Starting phenix.real_space_refine on Mon Jun 16 00:30:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duv_47180/06_2025/9duv_47180_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duv_47180/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9duv_47180/06_2025/9duv_47180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duv_47180/06_2025/9duv_47180.map" model { file = "/net/cci-nas-00/data/ceres_data/9duv_47180/06_2025/9duv_47180_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duv_47180/06_2025/9duv_47180_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.103 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.43, per 1000 atoms: 0.69 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: 4.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.55 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: 6.14 Time building geometry restraints manager: 5.54 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: 0.04 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: 5.140 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.730 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.720 ------------------------------------------------------------------------------- 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 : 11.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (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 TRP 0.012 0.002 TRP O 1 HIS 0.003 0.001 HIS D 173 PHE 0.014 0.001 PHE F 124 TYR 0.011 0.001 TYR B 337 ARG 0.004 0.000 ARG D 290 Details of bonding type rmsd link_TRANS : bond 0.00377 ( 14) link_TRANS : angle 3.72474 ( 42) hydrogen bonds : bond 0.20536 ( 808) hydrogen bonds : angle 7.08463 ( 2076) covalent geometry : bond 0.00609 (18344) covalent geometry : angle 0.87965 (24911) *********************** 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 : 2.008 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: F 283 MET cc_start: 0.8049 (mmm) cc_final: 0.7825 (mmt) outliers start: 20 outliers final: 15 residues processed: 207 average time/residue: 0.2438 time to fit residues: 83.7505 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 : 1.917 ------------------------------------------------------------------------------- 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 187 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 201 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.2932 r_free = 0.2932 target = 0.092519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.079924 restraints weight = 24247.061| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.89 r_work: 0.2984 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18358 Z= 0.142 Angle : 0.624 7.789 24953 Z= 0.292 Chirality : 0.046 0.198 2776 Planarity : 0.004 0.091 3156 Dihedral : 11.707 144.608 2636 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.17 % Allowed : 27.64 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2196 helix: 0.76 (0.18), residues: 936 sheet: 0.10 (0.32), residues: 282 loop : 0.32 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 1 HIS 0.004 0.001 HIS F 254 PHE 0.012 0.001 PHE A 255 TYR 0.008 0.001 TYR B 198 ARG 0.003 0.000 ARG D 290 Details of bonding type rmsd link_TRANS : bond 0.00249 ( 14) link_TRANS : angle 0.58064 ( 42) hydrogen bonds : bond 0.03837 ( 808) hydrogen bonds : angle 5.39196 ( 2076) covalent geometry : bond 0.00322 (18344) covalent geometry : angle 0.62453 (24911) *********************** 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 262 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 1.903 Fit side-chains REVERT: C 225 ASN cc_start: 0.8950 (t0) cc_final: 0.8506 (t0) REVERT: C 325 MET cc_start: 0.8056 (tpt) cc_final: 0.7202 (tpt) REVERT: C 354 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8732 (tm-30) REVERT: D 227 MET cc_start: 0.8327 (mmm) cc_final: 0.7935 (tpp) outliers start: 60 outliers final: 32 residues processed: 248 average time/residue: 0.2325 time to fit residues: 96.0437 Evaluate side-chains 223 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 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 119 MET Chi-restraints excluded: chain E residue 267 ILE 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 49 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 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 = 0.3297 r_free = 0.3297 target = 0.106333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092280 restraints weight = 24070.853| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.38 r_work: 0.2965 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18358 Z= 0.141 Angle : 0.601 8.368 24953 Z= 0.278 Chirality : 0.046 0.232 2776 Planarity : 0.004 0.071 3156 Dihedral : 10.553 129.557 2624 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.01 % Allowed : 27.80 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 2196 helix: 0.84 (0.18), residues: 936 sheet: -0.19 (0.31), residues: 312 loop : 0.40 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.005 0.001 HIS A 161 PHE 0.012 0.001 PHE F 255 TYR 0.008 0.001 TYR B 337 ARG 0.006 0.000 ARG B 116 Details of bonding type rmsd link_TRANS : bond 0.00161 ( 14) link_TRANS : angle 0.54480 ( 42) hydrogen bonds : bond 0.03532 ( 808) hydrogen bonds : angle 4.98908 ( 2076) covalent geometry : bond 0.00331 (18344) covalent geometry : angle 0.60149 (24911) *********************** 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 257 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 1.908 Fit side-chains REVERT: A 123 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7895 (tpp) REVERT: A 124 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7853 (t80) REVERT: B 53 TYR cc_start: 0.9021 (m-80) cc_final: 0.8593 (m-80) REVERT: C 124 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: C 225 ASN cc_start: 0.8765 (t0) cc_final: 0.8427 (t0) REVERT: D 44 MET cc_start: 0.8576 (tpp) cc_final: 0.8370 (mmm) REVERT: F 283 MET cc_start: 0.8164 (mmm) cc_final: 0.7896 (mmt) outliers start: 57 outliers final: 35 residues processed: 239 average time/residue: 0.2315 time to fit residues: 91.7557 Evaluate side-chains 237 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 123 MET 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 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 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 D residue 236 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 124 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 43 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.098572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.084861 restraints weight = 25156.267| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.36 r_work: 0.2874 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 18358 Z= 0.283 Angle : 0.706 10.203 24953 Z= 0.333 Chirality : 0.051 0.258 2776 Planarity : 0.004 0.057 3156 Dihedral : 10.826 135.205 2622 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.81 % Allowed : 26.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2196 helix: 0.60 (0.17), residues: 936 sheet: -0.42 (0.30), residues: 324 loop : 0.18 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 1 HIS 0.006 0.001 HIS E 254 PHE 0.014 0.001 PHE F 255 TYR 0.010 0.001 TYR E 143 ARG 0.004 0.000 ARG E 290 Details of bonding type rmsd link_TRANS : bond 0.00315 ( 14) link_TRANS : angle 0.80792 ( 42) hydrogen bonds : bond 0.04104 ( 808) hydrogen bonds : angle 5.09562 ( 2076) covalent geometry : bond 0.00689 (18344) covalent geometry : angle 0.70593 (24911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 180 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8002 (tpp) REVERT: A 124 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 305 MET cc_start: 0.8847 (mmm) cc_final: 0.8625 (mmm) REVERT: C 116 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: C 354 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8619 (tm-30) REVERT: D 44 MET cc_start: 0.8750 (tpp) cc_final: 0.8488 (mmm) REVERT: D 184 ASP cc_start: 0.8816 (m-30) cc_final: 0.8567 (m-30) REVERT: D 337 TYR cc_start: 0.8797 (m-80) cc_final: 0.8573 (m-80) REVERT: E 178 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8002 (tp) REVERT: F 203 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7778 (m) outliers start: 72 outliers final: 50 residues processed: 229 average time/residue: 0.2548 time to fit residues: 96.5211 Evaluate side-chains 231 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 2.175 ------------------------------------------------------------------------------- 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 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE 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 201 VAL 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 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 116 ARG 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 25 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 178 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 11 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 69 optimal weight: 0.0000 chunk 60 optimal weight: 0.0570 chunk 146 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 216 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090419 restraints weight = 24420.587| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.36 r_work: 0.2959 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18358 Z= 0.100 Angle : 0.574 8.792 24953 Z= 0.264 Chirality : 0.045 0.240 2776 Planarity : 0.004 0.049 3156 Dihedral : 10.399 133.832 2622 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.38 % Allowed : 27.64 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 2196 helix: 0.80 (0.18), residues: 948 sheet: -0.35 (0.30), residues: 312 loop : 0.35 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 79 HIS 0.003 0.001 HIS C 161 PHE 0.013 0.001 PHE F 255 TYR 0.006 0.001 TYR C 306 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd link_TRANS : bond 0.00092 ( 14) link_TRANS : angle 0.32130 ( 42) hydrogen bonds : bond 0.02950 ( 808) hydrogen bonds : angle 4.80222 ( 2076) covalent geometry : bond 0.00224 (18344) covalent geometry : angle 0.57416 (24911) *********************** 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 264 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 2.439 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8018 (t80) REVERT: B 203 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7628 (m) REVERT: B 225 ASN cc_start: 0.8991 (t0) cc_final: 0.8323 (t0) REVERT: C 16 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7804 (mp) REVERT: C 225 ASN cc_start: 0.8824 (t0) cc_final: 0.8452 (t0) REVERT: D 227 MET cc_start: 0.8128 (mmm) cc_final: 0.7716 (tpp) REVERT: D 337 TYR cc_start: 0.8786 (m-80) cc_final: 0.8561 (m-80) REVERT: E 178 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7899 (tp) REVERT: F 203 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7538 (m) outliers start: 64 outliers final: 36 residues processed: 248 average time/residue: 0.2561 time to fit residues: 106.4390 Evaluate side-chains 234 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 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 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 124 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL 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 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 113 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.089554 restraints weight = 24593.634| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.37 r_work: 0.2945 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18358 Z= 0.123 Angle : 0.579 8.188 24953 Z= 0.265 Chirality : 0.046 0.240 2776 Planarity : 0.004 0.041 3156 Dihedral : 10.127 134.857 2620 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.44 % Allowed : 27.06 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 2196 helix: 0.86 (0.18), residues: 948 sheet: -0.31 (0.30), residues: 312 loop : 0.38 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 79 HIS 0.003 0.001 HIS C 161 PHE 0.014 0.001 PHE F 255 TYR 0.008 0.001 TYR B 337 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd link_TRANS : bond 0.00120 ( 14) link_TRANS : angle 0.43080 ( 42) hydrogen bonds : bond 0.03008 ( 808) hydrogen bonds : angle 4.72849 ( 2076) covalent geometry : bond 0.00290 (18344) covalent geometry : angle 0.57948 (24911) *********************** 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 259 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 194 time to evaluate : 1.961 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7981 (t80) REVERT: B 225 ASN cc_start: 0.8933 (t0) cc_final: 0.8275 (t0) REVERT: C 16 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7888 (mp) REVERT: D 44 MET cc_start: 0.8537 (tpp) cc_final: 0.8293 (mmm) REVERT: D 227 MET cc_start: 0.8076 (mmm) cc_final: 0.7661 (tpp) REVERT: D 337 TYR cc_start: 0.8793 (m-80) cc_final: 0.8574 (m-80) REVERT: E 222 ASP cc_start: 0.7395 (p0) cc_final: 0.7153 (p0) REVERT: F 203 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7549 (m) REVERT: F 270 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8077 (tp30) REVERT: F 283 MET cc_start: 0.8304 (mmm) cc_final: 0.8091 (mmt) outliers start: 65 outliers final: 50 residues processed: 240 average time/residue: 0.2530 time to fit residues: 101.1002 Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 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 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 123 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 14 SER 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 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 358 THR 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 270 GLU Chi-restraints excluded: chain F residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.097692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.084069 restraints weight = 25063.944| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.33 r_work: 0.2861 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 18358 Z= 0.288 Angle : 0.697 10.183 24953 Z= 0.329 Chirality : 0.051 0.260 2776 Planarity : 0.004 0.039 3156 Dihedral : 10.573 157.074 2618 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.07 % Allowed : 26.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2196 helix: 0.61 (0.17), residues: 942 sheet: -0.59 (0.29), residues: 330 loop : 0.23 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 1 HIS 0.006 0.002 HIS A 254 PHE 0.015 0.001 PHE F 255 TYR 0.011 0.001 TYR E 143 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd link_TRANS : bond 0.00320 ( 14) link_TRANS : angle 0.82627 ( 42) hydrogen bonds : bond 0.03948 ( 808) hydrogen bonds : angle 4.97064 ( 2076) covalent geometry : bond 0.00699 (18344) covalent geometry : angle 0.69661 (24911) *********************** 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 253 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 176 time to evaluate : 2.194 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7928 (t80) REVERT: D 44 MET cc_start: 0.8738 (tpp) cc_final: 0.8462 (mmm) REVERT: E 178 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8000 (tp) REVERT: E 222 ASP cc_start: 0.7572 (p0) cc_final: 0.7321 (p0) REVERT: E 363 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: F 123 MET cc_start: 0.7875 (ttp) cc_final: 0.7659 (ttm) REVERT: F 203 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7786 (m) REVERT: F 270 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8219 (tp30) outliers start: 77 outliers final: 60 residues processed: 233 average time/residue: 0.2473 time to fit residues: 96.5050 Evaluate side-chains 239 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 174 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 14 SER 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 149 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 C residue 338 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 34 ILE 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 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 VAL 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 265 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 363 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 270 GLU 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 53 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.099402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.085605 restraints weight = 24927.122| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.36 r_work: 0.2891 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18358 Z= 0.191 Angle : 0.628 9.614 24953 Z= 0.292 Chirality : 0.048 0.255 2776 Planarity : 0.004 0.041 3156 Dihedral : 10.683 178.041 2618 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.65 % Allowed : 26.74 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 2196 helix: 0.68 (0.18), residues: 942 sheet: -0.50 (0.29), residues: 324 loop : 0.19 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 340 HIS 0.004 0.001 HIS E 254 PHE 0.015 0.001 PHE F 255 TYR 0.009 0.001 TYR E 143 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd link_TRANS : bond 0.00228 ( 14) link_TRANS : angle 0.60151 ( 42) hydrogen bonds : bond 0.03426 ( 808) hydrogen bonds : angle 4.87651 ( 2076) covalent geometry : bond 0.00461 (18344) covalent geometry : angle 0.62767 (24911) *********************** 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 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 2.649 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8290 (ttm) cc_final: 0.7987 (tpp) REVERT: A 124 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8005 (t80) REVERT: D 44 MET cc_start: 0.8646 (tpp) cc_final: 0.8378 (mmm) REVERT: D 337 TYR cc_start: 0.8804 (m-80) cc_final: 0.8589 (m-80) REVERT: E 178 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7935 (tp) REVERT: E 222 ASP cc_start: 0.7423 (p0) cc_final: 0.7178 (p0) REVERT: E 363 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: F 123 MET cc_start: 0.7802 (ttp) cc_final: 0.7572 (ttm) REVERT: F 203 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7661 (m) REVERT: F 270 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: F 283 MET cc_start: 0.8469 (mmm) cc_final: 0.8214 (mmt) outliers start: 69 outliers final: 59 residues processed: 226 average time/residue: 0.2848 time to fit residues: 108.5678 Evaluate side-chains 240 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 3.160 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER 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 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 34 ILE 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 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE 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 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET 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 E residue 338 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 363 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 270 GLU 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 23 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.099715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.086011 restraints weight = 24866.035| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.36 r_work: 0.2893 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18358 Z= 0.188 Angle : 0.622 9.427 24953 Z= 0.290 Chirality : 0.048 0.254 2776 Planarity : 0.004 0.040 3156 Dihedral : 10.701 177.322 2618 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.75 % Allowed : 26.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2196 helix: 0.71 (0.18), residues: 942 sheet: -0.59 (0.29), residues: 330 loop : 0.23 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 340 HIS 0.004 0.001 HIS E 254 PHE 0.015 0.001 PHE F 255 TYR 0.008 0.001 TYR E 143 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_TRANS : bond 0.00215 ( 14) link_TRANS : angle 0.59487 ( 42) hydrogen bonds : bond 0.03380 ( 808) hydrogen bonds : angle 4.83685 ( 2076) covalent geometry : bond 0.00454 (18344) covalent geometry : angle 0.62248 (24911) *********************** 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 251 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 4.361 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8268 (ttm) cc_final: 0.7974 (tpp) REVERT: A 124 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8051 (t80) REVERT: D 44 MET cc_start: 0.8624 (tpp) cc_final: 0.8349 (mmm) REVERT: D 82 MET cc_start: 0.8332 (mmt) cc_final: 0.8069 (tpp) REVERT: D 227 MET cc_start: 0.8031 (mmm) cc_final: 0.7674 (tpp) REVERT: D 337 TYR cc_start: 0.8801 (m-80) cc_final: 0.8588 (m-80) REVERT: E 178 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7913 (tp) REVERT: E 222 ASP cc_start: 0.7401 (p0) cc_final: 0.7155 (p0) REVERT: E 363 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: F 203 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7669 (m) REVERT: F 270 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: F 283 MET cc_start: 0.8471 (mmm) cc_final: 0.8246 (mmt) outliers start: 71 outliers final: 64 residues processed: 232 average time/residue: 0.3650 time to fit residues: 140.2203 Evaluate side-chains 244 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 175 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER 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 149 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 334 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 34 ILE 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 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE 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 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 265 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 E residue 338 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 338 SER 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 119 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.100996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087310 restraints weight = 24644.409| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.34 r_work: 0.2913 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18358 Z= 0.153 Angle : 0.599 9.007 24953 Z= 0.277 Chirality : 0.047 0.250 2776 Planarity : 0.004 0.041 3156 Dihedral : 10.545 179.263 2618 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.44 % Allowed : 27.38 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2196 helix: 0.78 (0.18), residues: 942 sheet: -0.58 (0.29), residues: 330 loop : 0.27 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.003 0.001 HIS E 254 PHE 0.015 0.001 PHE F 255 TYR 0.008 0.001 TYR E 143 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_TRANS : bond 0.00175 ( 14) link_TRANS : angle 0.52626 ( 42) hydrogen bonds : bond 0.03151 ( 808) hydrogen bonds : angle 4.76304 ( 2076) covalent geometry : bond 0.00365 (18344) covalent geometry : angle 0.59867 (24911) ********************** 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 248 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8241 (ttm) cc_final: 0.7986 (tpp) REVERT: A 124 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 225 ASN cc_start: 0.8850 (t0) cc_final: 0.8347 (t0) REVERT: D 227 MET cc_start: 0.7965 (mmm) cc_final: 0.7628 (tpp) REVERT: D 337 TYR cc_start: 0.8790 (m-80) cc_final: 0.8586 (m-80) REVERT: E 178 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7896 (tp) REVERT: E 222 ASP cc_start: 0.7348 (p0) cc_final: 0.7104 (p0) REVERT: E 363 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: F 203 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7622 (m) REVERT: F 270 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: F 283 MET cc_start: 0.8416 (mmm) cc_final: 0.8179 (mmt) outliers start: 65 outliers final: 60 residues processed: 230 average time/residue: 0.2672 time to fit residues: 102.8624 Evaluate side-chains 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 182 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER 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 123 MET Chi-restraints excluded: chain C residue 149 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 334 GLU Chi-restraints excluded: chain D residue 14 SER 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 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 34 ILE 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 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET 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 E residue 338 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 338 SER 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 184 optimal weight: 0.0030 chunk 32 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 180 optimal weight: 0.0470 chunk 126 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 overall best weight: 0.6690 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.102251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.088427 restraints weight = 24606.849| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.35 r_work: 0.2930 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1852 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= 0.129 Angle : 0.579 9.838 24953 Z= 0.268 Chirality : 0.046 0.245 2776 Planarity : 0.004 0.041 3156 Dihedral : 10.136 159.028 2618 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.33 % Allowed : 27.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2196 helix: 0.82 (0.18), residues: 948 sheet: -0.52 (0.29), residues: 318 loop : 0.30 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS C 173 PHE 0.014 0.001 PHE F 255 TYR 0.007 0.001 TYR E 143 ARG 0.003 0.000 ARG E 177 Details of bonding type rmsd link_TRANS : bond 0.00136 ( 14) link_TRANS : angle 0.42184 ( 42) hydrogen bonds : bond 0.02949 ( 808) hydrogen bonds : angle 4.68902 ( 2076) covalent geometry : bond 0.00307 (18344) covalent geometry : angle 0.57950 (24911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7748.37 seconds wall clock time: 139 minutes 10.98 seconds (8350.98 seconds total)