaluate : 1.469 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. REVERT: A 137 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8082 (ttt) REVERT: A 177 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8289 (ttp80) REVERT: A 218 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 320 GLU cc_start: 0.7239 (mp0) cc_final: 0.6917 (mp0) REVERT: A 378 GLU cc_start: 0.8029 (tt0) cc_final: 0.7449 (mt-10) REVERT: B 146 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7776 (t0) REVERT: B 320 GLU cc_start: 0.7964 (tp30) cc_final: 0.7663 (tp30) REVERT: B 400 LYS cc_start: 0.8303 (mppt) cc_final: 0.8018 (mppt) REVERT: B 404 GLN cc_start: 0.6752 (mt0) cc_final: 0.6430 (mp10) REVERT: C 377 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7958 (mm-30) REVERT: C 401 GLU cc_start: 0.5862 (mt-10) cc_final: 0.3775 (tt0) REVERT: D 146 ASP cc_start: 0.7271 (p0) cc_final: 0.6844 (p0) REVERT: D 190 LYS cc_start: 0.6904 (mttm) cc_final: 0.6629 (mttt) REVERT: D 347 GLU cc_start: 0.8636 (tt0) cc_final: 0.8300 (pp20) REVERT: D 400 LYS cc_start: 0.8774 (mppt) cc_final: 0.8252 (mppt) REVERT: E 128 THR cc_start: 0.4378 (OUTLIER) cc_final: 0.3924 (m) REVERT: E 166 LYS cc_start: 0.8781 (mtmp) cc_final: 0.8471 (mtmm) REVERT: E 186 ASP cc_start: 0.6684 (p0) cc_final: 0.6454 (t0) REVERT: E 263 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8264 (ttp-110) REVERT: E 291 MET cc_start: 0.6876 (tpp) cc_final: 0.6599 (mmm) REVERT: E 320 GLU cc_start: 0.7924 (pm20) cc_final: 0.7625 (pm20) REVERT: E 349 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7090 (mt-10) REVERT: E 356 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7070 (mm-30) REVERT: E 386 ASP cc_start: 0.7860 (m-30) cc_final: 0.7485 (t0) REVERT: F 218 GLU cc_start: 0.7127 (tt0) cc_final: 0.6844 (tp30) REVERT: F 301 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.6053 (pt) REVERT: F 361 GLN cc_start: 0.6156 (mm-40) cc_final: 0.5834 (mm-40) REVERT: H 38 GLU cc_start: 0.8321 (tp30) cc_final: 0.8004 (mp0) REVERT: H 144 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: K 39 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: L 144 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8326 (mp10) REVERT: M 20 ILE cc_start: 0.9218 (mt) cc_final: 0.8922 (mm) REVERT: P 35 GLU cc_start: 0.8522 (tt0) cc_final: 0.8256 (tm-30) REVERT: Q 35 GLU cc_start: 0.8528 (tt0) cc_final: 0.8298 (tp30) REVERT: R 22 GLU cc_start: 0.8426 (tt0) cc_final: 0.7876 (tm-30) REVERT: S 120 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9262 (mp) REVERT: S 164 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8756 (tpt90) REVERT: U 43 ARG cc_start: 0.8677 (ttp80) cc_final: 0.8361 (tmm160) REVERT: U 55 ASP cc_start: 0.8660 (t0) cc_final: 0.8446 (t0) REVERT: V 144 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8041 (mp10) outliers start: 102 outliers final: 38 residues processed: 736 average time/residue: 0.8204 time to fit residues: 712.5382 Evaluate side-chains 678 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 629 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 164 ARG Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 ASP Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 144 GLN Chi-restraints excluded: chain V residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 198 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 266 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS B 97 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN K 136 GLN L 101 GLN L 136 GLN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087713 restraints weight = 54575.703| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.92 r_work: 0.3219 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36708 Z= 0.172 Angle : 0.573 15.577 49647 Z= 0.288 Chirality : 0.043 0.256 5770 Planarity : 0.004 0.054 6398 Dihedral : 8.272 120.873 5409 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.75 % Allowed : 13.95 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.12), residues: 4553 helix: 1.10 (0.11), residues: 2367 sheet: -1.62 (0.22), residues: 459 loop : -1.49 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 276 TYR 0.018 0.001 TYR A 337 PHE 0.015 0.001 PHE K 43 TRP 0.001 0.000 TRP R 174 HIS 0.005 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00393 (36680) covalent geometry : angle 0.57334 (49647) hydrogen bonds : bond 0.03467 ( 1780) hydrogen bonds : angle 4.22223 ( 5388) Misc. bond : bond 0.00217 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 668 time to evaluate : 1.466 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 137 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8060 (ttt) REVERT: A 218 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 378 GLU cc_start: 0.8017 (tt0) cc_final: 0.7756 (mt-10) REVERT: B 146 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7672 (t0) REVERT: B 320 GLU cc_start: 0.7933 (tp30) cc_final: 0.7655 (tp30) REVERT: B 400 LYS cc_start: 0.8290 (mppt) cc_final: 0.7995 (mppt) REVERT: B 404 GLN cc_start: 0.6810 (mt0) cc_final: 0.6463 (mp10) REVERT: C 146 ASP cc_start: 0.8269 (t70) cc_final: 0.8015 (t70) REVERT: C 378 GLU cc_start: 0.8532 (tt0) cc_final: 0.8015 (mp0) REVERT: C 401 GLU cc_start: 0.5766 (mt-10) cc_final: 0.3817 (tt0) REVERT: D 146 ASP cc_start: 0.7187 (p0) cc_final: 0.6758 (p0) REVERT: D 347 GLU cc_start: 0.8630 (tt0) cc_final: 0.8342 (pp20) REVERT: D 377 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7914 (mm-30) REVERT: E 100 GLU cc_start: 0.6982 (mp0) cc_final: 0.6414 (pp20) REVERT: E 128 THR cc_start: 0.4231 (OUTLIER) cc_final: 0.3785 (m) REVERT: E 166 LYS cc_start: 0.8791 (mtmp) cc_final: 0.8464 (mtmm) REVERT: E 186 ASP cc_start: 0.6711 (p0) cc_final: 0.6438 (t0) REVERT: E 291 MET cc_start: 0.6910 (tpp) cc_final: 0.6684 (mmm) REVERT: E 320 GLU cc_start: 0.8137 (pm20) cc_final: 0.7857 (pm20) REVERT: E 349 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7192 (mt-10) REVERT: E 353 ASP cc_start: 0.8400 (m-30) cc_final: 0.8178 (m-30) REVERT: E 356 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7032 (mm-30) REVERT: E 386 ASP cc_start: 0.7832 (m-30) cc_final: 0.7468 (t0) REVERT: F 218 GLU cc_start: 0.7210 (tt0) cc_final: 0.6913 (tp30) REVERT: F 361 GLN cc_start: 0.6210 (mm-40) cc_final: 0.5925 (mm-40) REVERT: F 395 LYS cc_start: 0.7962 (tppt) cc_final: 0.7136 (tptt) REVERT: H 144 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: I 144 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: K 39 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: L 144 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: M 20 ILE cc_start: 0.9259 (mt) cc_final: 0.9025 (mm) REVERT: P 35 GLU cc_start: 0.8446 (tt0) cc_final: 0.8165 (tm-30) REVERT: Q 35 GLU cc_start: 0.8514 (tt0) cc_final: 0.8284 (tp30) REVERT: R 22 GLU cc_start: 0.8431 (tt0) cc_final: 0.7865 (tm-30) REVERT: S 40 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8836 (mp) REVERT: S 43 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8342 (ttp80) REVERT: S 120 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9241 (mp) REVERT: S 164 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8690 (tpt90) REVERT: U 43 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8254 (tmm160) outliers start: 104 outliers final: 38 residues processed: 721 average time/residue: 0.7788 time to fit residues: 662.6545 Evaluate side-chains 689 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 641 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain S residue 35 GLU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 162 ILE Chi-restraints excluded: chain S residue 164 ARG Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 ASP Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 247 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 324 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 443 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 416 optimal weight: 0.9990 chunk 406 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN I 136 GLN L 136 GLN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.112432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087458 restraints weight = 54590.758| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.00 r_work: 0.3210 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36708 Z= 0.175 Angle : 0.576 15.736 49647 Z= 0.289 Chirality : 0.043 0.284 5770 Planarity : 0.004 0.061 6398 Dihedral : 8.285 122.967 5408 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 2.65 % Allowed : 14.72 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.12), residues: 4553 helix: 1.25 (0.11), residues: 2364 sheet: -1.63 (0.21), residues: 466 loop : -1.40 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 276 TYR 0.018 0.001 TYR A 337 PHE 0.014 0.001 PHE C 341 TRP 0.001 0.000 TRP S 174 HIS 0.005 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00401 (36680) covalent geometry : angle 0.57582 (49647) hydrogen bonds : bond 0.03468 ( 1780) hydrogen bonds : angle 4.18465 ( 5388) Misc. bond : bond 0.00231 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 676 time to evaluate : 1.529 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 137 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8119 (ttt) REVERT: A 218 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 378 GLU cc_start: 0.8001 (tt0) cc_final: 0.7777 (mt-10) REVERT: B 146 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7804 (t0) REVERT: B 320 GLU cc_start: 0.7932 (tp30) cc_final: 0.7665 (tp30) REVERT: B 400 LYS cc_start: 0.8306 (mppt) cc_final: 0.7996 (mppt) REVERT: B 404 GLN cc_start: 0.6977 (mt0) cc_final: 0.6598 (mp10) REVERT: C 146 ASP cc_start: 0.8353 (t70) cc_final: 0.8062 (t70) REVERT: C 158 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6872 (mm-30) REVERT: C 303 GLU cc_start: 0.6798 (mp0) cc_final: 0.6591 (mp0) REVERT: C 378 GLU cc_start: 0.8519 (tt0) cc_final: 0.7922 (mp0) REVERT: C 401 GLU cc_start: 0.5845 (mt-10) cc_final: 0.3923 (tt0) REVERT: D 146 ASP cc_start: 0.7166 (p0) cc_final: 0.6740 (p0) REVERT: D 303 GLU cc_start: 0.4852 (tp30) cc_final: 0.3631 (pm20) REVERT: D 347 GLU cc_start: 0.8659 (tt0) cc_final: 0.8352 (pp20) REVERT: D 356 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7525 (mp0) REVERT: D 377 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7876 (mm-30) REVERT: D 400 LYS cc_start: 0.8571 (mppt) cc_final: 0.8353 (mppt) REVERT: E 100 GLU cc_start: 0.6940 (mp0) cc_final: 0.6334 (pp20) REVERT: E 128 THR cc_start: 0.4593 (OUTLIER) cc_final: 0.4224 (m) REVERT: E 166 LYS cc_start: 0.8798 (mtmp) cc_final: 0.8446 (mtmm) REVERT: E 186 ASP cc_start: 0.6687 (p0) cc_final: 0.6412 (t0) REVERT: E 291 MET cc_start: 0.6883 (tpp) cc_final: 0.6671 (mmm) REVERT: E 320 GLU cc_start: 0.8117 (pm20) cc_final: 0.7825 (pm20) REVERT: E 349 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7240 (mt-10) REVERT: E 353 ASP cc_start: 0.8416 (m-30) cc_final: 0.8193 (m-30) REVERT: E 356 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7038 (mm-30) REVERT: E 386 ASP cc_start: 0.7866 (m-30) cc_final: 0.7470 (t0) REVERT: F 361 GLN cc_start: 0.6249 (mm-40) cc_final: 0.5956 (mm-40) REVERT: F 395 LYS cc_start: 0.7946 (tppt) cc_final: 0.7105 (tptt) REVERT: I 187 LYS cc_start: 0.9098 (tppt) cc_final: 0.8879 (tttp) REVERT: K 39 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8532 (mp0) REVERT: L 144 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: M 20 ILE cc_start: 0.9264 (mt) cc_final: 0.9039 (mm) REVERT: O 17 THR cc_start: 0.9198 (m) cc_final: 0.8955 (t) REVERT: O 166 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: P 35 GLU cc_start: 0.8480 (tt0) cc_final: 0.8185 (tm-30) REVERT: Q 35 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: Q 58 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8937 (mtpp) REVERT: R 22 GLU cc_start: 0.8422 (tt0) cc_final: 0.7848 (tm-30) REVERT: S 40 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8836 (mp) REVERT: S 120 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9225 (mp) REVERT: S 164 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8724 (tpt90) REVERT: U 43 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8235 (tmm160) outliers start: 100 outliers final: 38 residues processed: 731 average time/residue: 0.8288 time to fit residues: 711.8765 Evaluate side-chains 674 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 626 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain S residue 35 GLU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 162 ILE Chi-restraints excluded: chain S residue 164 ARG Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 ASP Chi-restraints excluded: chain V residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 255 optimal weight: 1.9990 chunk 66 optimal weight: 0.0000 chunk 191 optimal weight: 1.9990 chunk 427 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN H 94 GLN I 136 GLN L 101 GLN L 136 GLN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS V 22 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086838 restraints weight = 54715.872| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.94 r_work: 0.3199 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36708 Z= 0.194 Angle : 0.599 15.386 49647 Z= 0.298 Chirality : 0.044 0.330 5770 Planarity : 0.004 0.049 6398 Dihedral : 8.385 125.027 5408 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 2.57 % Allowed : 15.22 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.12), residues: 4553 helix: 1.25 (0.11), residues: 2375 sheet: -1.57 (0.22), residues: 464 loop : -1.36 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 43 TYR 0.019 0.001 TYR C 337 PHE 0.021 0.001 PHE A 70 TRP 0.001 0.000 TRP S 174 HIS 0.005 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00445 (36680) covalent geometry : angle 0.59851 (49647) hydrogen bonds : bond 0.03547 ( 1780) hydrogen bonds : angle 4.21978 ( 5388) Misc. bond : bond 0.00263 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 650 time to evaluate : 1.433 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 137 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8144 (ttt) REVERT: A 218 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7818 (mm-30) REVERT: A 378 GLU cc_start: 0.8057 (tt0) cc_final: 0.7832 (mt-10) REVERT: B 146 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7838 (t0) REVERT: B 320 GLU cc_start: 0.7940 (tp30) cc_final: 0.7671 (tp30) REVERT: B 400 LYS cc_start: 0.8340 (mppt) cc_final: 0.8023 (mppt) REVERT: B 404 GLN cc_start: 0.7009 (mt0) cc_final: 0.6637 (mp10) REVERT: C 146 ASP cc_start: 0.8314 (t70) cc_final: 0.8018 (t70) REVERT: C 303 GLU cc_start: 0.6838 (mp0) cc_final: 0.6496 (mp0) REVERT: C 378 GLU cc_start: 0.8545 (tt0) cc_final: 0.8001 (mp0) REVERT: C 401 GLU cc_start: 0.5903 (mt-10) cc_final: 0.3958 (tt0) REVERT: D 146 ASP cc_start: 0.7178 (p0) cc_final: 0.6752 (p0) REVERT: D 303 GLU cc_start: 0.4808 (tp30) cc_final: 0.4168 (mm-30) REVERT: D 356 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7558 (mp0) REVERT: D 377 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7948 (mm-30) REVERT: E 128 THR cc_start: 0.4809 (OUTLIER) cc_final: 0.4443 (m) REVERT: E 166 LYS cc_start: 0.8834 (mtmp) cc_final: 0.8511 (mtmp) REVERT: E 186 ASP cc_start: 0.6699 (p0) cc_final: 0.6386 (t0) REVERT: E 220 THR cc_start: 0.8578 (t) cc_final: 0.8356 (p) REVERT: E 291 MET cc_start: 0.6914 (tpp) cc_final: 0.6694 (mmm) REVERT: E 320 GLU cc_start: 0.8111 (pm20) cc_final: 0.7816 (pm20) REVERT: E 353 ASP cc_start: 0.8443 (m-30) cc_final: 0.8215 (m-30) REVERT: E 356 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7087 (mm-30) REVERT: E 386 ASP cc_start: 0.7867 (m-30) cc_final: 0.7492 (t0) REVERT: F 303 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5912 (mp0) REVERT: F 361 GLN cc_start: 0.6301 (mm-40) cc_final: 0.6055 (mm-40) REVERT: H 144 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8305 (mp10) REVERT: I 144 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: I 187 LYS cc_start: 0.9099 (tppt) cc_final: 0.8889 (tttp) REVERT: K 39 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: L 144 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: L 207 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7848 (ptt-90) REVERT: O 17 THR cc_start: 0.9200 (m) cc_final: 0.8993 (t) REVERT: O 166 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: P 35 GLU cc_start: 0.8507 (tt0) cc_final: 0.8226 (tm-30) REVERT: Q 35 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8304 (tp30) REVERT: Q 58 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8959 (mtpp) REVERT: R 22 GLU cc_start: 0.8434 (tt0) cc_final: 0.7901 (tm-30) REVERT: S 40 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8865 (mp) REVERT: S 58 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8943 (mttt) REVERT: S 109 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8622 (mptp) REVERT: S 120 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9235 (mp) REVERT: S 164 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8730 (tpt90) REVERT: U 43 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8358 (tmm160) REVERT: U 58 LYS cc_start: 0.9119 (mttm) cc_final: 0.8886 (mtpt) outliers start: 97 outliers final: 40 residues processed: 701 average time/residue: 0.7836 time to fit residues: 647.1062 Evaluate side-chains 675 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 621 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain S residue 35 GLU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 58 LYS Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 162 ILE Chi-restraints excluded: chain S residue 164 ARG Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 ASP Chi-restraints excluded: chain V residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 213 optimal weight: 0.6980 chunk 255 optimal weight: 0.7980 chunk 280 optimal weight: 0.7980 chunk 318 optimal weight: 2.9990 chunk 157 optimal weight: 0.0020 chunk 234 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 365 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN I 136 GLN L 136 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN V 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.113181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088151 restraints weight = 54586.329| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.04 r_work: 0.3222 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36708 Z= 0.146 Angle : 0.583 15.097 49647 Z= 0.292 Chirality : 0.043 0.302 5770 Planarity : 0.004 0.075 6398 Dihedral : 8.231 126.100 5408 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 2.12 % Allowed : 16.26 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.12), residues: 4553 helix: 1.38 (0.11), residues: 2374 sheet: -1.56 (0.22), residues: 464 loop : -1.28 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 276 TYR 0.020 0.001 TYR C 337 PHE 0.029 0.001 PHE B 237 TRP 0.001 0.000 TRP S 174 HIS 0.005 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00333 (36680) covalent geometry : angle 0.58313 (49647) hydrogen bonds : bond 0.03298 ( 1780) hydrogen bonds : angle 4.15022 ( 5388) Misc. bond : bond 0.00243 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 653 time to evaluate : 1.601 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 377 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 378 GLU cc_start: 0.8023 (tt0) cc_final: 0.7759 (mt-10) REVERT: B 146 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7833 (t0) REVERT: B 320 GLU cc_start: 0.7936 (tp30) cc_final: 0.7671 (tp30) REVERT: B 400 LYS cc_start: 0.8323 (mppt) cc_final: 0.8002 (mppt) REVERT: B 404 GLN cc_start: 0.6994 (mt0) cc_final: 0.6608 (mp10) REVERT: C 146 ASP cc_start: 0.8316 (t70) cc_final: 0.8042 (t70) REVERT: C 158 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6864 (mm-30) REVERT: C 303 GLU cc_start: 0.6819 (mp0) cc_final: 0.6486 (mp0) REVERT: C 378 GLU cc_start: 0.8516 (tt0) cc_final: 0.7988 (mp0) REVERT: C 401 GLU cc_start: 0.5833 (mt-10) cc_final: 0.4013 (tt0) REVERT: D 146 ASP cc_start: 0.7109 (p0) cc_final: 0.6677 (p0) REVERT: D 303 GLU cc_start: 0.4837 (tp30) cc_final: 0.3777 (mp0) REVERT: D 356 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7549 (mp0) REVERT: E 128 THR cc_start: 0.4582 (OUTLIER) cc_final: 0.4171 (m) REVERT: E 166 LYS cc_start: 0.8830 (mtmp) cc_final: 0.8508 (mtmp) REVERT: E 186 ASP cc_start: 0.6644 (p0) cc_final: 0.6391 (t0) REVERT: E 220 THR cc_start: 0.8568 (t) cc_final: 0.8353 (p) REVERT: E 320 GLU cc_start: 0.8103 (pm20) cc_final: 0.7790 (pm20) REVERT: E 353 ASP cc_start: 0.8435 (m-30) cc_final: 0.8207 (m-30) REVERT: E 356 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6991 (mm-30) REVERT: E 386 ASP cc_start: 0.7841 (m-30) cc_final: 0.7449 (t0) REVERT: F 361 GLN cc_start: 0.6281 (mm-40) cc_final: 0.6069 (mm-40) REVERT: H 144 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8279 (mp10) REVERT: I 29 GLU cc_start: 0.8027 (tt0) cc_final: 0.7596 (tp30) REVERT: I 187 LYS cc_start: 0.9097 (tppt) cc_final: 0.8885 (tttp) REVERT: K 144 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: L 144 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: L 207 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7835 (ptt-90) REVERT: P 35 GLU cc_start: 0.8437 (tt0) cc_final: 0.8157 (tm-30) REVERT: Q 35 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: Q 58 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8936 (mtpp) REVERT: R 22 GLU cc_start: 0.8432 (tt0) cc_final: 0.7894 (tm-30) REVERT: S 40 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8847 (mp) REVERT: S 58 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8931 (mttt) REVERT: S 164 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8701 (tpt90) REVERT: U 43 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8358 (tmm160) REVERT: U 58 LYS cc_start: 0.9116 (mttm) cc_final: 0.8891 (mtpt) outliers start: 80 outliers final: 37 residues processed: 699 average time/residue: 0.8331 time to fit residues: 688.0685 Evaluate side-chains 670 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 624 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 58 LYS Chi-restraints excluded: chain S residue 164 ARG Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 ASP Chi-restraints excluded: chain V residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 222 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 228 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 279 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 306 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 313 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN L 101 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN V 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088992 restraints weight = 54534.210| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.99 r_work: 0.3237 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36708 Z= 0.143 Angle : 0.585 16.165 49647 Z= 0.293 Chirality : 0.043 0.352 5770 Planarity : 0.004 0.043 6398 Dihedral : 8.093 127.603 5408 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.83 % Allowed : 16.65 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.12), residues: 4553 helix: 1.48 (0.11), residues: 2369 sheet: -1.46 (0.22), residues: 470 loop : -1.21 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 207 TYR 0.021 0.001 TYR C 337 PHE 0.021 0.001 PHE I 25 TRP 0.001 0.000 TRP O 174 HIS 0.004 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00324 (36680) covalent geometry : angle 0.58491 (49647) hydrogen bonds : bond 0.03237 ( 1780) hydrogen bonds : angle 4.11457 ( 5388) Misc. bond : bond 0.00259 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 650 time to evaluate : 1.606 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 378 GLU cc_start: 0.7965 (tt0) cc_final: 0.7744 (mt-10) REVERT: B 146 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7810 (t0) REVERT: B 320 GLU cc_start: 0.7907 (tp30) cc_final: 0.7641 (tp30) REVERT: B 400 LYS cc_start: 0.8309 (mppt) cc_final: 0.7959 (mppt) REVERT: B 404 GLN cc_start: 0.7034 (mt0) cc_final: 0.6617 (mp10) REVERT: C 146 ASP cc_start: 0.8304 (t70) cc_final: 0.8002 (t70) REVERT: C 158 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6824 (mm-30) REVERT: C 303 GLU cc_start: 0.6774 (mp0) cc_final: 0.6431 (mp0) REVERT: C 378 GLU cc_start: 0.8438 (tt0) cc_final: 0.7995 (mp0) REVERT: C 401 GLU cc_start: 0.5790 (mt-10) cc_final: 0.4051 (tt0) REVERT: D 146 ASP cc_start: 0.7102 (p0) cc_final: 0.6674 (p0) REVERT: D 303 GLU cc_start: 0.4795 (tp30) cc_final: 0.4257 (mm-30) REVERT: D 347 GLU cc_start: 0.8683 (tt0) cc_final: 0.8370 (pp20) REVERT: D 356 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7501 (mp0) REVERT: E 128 THR cc_start: 0.4970 (OUTLIER) cc_final: 0.4620 (m) REVERT: E 166 LYS cc_start: 0.8803 (mtmp) cc_final: 0.8475 (mtmp) REVERT: E 186 ASP cc_start: 0.6654 (p0) cc_final: 0.6405 (t0) REVERT: E 220 THR cc_start: 0.8569 (t) cc_final: 0.8358 (p) REVERT: E 320 GLU cc_start: 0.8064 (pm20) cc_final: 0.7778 (pm20) REVERT: E 356 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6953 (mm-30) REVERT: F 137 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8388 (ttp) REVERT: F 377 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7146 (mm-30) REVERT: F 401 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7373 (tm-30) REVERT: H 144 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: I 187 LYS cc_start: 0.9097 (tppt) cc_final: 0.8884 (tttp) REVERT: K 144 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: L 144 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: L 207 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7732 (ptt180) REVERT: P 35 GLU cc_start: 0.8425 (tt0) cc_final: 0.8125 (tm-30) REVERT: Q 35 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8202 (tp30) REVERT: Q 58 LYS cc_start: 0.9141 (mtmm) cc_final: 0.8924 (mtpp) REVERT: R 22 GLU cc_start: 0.8395 (tt0) cc_final: 0.7839 (tm-30) REVERT: S 40 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8845 (mp) REVERT: S 164 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8666 (tpt90) REVERT: U 43 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8340 (tmm160) REVERT: V 50 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8175 (t0) outliers start: 69 outliers final: 36 residues processed: 689 average time/residue: 0.7719 time to fit residues: 630.1508 Evaluate side-chains 683 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 637 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 164 ARG Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 ASP Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 9 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 411 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 436 optimal weight: 0.9980 chunk 387 optimal weight: 0.9990 chunk 267 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 399 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN L 101 GLN L 136 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 136 GLN V 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087558 restraints weight = 54497.331| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.00 r_work: 0.3210 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36708 Z= 0.184 Angle : 0.612 15.615 49647 Z= 0.305 Chirality : 0.044 0.337 5770 Planarity : 0.004 0.054 6398 Dihedral : 8.179 128.647 5408 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 1.54 % Allowed : 17.10 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.12), residues: 4553 helix: 1.43 (0.11), residues: 2371 sheet: -1.58 (0.21), residues: 484 loop : -1.17 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 207 TYR 0.018 0.001 TYR C 337 PHE 0.021 0.001 PHE I 25 TRP 0.001 0.000 TRP Q 174 HIS 0.005 0.001 HIS L 171 Details of bonding type rmsd covalent geometry : bond 0.00423 (36680) covalent geometry : angle 0.61153 (49647) hydrogen bonds : bond 0.03444 ( 1780) hydrogen bonds : angle 4.16083 ( 5388) Misc. bond : bond 0.00275 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9106 Ramachandran restraints generated. 4553 Oldfield, 0 Emsley, 4553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 633 time to evaluate : 1.483 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 410 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL E 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE K 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER K 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER L 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 378 GLU cc_start: 0.8038 (tt0) cc_final: 0.7821 (mt-10) REVERT: B 146 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7781 (t0) REVERT: B 320 GLU cc_start: 0.7914 (tp30) cc_final: 0.7645 (tp30) REVERT: B 400 LYS cc_start: 0.8316 (mppt) cc_final: 0.7950 (mppt) REVERT: B 404 GLN cc_start: 0.7128 (mt0) cc_final: 0.6702 (mp10) REVERT: C 146 ASP cc_start: 0.8324 (t70) cc_final: 0.8017 (t70) REVERT: C 158 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6838 (mm-30) REVERT: C 303 GLU cc_start: 0.6789 (mp0) cc_final: 0.6450 (mp0) REVERT: C 378 GLU cc_start: 0.8471 (tt0) cc_final: 0.8078 (mp0) REVERT: C 401 GLU cc_start: 0.5900 (mt-10) cc_final: 0.4133 (tt0) REVERT: D 146 ASP cc_start: 0.7137 (p0) cc_final: 0.6702 (p0) REVERT: D 303 GLU cc_start: 0.4786 (tp30) cc_final: 0.4149 (mm-30) REVERT: D 347 GLU cc_start: 0.8690 (tt0) cc_final: 0.8375 (pp20) REVERT: D 356 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7558 (mp0) REVERT: E 128 THR cc_start: 0.5165 (OUTLIER) cc_final: 0.4803 (m) REVERT: E 166 LYS cc_start: 0.8813 (mtmp) cc_final: 0.8476 (mtmp) REVERT: E 186 ASP cc_start: 0.6635 (p0) cc_final: 0.6338 (t0) REVERT: E 220 THR cc_start: 0.8586 (t) cc_final: 0.8357 (p) REVERT: E 263 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8038 (ttp-110) REVERT: E 320 GLU cc_start: 0.8057 (pm20) cc_final: 0.7738 (pm20) REVERT: E 356 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6983 (mm-30) REVERT: F 137 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8215 (ttp) REVERT: F 395 LYS cc_start: 0.7788 (tptt) cc_final: 0.7201 (tptt) REVERT: F 401 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7073 (tp30) REVERT: H 144 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: I 144 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: K 144 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: L 144 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: L 207 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7813 (ptt-90) REVERT: N 28 LYS cc_start: 0.7887 (ptpt) cc_final: 0.7686 (pttt) REVERT: P 35 GLU cc_start: 0.8457 (tt0) cc_final: 0.8158 (tm-30) REVERT: Q 35 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: Q 58 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8933 (mtpp) REVERT: R 22 GLU cc_start: 0.8413 (tt0) cc_final: 0.7856 (tm-30) REVERT: S 40 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8858 (mp) REVERT: S 120 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9178 (mt) REVERT: S 164 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8700 (tpt90) REVERT: U 43 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8338 (tmm160) outliers start: 58 outliers final: 35 residues processed: 666 average time/residue: 0.7481 time to fit residues: 589.7871 Evaluate side-chains 651 residues out of total 3777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 605 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 164 ARG Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 ASP Chi-restraints excluded: chain V residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 308 optimal weight: 0.8980 chunk 156 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 415 optimal weight: 0.8980 chunk 259 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 262 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 chunk 332 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN L 136 GLN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 136 GLN V 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.114186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088997 restraints weight = 53938.289| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.97 r_work: 0.3231 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36708 Z= 0.150 Angle : 0.594 15.667 49647 Z= 0.296 Chirality : 0.043 0.317 5770 Planarity : 0.004 0.051 6398 Dihedral : 8.099 129.053 5408 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 1.51 % Allowed : 17.37 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.13), residues: 4553 helix: 1.50 (0.11), residues: 2367 sheet: -1.48 (0.22), residues: 476 loop : -1.17 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 207 TYR 0.018 0.001 TYR C 337 PHE 0.019 0.001 PHE A 70 TRP 0.001 0.000 TRP Q 174 HIS 0.005 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00345 (36680) covalent geometry : angle 0.59363 (49647) hydrogen bonds : bond 0.03271 ( 1780) hydrogen bonds : angle 4.12319 ( 5388) Misc. bond : bond 0.00247 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19686.44 seconds wall clock time: 334 minutes 21.18 seconds (20061.18 seconds total)