Starting phenix.real_space_refine on Mon May 4 03:33:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duv_47180/05_2026/9duv_47180_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duv_47180/05_2026/9duv_47180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9duv_47180/05_2026/9duv_47180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duv_47180/05_2026/9duv_47180.map" model { file = "/net/cci-nas-00/data/ceres_data/9duv_47180/05_2026/9duv_47180_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duv_47180/05_2026/9duv_47180_neut.cif" } resolution = 3.3 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= 0.003 sd= 0.103 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 133 5.16 5 C 11327 2.51 5 N 3014 2.21 5 O 3455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17947 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" 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: "B" 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: "C" 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: "D" 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: "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: 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} Time building chain proxies: 4.72, per 1000 atoms: 0.26 Number of scatterers: 17947 At special positions: 0 Unit cell: (79.328, 98.272, 220.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 12 15.00 Mg 6 11.99 O 3455 8.00 N 3014 7.00 C 11327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP M 1 " - " ALA M 7 " " DTH M 4 " - " ALA M 3 " " TRP N 1 " - " ALA N 7 " " DTH N 4 " - " ALA N 3 " " TRP O 1 " - " ALA O 7 " " DTH O 4 " - " ALA O 3 " " TRP P 1 " - " ALA P 7 " " DTH P 4 " - " ALA P 3 " " TRP Q 1 " - " ALA Q 7 " " DTH Q 4 " - " ALA Q 3 " " TRP R 1 " - " ALA R 7 " " DTH R 4 " - " ALA R 3 " " TRP S 1 " - " ALA S 7 " " DTH S 4 " - " ALA S 3 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 789.9 milliseconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH M 4 " pdb=" CB DTH N 4 " pdb=" CB DTH O 4 " pdb=" CB DTH P 4 " pdb=" CB DTH Q 4 " pdb=" CB DTH R 4 " pdb=" CB DTH S 4 " Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 35 sheets defined 46.9% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.661A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.528A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.646A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.678A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.596A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.506A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 257 through 261 removed outlier: 3.502A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.542A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.578A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.729A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.753A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.505A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.584A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.511A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.772A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 251 through 255 removed outlier: 4.196A pdb=" N HIS C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.604A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 removed outlier: 4.042A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.681A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.569A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.563A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.543A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 251 through 255 removed outlier: 4.121A pdb=" N HIS D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 255' Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.578A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.843A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.680A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 232 Processing helix chain 'E' and resid 257 through 261 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.503A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 296 removed outlier: 3.795A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.683A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.761A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.778A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.549A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.539A pdb=" N GLY F 146 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 232 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 296 removed outlier: 4.046A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 removed outlier: 3.568A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.598A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.573A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.636A pdb=" N HIS F 371 " --> pdb=" O SER F 368 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.491A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.529A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.529A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.378A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.525A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.393A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.664A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.664A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.407A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.605A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.605A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.492A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC8, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.554A pdb=" N TYR E 166 " --> pdb=" O TYR E 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.554A pdb=" N TYR E 166 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS E 161 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.539A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AD5, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.648A pdb=" N TYR F 166 " --> pdb=" O TYR F 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.648A pdb=" N TYR F 166 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS F 161 " --> pdb=" O ASP F 154 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 238 through 241 815 hydrogen bonds defined for protein. 2076 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: 3.14 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3253 1.33 - 1.45: 4593 1.45 - 1.57: 10251 1.57 - 1.69: 18 1.69 - 1.81: 229 Bond restraints: 18344 Sorted by residual: bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 ... (remaining 18339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 24467 2.90 - 5.81: 345 5.81 - 8.71: 65 8.71 - 11.62: 22 11.62 - 14.52: 12 Bond angle restraints: 24911 Sorted by residual: angle pdb=" N THR E 303 " pdb=" CA THR E 303 " pdb=" C THR E 303 " ideal model delta sigma weight residual 113.01 104.28 8.73 1.20e+00 6.94e-01 5.29e+01 angle pdb=" N THR B 303 " pdb=" CA THR B 303 " pdb=" C THR B 303 " ideal model delta sigma weight residual 111.82 104.12 7.70 1.16e+00 7.43e-01 4.40e+01 angle pdb=" N THR C 303 " pdb=" CA THR C 303 " pdb=" C THR C 303 " ideal model delta sigma weight residual 111.14 105.32 5.82 1.08e+00 8.57e-01 2.90e+01 angle pdb=" N THR D 303 " pdb=" CA THR D 303 " pdb=" C THR D 303 " ideal model delta sigma weight residual 111.40 104.99 6.41 1.22e+00 6.72e-01 2.76e+01 angle pdb=" N THR E 304 " pdb=" CA THR E 304 " pdb=" C THR E 304 " ideal model delta sigma weight residual 113.17 106.65 6.52 1.26e+00 6.30e-01 2.67e+01 ... (remaining 24906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.98: 10194 28.98 - 57.95: 785 57.95 - 86.93: 42 86.93 - 115.90: 9 115.90 - 144.88: 12 Dihedral angle restraints: 11042 sinusoidal: 4477 harmonic: 6565 Sorted by residual: dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.87 -144.88 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 80.68 -140.68 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 80.57 -140.58 1 2.00e+01 2.50e-03 4.25e+01 ... (remaining 11039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1882 0.038 - 0.076: 572 0.076 - 0.113: 282 0.113 - 0.151: 24 0.151 - 0.189: 16 Chirality restraints: 2776 Sorted by residual: chirality pdb=" CA CYS Q 5 " pdb=" N CYS Q 5 " pdb=" C CYS Q 5 " pdb=" CB CYS Q 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CA CYS S 5 " pdb=" N CYS S 5 " pdb=" C CYS S 5 " pdb=" CB CYS S 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CA CYS N 5 " pdb=" N CYS N 5 " pdb=" C CYS N 5 " pdb=" CB CYS N 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 2773 not shown) Planarity restraints: 3170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 366 " -0.084 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO C 367 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 300 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C SER D 300 " -0.070 2.00e-02 2.50e+03 pdb=" O SER D 300 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY D 301 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 300 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C SER C 300 " 0.065 2.00e-02 2.50e+03 pdb=" O SER C 300 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C 301 " -0.021 2.00e-02 2.50e+03 ... (remaining 3167 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 89 2.38 - 3.01: 9932 3.01 - 3.64: 26582 3.64 - 4.27: 40509 4.27 - 4.90: 69998 Nonbonded interactions: 147110 Sorted by model distance: nonbonded pdb=" CD1 TRP N 1 " pdb=" SG CYS N 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP S 1 " pdb=" SG CYS S 5 " model vdw 1.753 3.620 nonbonded pdb=" CD1 TRP R 1 " pdb=" SG CYS R 5 " model vdw 1.753 3.620 nonbonded pdb=" CD1 TRP P 1 " pdb=" SG CYS P 5 " model vdw 1.753 3.620 nonbonded pdb=" CD1 TRP O 1 " pdb=" SG CYS O 5 " model vdw 1.753 3.620 ... (remaining 147105 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 6.560 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.110 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 18358 Z= 0.291 Angle : 0.882 14.521 24953 Z= 0.431 Chirality : 0.046 0.189 2776 Planarity : 0.004 0.127 3156 Dihedral : 18.943 144.876 6800 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.01 % Favored : 94.81 % Rotamer: Outliers : 1.06 % Allowed : 30.92 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.26 (0.19), residues: 2196 helix: 0.67 (0.18), residues: 942 sheet: -0.10 (0.32), residues: 288 loop : -0.10 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.011 0.001 TYR B 337 PHE 0.014 0.001 PHE F 124 TRP 0.012 0.002 TRP O 1 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00577 (18344) covalent geometry : angle 0.86985 (24911) hydrogen bonds : bond 0.20536 ( 808) hydrogen bonds : angle 7.08463 ( 2076) link_TRANS : bond 0.00377 ( 14) link_TRANS : angle 3.72474 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8954 (ttp) cc_final: 0.8646 (ttp) REVERT: C 350 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8872 (t) REVERT: D 227 MET cc_start: 0.7815 (mmm) cc_final: 0.7496 (tpp) REVERT: F 283 MET cc_start: 0.8049 (mmm) cc_final: 0.7824 (mmt) outliers start: 20 outliers final: 15 residues processed: 207 average time/residue: 0.1110 time to fit residues: 38.5550 Evaluate side-chains 203 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain M residue 5 CYS Chi-restraints excluded: chain N residue 5 CYS Chi-restraints excluded: chain O residue 5 CYS Chi-restraints excluded: chain P residue 5 CYS Chi-restraints excluded: chain Q residue 5 CYS Chi-restraints excluded: chain R residue 5 CYS Chi-restraints excluded: chain S residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.0040 chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.095183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.082429 restraints weight = 23972.172| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.89 r_work: 0.3023 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18358 Z= 0.112 Angle : 0.594 7.403 24953 Z= 0.279 Chirality : 0.045 0.204 2776 Planarity : 0.004 0.092 3156 Dihedral : 11.911 145.070 2636 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.22 % Allowed : 27.59 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 2196 helix: 0.83 (0.18), residues: 936 sheet: 0.14 (0.33), residues: 282 loop : 0.36 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.008 0.001 TYR B 306 PHE 0.013 0.001 PHE A 255 TRP 0.019 0.002 TRP M 1 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00240 (18344) covalent geometry : angle 0.59440 (24911) hydrogen bonds : bond 0.03620 ( 808) hydrogen bonds : angle 5.36602 ( 2076) link_TRANS : bond 0.00280 ( 14) link_TRANS : angle 0.60692 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 0.711 Fit side-chains REVERT: A 132 MET cc_start: 0.8658 (ttp) cc_final: 0.8080 (ttp) REVERT: C 225 ASN cc_start: 0.8932 (t0) cc_final: 0.8485 (t0) REVERT: C 325 MET cc_start: 0.7993 (tpt) cc_final: 0.7152 (tpt) outliers start: 61 outliers final: 30 residues processed: 260 average time/residue: 0.1122 time to fit residues: 48.8816 Evaluate side-chains 228 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 124 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 131 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 125 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 174 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092842 restraints weight = 24316.809| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.40 r_work: 0.2971 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18358 Z= 0.136 Angle : 0.595 8.087 24953 Z= 0.276 Chirality : 0.046 0.227 2776 Planarity : 0.004 0.071 3156 Dihedral : 10.799 132.065 2622 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.75 % Allowed : 27.64 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.67 (0.19), residues: 2196 helix: 0.92 (0.18), residues: 930 sheet: -0.16 (0.31), residues: 312 loop : 0.38 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.008 0.001 TYR B 198 PHE 0.012 0.001 PHE E 255 TRP 0.009 0.001 TRP F 79 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00319 (18344) covalent geometry : angle 0.59466 (24911) hydrogen bonds : bond 0.03526 ( 808) hydrogen bonds : angle 4.96811 ( 2076) link_TRANS : bond 0.00172 ( 14) link_TRANS : angle 0.51179 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.539 Fit side-chains REVERT: A 124 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7827 (t80) REVERT: C 124 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: C 132 MET cc_start: 0.8962 (tmm) cc_final: 0.8753 (ttp) REVERT: C 225 ASN cc_start: 0.8757 (t0) cc_final: 0.8417 (t0) REVERT: C 270 GLU cc_start: 0.9079 (tp30) cc_final: 0.8804 (tp30) REVERT: D 227 MET cc_start: 0.7878 (tpp) cc_final: 0.7605 (tpp) REVERT: D 337 TYR cc_start: 0.8730 (m-80) cc_final: 0.8458 (m-80) REVERT: E 283 MET cc_start: 0.8308 (mmm) cc_final: 0.8105 (mmm) outliers start: 52 outliers final: 33 residues processed: 238 average time/residue: 0.1062 time to fit residues: 42.4574 Evaluate side-chains 232 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 124 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 189 optimal weight: 0.0050 chunk 10 optimal weight: 0.0770 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 0.0170 chunk 148 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.090482 restraints weight = 24541.765| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.39 r_work: 0.2956 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18358 Z= 0.146 Angle : 0.589 8.023 24953 Z= 0.272 Chirality : 0.046 0.233 2776 Planarity : 0.004 0.058 3156 Dihedral : 10.568 126.282 2622 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.80 % Allowed : 27.27 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.66 (0.19), residues: 2196 helix: 0.85 (0.18), residues: 942 sheet: -0.21 (0.31), residues: 312 loop : 0.46 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 116 TYR 0.006 0.001 TYR E 143 PHE 0.013 0.001 PHE F 255 TRP 0.008 0.001 TRP F 79 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00348 (18344) covalent geometry : angle 0.58952 (24911) hydrogen bonds : bond 0.03262 ( 808) hydrogen bonds : angle 4.86484 ( 2076) link_TRANS : bond 0.00146 ( 14) link_TRANS : angle 0.43419 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7899 (t80) REVERT: B 203 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7790 (m) REVERT: C 225 ASN cc_start: 0.8806 (t0) cc_final: 0.8452 (t0) REVERT: C 270 GLU cc_start: 0.9087 (tp30) cc_final: 0.8809 (tp30) REVERT: D 227 MET cc_start: 0.7984 (tpp) cc_final: 0.7674 (tpp) REVERT: F 203 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7588 (m) outliers start: 53 outliers final: 43 residues processed: 237 average time/residue: 0.1042 time to fit residues: 41.7093 Evaluate side-chains 241 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 166 optimal weight: 0.9980 chunk 209 optimal weight: 0.0170 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 189 optimal weight: 0.0670 chunk 150 optimal weight: 0.0050 chunk 180 optimal weight: 0.0060 chunk 61 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095708 restraints weight = 23504.017| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.35 r_work: 0.2998 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18358 Z= 0.084 Angle : 0.544 7.144 24953 Z= 0.249 Chirality : 0.043 0.221 2776 Planarity : 0.004 0.049 3156 Dihedral : 9.847 125.241 2622 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.22 % Allowed : 27.54 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 2196 helix: 1.07 (0.18), residues: 942 sheet: -0.04 (0.28), residues: 372 loop : 0.51 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.008 0.001 TYR B 337 PHE 0.012 0.001 PHE F 255 TRP 0.008 0.001 TRP B 79 HIS 0.002 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00177 (18344) covalent geometry : angle 0.54491 (24911) hydrogen bonds : bond 0.02641 ( 808) hydrogen bonds : angle 4.65492 ( 2076) link_TRANS : bond 0.00056 ( 14) link_TRANS : angle 0.17794 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.683 Fit side-chains REVERT: A 124 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7860 (t80) REVERT: B 203 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7535 (m) REVERT: B 225 ASN cc_start: 0.8919 (t0) cc_final: 0.8263 (t0) REVERT: C 82 MET cc_start: 0.8393 (tpt) cc_final: 0.7979 (tpt) REVERT: C 124 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: C 132 MET cc_start: 0.8872 (tmm) cc_final: 0.8612 (ttp) REVERT: C 225 ASN cc_start: 0.8717 (t0) cc_final: 0.8376 (t0) REVERT: C 325 MET cc_start: 0.7800 (tpt) cc_final: 0.7158 (tpt) REVERT: D 227 MET cc_start: 0.7916 (tpp) cc_final: 0.7536 (tpp) REVERT: D 337 TYR cc_start: 0.8677 (m-80) cc_final: 0.8410 (m-80) REVERT: E 178 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7808 (tp) REVERT: E 222 ASP cc_start: 0.7204 (p0) cc_final: 0.6994 (p0) outliers start: 61 outliers final: 45 residues processed: 257 average time/residue: 0.1051 time to fit residues: 46.1386 Evaluate side-chains 245 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 28 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 195 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.091708 restraints weight = 24193.070| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.36 r_work: 0.2965 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18358 Z= 0.169 Angle : 0.601 7.815 24953 Z= 0.278 Chirality : 0.047 0.238 2776 Planarity : 0.004 0.039 3156 Dihedral : 9.806 124.519 2622 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.54 % Allowed : 27.48 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 2196 helix: 0.92 (0.18), residues: 948 sheet: -0.22 (0.30), residues: 312 loop : 0.48 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 116 TYR 0.007 0.001 TYR E 143 PHE 0.014 0.001 PHE F 255 TRP 0.009 0.002 TRP D 79 HIS 0.004 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00406 (18344) covalent geometry : angle 0.60114 (24911) hydrogen bonds : bond 0.03224 ( 808) hydrogen bonds : angle 4.70412 ( 2076) link_TRANS : bond 0.00154 ( 14) link_TRANS : angle 0.48718 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7914 (t80) REVERT: B 225 ASN cc_start: 0.8859 (t0) cc_final: 0.8216 (t0) REVERT: C 16 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7894 (mp) REVERT: C 225 ASN cc_start: 0.8792 (t0) cc_final: 0.8447 (t0) REVERT: D 227 MET cc_start: 0.7903 (tpp) cc_final: 0.7480 (tpp) REVERT: E 178 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7902 (tp) REVERT: F 203 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7519 (m) outliers start: 67 outliers final: 54 residues processed: 241 average time/residue: 0.1046 time to fit residues: 42.9076 Evaluate side-chains 252 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 127 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 214 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.089960 restraints weight = 24744.282| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.33 r_work: 0.2962 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18358 Z= 0.150 Angle : 0.590 8.067 24953 Z= 0.272 Chirality : 0.046 0.240 2776 Planarity : 0.004 0.039 3156 Dihedral : 9.426 123.224 2620 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.49 % Allowed : 27.22 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 2196 helix: 0.90 (0.18), residues: 948 sheet: -0.32 (0.30), residues: 312 loop : 0.45 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.007 0.001 TYR E 143 PHE 0.014 0.001 PHE F 255 TRP 0.010 0.001 TRP P 1 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00361 (18344) covalent geometry : angle 0.59066 (24911) hydrogen bonds : bond 0.03109 ( 808) hydrogen bonds : angle 4.70109 ( 2076) link_TRANS : bond 0.00133 ( 14) link_TRANS : angle 0.38303 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 191 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.8041 (tpp) REVERT: A 124 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7975 (t80) REVERT: B 225 ASN cc_start: 0.8915 (t0) cc_final: 0.8272 (t0) REVERT: C 16 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 132 MET cc_start: 0.8977 (tmm) cc_final: 0.8571 (ttp) REVERT: C 225 ASN cc_start: 0.8830 (t0) cc_final: 0.8478 (t0) REVERT: D 227 MET cc_start: 0.7982 (tpp) cc_final: 0.7637 (mmm) REVERT: E 178 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7943 (tp) REVERT: F 123 MET cc_start: 0.7728 (ttp) cc_final: 0.7499 (ttm) REVERT: F 203 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7595 (m) outliers start: 66 outliers final: 55 residues processed: 236 average time/residue: 0.1061 time to fit residues: 42.6846 Evaluate side-chains 249 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 219 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 0.2980 chunk 214 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.091659 restraints weight = 24199.345| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.36 r_work: 0.2965 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18358 Z= 0.131 Angle : 0.581 8.026 24953 Z= 0.267 Chirality : 0.046 0.239 2776 Planarity : 0.004 0.039 3156 Dihedral : 9.094 121.865 2620 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.54 % Allowed : 27.22 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 2196 helix: 0.93 (0.18), residues: 948 sheet: -0.34 (0.30), residues: 312 loop : 0.46 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.009 0.001 TYR B 337 PHE 0.014 0.001 PHE F 255 TRP 0.009 0.001 TRP P 1 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00312 (18344) covalent geometry : angle 0.58107 (24911) hydrogen bonds : bond 0.02989 ( 808) hydrogen bonds : angle 4.66646 ( 2076) link_TRANS : bond 0.00107 ( 14) link_TRANS : angle 0.34933 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7997 (tpp) REVERT: A 124 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7904 (t80) REVERT: B 225 ASN cc_start: 0.8832 (t0) cc_final: 0.8191 (t0) REVERT: C 16 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7877 (mp) REVERT: C 132 MET cc_start: 0.8908 (tmm) cc_final: 0.8493 (ttp) REVERT: D 227 MET cc_start: 0.7876 (tpp) cc_final: 0.7568 (mmm) REVERT: E 178 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7845 (tp) REVERT: F 123 MET cc_start: 0.7698 (ttp) cc_final: 0.7459 (ttm) REVERT: F 203 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7450 (m) outliers start: 67 outliers final: 59 residues processed: 240 average time/residue: 0.1067 time to fit residues: 43.5600 Evaluate side-chains 256 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 192 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 34 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 0.0050 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 104 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091298 restraints weight = 24153.383| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.35 r_work: 0.2964 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18358 Z= 0.138 Angle : 0.583 8.032 24953 Z= 0.269 Chirality : 0.046 0.239 2776 Planarity : 0.004 0.039 3156 Dihedral : 8.852 120.438 2620 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.44 % Allowed : 27.27 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 2196 helix: 0.93 (0.18), residues: 948 sheet: -0.34 (0.30), residues: 312 loop : 0.45 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 177 TYR 0.008 0.001 TYR B 337 PHE 0.014 0.001 PHE F 255 TRP 0.009 0.001 TRP Q 1 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00329 (18344) covalent geometry : angle 0.58360 (24911) hydrogen bonds : bond 0.02994 ( 808) hydrogen bonds : angle 4.65899 ( 2076) link_TRANS : bond 0.00102 ( 14) link_TRANS : angle 0.36717 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7861 (tpp) REVERT: A 124 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7918 (t80) REVERT: B 225 ASN cc_start: 0.8831 (t0) cc_final: 0.8267 (t0) REVERT: B 299 MET cc_start: 0.8784 (mmm) cc_final: 0.8492 (mmm) REVERT: C 16 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7840 (mp) REVERT: C 132 MET cc_start: 0.8910 (tmm) cc_final: 0.8499 (ttp) REVERT: D 227 MET cc_start: 0.7932 (tpp) cc_final: 0.7629 (mmm) REVERT: E 178 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7841 (tp) REVERT: F 123 MET cc_start: 0.7670 (ttp) cc_final: 0.7428 (ttm) REVERT: F 203 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7449 (m) outliers start: 65 outliers final: 58 residues processed: 233 average time/residue: 0.1037 time to fit residues: 41.0532 Evaluate side-chains 250 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 213 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.0030 chunk 2 optimal weight: 0.2980 chunk 151 optimal weight: 0.4980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091706 restraints weight = 24040.614| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.34 r_work: 0.2970 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18358 Z= 0.128 Angle : 0.577 8.007 24953 Z= 0.266 Chirality : 0.046 0.238 2776 Planarity : 0.004 0.039 3156 Dihedral : 8.642 116.512 2620 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.38 % Allowed : 27.43 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 2196 helix: 0.94 (0.18), residues: 948 sheet: -0.33 (0.30), residues: 312 loop : 0.47 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.010 0.001 TYR B 337 PHE 0.014 0.001 PHE F 255 TRP 0.009 0.001 TRP Q 1 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00304 (18344) covalent geometry : angle 0.57740 (24911) hydrogen bonds : bond 0.02944 ( 808) hydrogen bonds : angle 4.64170 ( 2076) link_TRANS : bond 0.00097 ( 14) link_TRANS : angle 0.34265 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7852 (tpp) REVERT: A 124 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7923 (t80) REVERT: B 225 ASN cc_start: 0.8823 (t0) cc_final: 0.8272 (t0) REVERT: B 299 MET cc_start: 0.8760 (mmm) cc_final: 0.8528 (mmm) REVERT: B 305 MET cc_start: 0.8690 (mmm) cc_final: 0.8462 (mmm) REVERT: C 132 MET cc_start: 0.8890 (tmm) cc_final: 0.8487 (ttp) REVERT: D 227 MET cc_start: 0.7938 (tpp) cc_final: 0.7640 (mmm) REVERT: E 178 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7840 (tp) REVERT: F 123 MET cc_start: 0.7692 (ttp) cc_final: 0.7451 (ttm) REVERT: F 203 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7429 (m) outliers start: 64 outliers final: 59 residues processed: 240 average time/residue: 0.1062 time to fit residues: 43.3412 Evaluate side-chains 252 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 170 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 191 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 169 optimal weight: 0.0270 chunk 215 optimal weight: 0.7980 chunk 212 optimal weight: 0.0870 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 ASN E 12 ASN E 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094247 restraints weight = 24116.500| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.39 r_work: 0.2986 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18358 Z= 0.101 Angle : 0.562 8.072 24953 Z= 0.258 Chirality : 0.045 0.234 2776 Planarity : 0.004 0.039 3156 Dihedral : 8.409 113.830 2620 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.38 % Allowed : 27.33 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 2196 helix: 1.00 (0.18), residues: 948 sheet: -0.17 (0.27), residues: 372 loop : 0.54 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 177 TYR 0.010 0.001 TYR B 337 PHE 0.014 0.001 PHE F 255 TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00233 (18344) covalent geometry : angle 0.56255 (24911) hydrogen bonds : bond 0.02753 ( 808) hydrogen bonds : angle 4.59444 ( 2076) link_TRANS : bond 0.00061 ( 14) link_TRANS : angle 0.25807 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.24 seconds wall clock time: 62 minutes 32.55 seconds (3752.55 seconds total)