Starting phenix.real_space_refine on Thu Sep 18 15:34:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duv_47180/09_2025/9duv_47180_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duv_47180/09_2025/9duv_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 { model { file = "/net/cci-nas-00/data/ceres_data/9duv_47180/09_2025/9duv_47180_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duv_47180/09_2025/9duv_47180_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9duv_47180/09_2025/9duv_47180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duv_47180/09_2025/9duv_47180.map" } 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-2.0-5805/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: 5.21, per 1000 atoms: 0.29 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: 1.60 Conformation dependent library (CDL) restraints added in 710.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.77 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: 3.01 Time building geometry restraints manager: 2.15 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: 24450 2.90 - 5.81: 355 5.81 - 8.71: 65 8.71 - 11.62: 36 11.62 - 14.52: 5 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: 10208 28.98 - 57.95: 771 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: 565 0.076 - 0.113: 282 0.113 - 0.151: 31 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.870 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- 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= 0.308 Angle : 0.892 14.521 24953 Z= 0.433 Chirality : 0.046 0.189 2776 Planarity : 0.004 0.127 3156 Dihedral : 18.913 144.876 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 aren 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 0.00609 (18344) covalent geometry : angle 0.87965 (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 : 0.719 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: 0.1127 time to fit residues: 39.0438 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 : 0.685 ------------------------------------------------------------------------------- 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 = 0.2979 r_free = 0.2979 target = 0.095717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.082849 restraints weight = 23884.052| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.90 r_work: 0.3019 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0942 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= 0.108 Angle : 0.601 7.497 24953 Z= 0.280 Chirality : 0.045 0.200 2776 Planarity : 0.004 0.092 3156 Dihedral : 11.678 145.641 2636 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.12 % Allowed : 27.43 % Favored : 69.45 % 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 aren not related in a simple way. whole: 0.68 (0.19), residues: 2196 helix: 0.82 (0.18), residues: 936 sheet: 0.15 (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 0.009 0.001 TYR B 306 PHE 0.012 0.001 PHE A 255 TRP 0.019 0.001 TRP M 1 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00233 (18344) covalent geometry : angle 0.60102 (24911) hydrogen bonds : bond 0.03507 ( 808) hydrogen bonds : angle 5.35856 ( 2076) link_TRANS : bond 0.00264 ( 14) link_TRANS : angle 0.70606 ( 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 269 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 0.621 Fit side-chains REVERT: A 132 MET cc_start: 0.8652 (ttp) cc_final: 0.8078 (ttp) REVERT: C 225 ASN cc_start: 0.8927 (t0) cc_final: 0.8481 (t0) REVERT: C 325 MET cc_start: 0.7975 (tpt) cc_final: 0.7149 (tpt) outliers start: 59 outliers final: 29 residues processed: 256 average time/residue: 0.1116 time to fit residues: 48.2961 Evaluate side-chains 228 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 67 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 110 optimal weight: 0.0870 chunk 174 optimal weight: 0.0980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.107508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093296 restraints weight = 24234.426| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.40 r_work: 0.2970 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18358 Z= 0.127 Angle : 0.592 8.009 24953 Z= 0.273 Chirality : 0.046 0.230 2776 Planarity : 0.004 0.071 3156 Dihedral : 10.367 130.261 2622 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.01 % Allowed : 27.06 % 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 aren not related in a simple way. whole: 0.71 (0.19), residues: 2196 helix: 0.95 (0.18), residues: 930 sheet: -0.15 (0.31), residues: 312 loop : 0.40 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.008 0.001 TYR B 337 PHE 0.012 0.001 PHE F 255 TRP 0.009 0.001 TRP F 79 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00293 (18344) covalent geometry : angle 0.59224 (24911) hydrogen bonds : bond 0.03442 ( 808) hydrogen bonds : angle 4.91445 ( 2076) link_TRANS : bond 0.00159 ( 14) link_TRANS : angle 0.56346 ( 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 258 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 0.731 Fit side-chains REVERT: A 124 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7874 (t80) REVERT: B 203 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7737 (m) REVERT: C 124 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: C 132 MET cc_start: 0.8942 (tmm) cc_final: 0.8731 (ttp) REVERT: C 225 ASN cc_start: 0.8785 (t0) cc_final: 0.8425 (t0) REVERT: C 270 GLU cc_start: 0.9012 (tp30) cc_final: 0.8727 (tp30) REVERT: D 44 MET cc_start: 0.8501 (mmt) cc_final: 0.8286 (mmm) REVERT: D 227 MET cc_start: 0.7939 (tpp) cc_final: 0.7596 (mpp) REVERT: D 337 TYR cc_start: 0.8756 (m-80) cc_final: 0.8476 (m-80) REVERT: E 283 MET cc_start: 0.8392 (mmm) cc_final: 0.8188 (mmm) outliers start: 57 outliers final: 35 residues processed: 240 average time/residue: 0.1117 time to fit residues: 44.9847 Evaluate side-chains 236 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP 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 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 Chi-restraints excluded: chain F residue 203 THR 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: 0.0170 chunk 10 optimal weight: 0.0770 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 0.0770 chunk 148 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.107524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.093386 restraints weight = 24017.323| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.39 r_work: 0.2982 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18358 Z= 0.117 Angle : 0.574 7.709 24953 Z= 0.263 Chirality : 0.045 0.230 2776 Planarity : 0.004 0.058 3156 Dihedral : 10.151 126.414 2622 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.85 % Allowed : 27.27 % Favored : 69.87 % 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 aren not related in a simple way. whole: 0.76 (0.19), residues: 2196 helix: 0.93 (0.18), residues: 942 sheet: -0.18 (0.31), residues: 312 loop : 0.51 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.005 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 C 161 Details of bonding type rmsd covalent geometry : bond 0.00274 (18344) covalent geometry : angle 0.57391 (24911) hydrogen bonds : bond 0.03041 ( 808) hydrogen bonds : angle 4.79375 ( 2076) link_TRANS : bond 0.00123 ( 14) link_TRANS : angle 0.40564 ( 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 257 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.699 Fit side-chains REVERT: A 124 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7795 (t80) REVERT: B 225 ASN cc_start: 0.8922 (t0) cc_final: 0.8274 (t0) REVERT: C 124 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: C 225 ASN cc_start: 0.8754 (t0) cc_final: 0.8411 (t0) REVERT: C 270 GLU cc_start: 0.9013 (tp30) cc_final: 0.8759 (tp30) REVERT: C 325 MET cc_start: 0.7959 (tpt) cc_final: 0.7342 (tpt) REVERT: D 44 MET cc_start: 0.8467 (mmt) cc_final: 0.8252 (mmm) REVERT: D 227 MET cc_start: 0.7918 (tpp) cc_final: 0.7602 (tpp) REVERT: E 222 ASP cc_start: 0.7358 (p0) cc_final: 0.7139 (p0) outliers start: 54 outliers final: 44 residues processed: 242 average time/residue: 0.1103 time to fit residues: 45.1268 Evaluate side-chains 245 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE 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 A residue 363 ASP 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 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 257 CYS Chi-restraints excluded: chain C residue 305 MET 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 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 344 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 166 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 189 optimal weight: 0.1980 chunk 150 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3269 r_free = 0.3269 target = 0.105415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.091356 restraints weight = 24410.634| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.37 r_work: 0.2975 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18358 Z= 0.125 Angle : 0.574 7.874 24953 Z= 0.263 Chirality : 0.045 0.232 2776 Planarity : 0.004 0.046 3156 Dihedral : 9.963 123.671 2622 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.65 % Allowed : 27.27 % Favored : 69.08 % 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 aren not related in a simple way. whole: 0.72 (0.19), residues: 2196 helix: 0.93 (0.18), residues: 948 sheet: -0.21 (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 D 290 TYR 0.007 0.001 TYR B 337 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 0.00295 (18344) covalent geometry : angle 0.57409 (24911) hydrogen bonds : bond 0.03006 ( 808) hydrogen bonds : angle 4.72053 ( 2076) link_TRANS : bond 0.00132 ( 14) link_TRANS : angle 0.41763 ( 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 270 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 201 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7913 (t80) REVERT: B 203 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7810 (m) REVERT: B 225 ASN cc_start: 0.8944 (t0) cc_final: 0.8283 (t0) REVERT: B 305 MET cc_start: 0.8726 (mmm) cc_final: 0.8516 (mmm) REVERT: C 16 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7884 (mp) REVERT: C 124 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: C 132 MET cc_start: 0.8991 (tmm) cc_final: 0.8766 (ttp) REVERT: C 225 ASN cc_start: 0.8810 (t0) cc_final: 0.8448 (t0) REVERT: D 44 MET cc_start: 0.8465 (mmt) cc_final: 0.8218 (mmm) REVERT: D 227 MET cc_start: 0.7989 (tpp) cc_final: 0.7597 (tpp) REVERT: E 178 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7956 (tp) REVERT: E 222 ASP cc_start: 0.7339 (p0) cc_final: 0.7125 (p0) outliers start: 69 outliers final: 53 residues processed: 253 average time/residue: 0.1061 time to fit residues: 45.3019 Evaluate side-chains 253 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 344 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 28 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 198 optimal weight: 0.3980 chunk 202 optimal weight: 0.8980 chunk 195 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.104727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090695 restraints weight = 24309.505| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.36 r_work: 0.2965 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18358 Z= 0.132 Angle : 0.579 7.723 24953 Z= 0.265 Chirality : 0.046 0.236 2776 Planarity : 0.004 0.040 3156 Dihedral : 9.768 120.912 2622 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.91 % Allowed : 27.06 % Favored : 69.03 % 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 aren not related in a simple way. whole: 0.72 (0.19), residues: 2196 helix: 0.93 (0.18), residues: 948 sheet: -0.24 (0.30), residues: 312 loop : 0.47 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.006 0.001 TYR E 143 PHE 0.014 0.001 PHE F 255 TRP 0.008 0.001 TRP D 79 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00313 (18344) covalent geometry : angle 0.57919 (24911) hydrogen bonds : bond 0.03013 ( 808) hydrogen bonds : angle 4.69309 ( 2076) link_TRANS : bond 0.00144 ( 14) link_TRANS : angle 0.42072 ( 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 272 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 198 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 225 ASN cc_start: 0.8912 (t0) cc_final: 0.8244 (t0) REVERT: C 16 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7926 (mp) REVERT: C 225 ASN cc_start: 0.8814 (t0) cc_final: 0.8452 (t0) REVERT: D 44 MET cc_start: 0.8420 (mmt) cc_final: 0.8170 (mmm) REVERT: D 227 MET cc_start: 0.7989 (tpp) cc_final: 0.7742 (mmm) REVERT: E 178 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7956 (tp) REVERT: E 222 ASP cc_start: 0.7279 (p0) cc_final: 0.7075 (p0) REVERT: F 203 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7578 (m) outliers start: 74 outliers final: 62 residues processed: 251 average time/residue: 0.0989 time to fit residues: 42.0327 Evaluate side-chains 262 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 196 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 43 VAL 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 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 363 ASP 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 85 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 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 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: 1.9990 chunk 220 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.101246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087361 restraints weight = 24907.627| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.37 r_work: 0.2908 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18358 Z= 0.202 Angle : 0.629 8.690 24953 Z= 0.292 Chirality : 0.048 0.248 2776 Planarity : 0.004 0.038 3156 Dihedral : 9.680 127.194 2620 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.75 % Allowed : 26.69 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2196 helix: 0.81 (0.18), residues: 948 sheet: -0.33 (0.30), residues: 312 loop : 0.38 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 116 TYR 0.008 0.001 TYR E 143 PHE 0.015 0.001 PHE F 255 TRP 0.010 0.002 TRP P 1 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00490 (18344) covalent geometry : angle 0.62903 (24911) hydrogen bonds : bond 0.03397 ( 808) hydrogen bonds : angle 4.77850 ( 2076) link_TRANS : bond 0.00223 ( 14) link_TRANS : angle 0.58873 ( 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 258 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 187 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8082 (tpp) REVERT: A 124 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8016 (t80) REVERT: B 47 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5645 (tmm) REVERT: B 225 ASN cc_start: 0.8949 (t0) cc_final: 0.8280 (t0) REVERT: C 16 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8041 (mp) REVERT: C 132 MET cc_start: 0.8989 (tmm) cc_final: 0.8643 (ttp) REVERT: D 44 MET cc_start: 0.8622 (mmt) cc_final: 0.8370 (mmm) REVERT: D 227 MET cc_start: 0.8009 (tpp) cc_final: 0.7618 (tpp) REVERT: E 178 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7986 (tp) REVERT: F 123 MET cc_start: 0.7742 (ttp) cc_final: 0.7535 (ttm) REVERT: F 203 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7697 (m) outliers start: 71 outliers final: 55 residues processed: 237 average time/residue: 0.1020 time to fit residues: 40.8432 Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 43 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 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 363 ASP 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 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 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 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 115 ASN Chi-restraints excluded: chain D residue 132 MET 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 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 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: 1.9990 chunk 66 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.102863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.088950 restraints weight = 24520.989| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.36 r_work: 0.2934 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18358 Z= 0.137 Angle : 0.589 8.396 24953 Z= 0.271 Chirality : 0.046 0.243 2776 Planarity : 0.004 0.039 3156 Dihedral : 9.367 124.373 2620 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.75 % Allowed : 26.69 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2196 helix: 0.86 (0.18), residues: 948 sheet: -0.37 (0.29), residues: 312 loop : 0.41 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.007 0.001 TYR E 143 PHE 0.014 0.001 PHE F 255 TRP 0.009 0.001 TRP E 340 HIS 0.003 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00328 (18344) covalent geometry : angle 0.58951 (24911) hydrogen bonds : bond 0.03056 ( 808) hydrogen bonds : angle 4.71462 ( 2076) link_TRANS : bond 0.00144 ( 14) link_TRANS : angle 0.43067 ( 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 266 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 195 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.8048 (tpp) REVERT: A 124 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7936 (t80) REVERT: B 47 MET cc_start: 0.5783 (OUTLIER) cc_final: 0.5567 (tmm) REVERT: B 225 ASN cc_start: 0.8936 (t0) cc_final: 0.8269 (t0) REVERT: C 16 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7987 (mp) REVERT: C 132 MET cc_start: 0.8955 (tmm) cc_final: 0.8544 (ttp) REVERT: D 44 MET cc_start: 0.8571 (mmt) cc_final: 0.8336 (mmm) REVERT: D 227 MET cc_start: 0.7958 (tpp) cc_final: 0.7660 (mmm) REVERT: E 178 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7911 (tp) REVERT: F 203 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7613 (m) outliers start: 71 outliers final: 58 residues processed: 245 average time/residue: 0.1068 time to fit residues: 43.7300 Evaluate side-chains 252 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 188 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 43 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 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 180 LEU 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 47 MET 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 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 115 ASN Chi-restraints excluded: chain D residue 132 MET 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 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: 0.5980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 0.0000 chunk 104 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.102962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.089069 restraints weight = 24426.209| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.35 r_work: 0.2939 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18358 Z= 0.136 Angle : 0.586 8.247 24953 Z= 0.270 Chirality : 0.046 0.243 2776 Planarity : 0.004 0.040 3156 Dihedral : 9.118 123.006 2620 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.65 % Allowed : 26.96 % Favored : 69.40 % 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 aren not related in a simple way. whole: 0.61 (0.18), residues: 2196 helix: 0.87 (0.18), residues: 948 sheet: -0.37 (0.29), residues: 312 loop : 0.40 (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 0.009 0.001 TRP E 340 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00324 (18344) covalent geometry : angle 0.58594 (24911) hydrogen bonds : bond 0.03019 ( 808) hydrogen bonds : angle 4.68051 ( 2076) link_TRANS : bond 0.00143 ( 14) link_TRANS : angle 0.42735 ( 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 260 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.8010 (tpp) REVERT: A 124 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7914 (t80) REVERT: B 47 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5557 (tmm) REVERT: B 225 ASN cc_start: 0.8858 (t0) cc_final: 0.8328 (t0) REVERT: B 299 MET cc_start: 0.8869 (mmm) cc_final: 0.8584 (mmm) REVERT: C 16 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7953 (mp) REVERT: C 132 MET cc_start: 0.8950 (tmm) cc_final: 0.8520 (ttp) REVERT: D 44 MET cc_start: 0.8511 (mmt) cc_final: 0.8276 (mmm) REVERT: D 227 MET cc_start: 0.8027 (tpp) cc_final: 0.7732 (mmm) REVERT: E 178 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7909 (tp) REVERT: F 203 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7599 (m) outliers start: 69 outliers final: 59 residues processed: 237 average time/residue: 0.1069 time to fit residues: 42.8209 Evaluate side-chains 252 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 43 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 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 47 MET 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 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 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 E residue 325 MET 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: 0.8980 chunk 218 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 95 optimal weight: 0.0370 chunk 65 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 ASN E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.089794 restraints weight = 24273.833| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.34 r_work: 0.2950 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18358 Z= 0.121 Angle : 0.576 8.018 24953 Z= 0.265 Chirality : 0.046 0.241 2776 Planarity : 0.004 0.040 3156 Dihedral : 8.866 119.232 2620 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.49 % Allowed : 27.17 % Favored : 69.34 % 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 aren not related in a simple way. whole: 0.65 (0.18), residues: 2196 helix: 0.91 (0.18), residues: 948 sheet: -0.36 (0.29), residues: 312 loop : 0.42 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 177 TYR 0.006 0.001 TYR E 143 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 0.00285 (18344) covalent geometry : angle 0.57648 (24911) hydrogen bonds : bond 0.02911 ( 808) hydrogen bonds : angle 4.64522 ( 2076) link_TRANS : bond 0.00122 ( 14) link_TRANS : angle 0.38425 ( 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 258 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7984 (tpp) REVERT: A 124 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7910 (t80) REVERT: B 47 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5534 (tmm) REVERT: B 225 ASN cc_start: 0.8816 (t0) cc_final: 0.8307 (t0) REVERT: B 305 MET cc_start: 0.8738 (mmm) cc_final: 0.8503 (mmm) REVERT: C 16 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7884 (mp) REVERT: C 132 MET cc_start: 0.8925 (tmm) cc_final: 0.8486 (ttp) REVERT: D 44 MET cc_start: 0.8472 (mmt) cc_final: 0.8250 (mmm) REVERT: D 227 MET cc_start: 0.8012 (tpp) cc_final: 0.7723 (mmm) REVERT: E 178 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7886 (tp) REVERT: F 123 MET cc_start: 0.8066 (ttm) cc_final: 0.7782 (tpp) REVERT: F 203 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7550 (m) outliers start: 66 outliers final: 59 residues processed: 236 average time/residue: 0.1111 time to fit residues: 44.2792 Evaluate side-chains 254 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 43 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 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 47 MET 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 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 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 E residue 325 MET 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: 0.9990 chunk 36 optimal weight: 0.4980 chunk 191 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 201 optimal weight: 0.0770 chunk 52 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 169 optimal weight: 0.1980 chunk 215 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 ASN E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090863 restraints weight = 24260.032| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.36 r_work: 0.2967 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18358 Z= 0.106 Angle : 0.565 8.075 24953 Z= 0.259 Chirality : 0.045 0.239 2776 Planarity : 0.004 0.040 3156 Dihedral : 8.585 114.393 2620 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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 aren not related in a simple way. whole: 0.71 (0.19), residues: 2196 helix: 0.97 (0.18), residues: 948 sheet: -0.35 (0.29), 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 0.006 0.001 TYR E 143 PHE 0.014 0.001 PHE F 255 TRP 0.010 0.001 TRP E 79 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00244 (18344) covalent geometry : angle 0.56502 (24911) hydrogen bonds : bond 0.02775 ( 808) hydrogen bonds : angle 4.59899 ( 2076) link_TRANS : bond 0.00097 ( 14) link_TRANS : angle 0.33036 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.97 seconds wall clock time: 65 minutes 27.73 seconds (3927.73 seconds total)