Starting phenix.real_space_refine on Tue Nov 19 00:30:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duv_47180/11_2024/9duv_47180_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duv_47180/11_2024/9duv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duv_47180/11_2024/9duv_47180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duv_47180/11_2024/9duv_47180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duv_47180/11_2024/9duv_47180_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duv_47180/11_2024/9duv_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-5513/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: 11.02, per 1000 atoms: 0.61 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 2.5 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: 2.41 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: 6.07 Time building geometry restraints manager: 5.39 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 41.190 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.920 ------------------------------------------------------------------------------- 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 18344 Z= 0.416 Angle : 0.880 14.521 24911 Z= 0.425 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 *********************** 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 : 1.806 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: 0.2461 time to fit residues: 84.1860 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 : 1.903 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 18344 Z= 0.213 Angle : 0.625 7.788 24911 Z= 0.292 Chirality : 0.046 0.198 2776 Planarity : 0.004 0.091 3156 Dihedral : 11.707 144.607 2636 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.28 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 *********************** 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 : 2.140 Fit side-chains REVERT: B 107 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: C 225 ASN cc_start: 0.8865 (t0) cc_final: 0.8456 (t0) REVERT: C 325 MET cc_start: 0.8196 (tpt) cc_final: 0.7367 (tpt) REVERT: C 354 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8628 (tm-30) REVERT: D 41 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: D 227 MET cc_start: 0.8086 (mmm) cc_final: 0.7589 (tpp) outliers start: 60 outliers final: 32 residues processed: 248 average time/residue: 0.2421 time to fit residues: 99.5772 Evaluate side-chains 225 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 107 GLU 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 41 GLN 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 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 179 optimal weight: 0.0770 chunk 200 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18344 Z= 0.201 Angle : 0.594 8.508 24911 Z= 0.274 Chirality : 0.046 0.230 2776 Planarity : 0.004 0.072 3156 Dihedral : 10.596 130.856 2624 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.07 % Allowed : 27.64 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.19), residues: 2196 helix: 0.85 (0.18), residues: 936 sheet: -0.17 (0.31), residues: 312 loop : 0.41 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 79 HIS 0.004 0.001 HIS A 161 PHE 0.012 0.001 PHE F 255 TYR 0.007 0.001 TYR B 337 ARG 0.002 0.000 ARG D 290 *********************** 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 255 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 1.923 Fit side-chains REVERT: A 124 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7932 (t80) REVERT: B 107 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: C 116 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7639 (ttm170) REVERT: C 124 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: C 225 ASN cc_start: 0.8866 (t0) cc_final: 0.8457 (t0) outliers start: 58 outliers final: 36 residues processed: 237 average time/residue: 0.2536 time to fit residues: 99.1334 Evaluate side-chains 234 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain 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 107 GLU 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 116 ARG 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 199 optimal weight: 0.0970 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 41 GLN E 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18344 Z= 0.205 Angle : 0.587 8.058 24911 Z= 0.269 Chirality : 0.046 0.231 2776 Planarity : 0.004 0.057 3156 Dihedral : 10.311 127.844 2622 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.96 % Allowed : 27.43 % 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: 0.68 (0.19), residues: 2196 helix: 0.86 (0.18), residues: 942 sheet: -0.21 (0.31), residues: 312 loop : 0.48 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.003 0.001 HIS A 254 PHE 0.013 0.001 PHE F 255 TYR 0.006 0.001 TYR E 143 ARG 0.003 0.000 ARG D 290 *********************** 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 254 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 198 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 107 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: C 225 ASN cc_start: 0.8870 (t0) cc_final: 0.8491 (t0) REVERT: C 354 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8498 (tm-30) REVERT: D 41 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: F 203 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7738 (m) outliers start: 56 outliers final: 40 residues processed: 240 average time/residue: 0.2460 time to fit residues: 97.8147 Evaluate side-chains 236 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 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 41 GLN Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain 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 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 0.0270 chunk 183 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18344 Z= 0.241 Angle : 0.595 8.467 24911 Z= 0.273 Chirality : 0.046 0.238 2776 Planarity : 0.004 0.046 3156 Dihedral : 10.211 125.530 2622 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.18 % Allowed : 26.43 % 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: 0.61 (0.19), residues: 2196 helix: 0.82 (0.18), residues: 948 sheet: -0.26 (0.30), residues: 312 loop : 0.41 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.003 0.001 HIS A 254 PHE 0.013 0.001 PHE F 255 TYR 0.007 0.001 TYR B 337 ARG 0.002 0.000 ARG D 290 *********************** 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 272 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 193 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7980 (t80) REVERT: B 107 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: B 203 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7971 (m) REVERT: B 225 ASN cc_start: 0.8959 (t0) cc_final: 0.8283 (t0) REVERT: C 225 ASN cc_start: 0.8890 (t0) cc_final: 0.8491 (t0) REVERT: C 325 MET cc_start: 0.7995 (tpt) cc_final: 0.7345 (tpt) REVERT: C 354 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8459 (tm-30) REVERT: D 41 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: D 44 MET cc_start: 0.8495 (mmm) cc_final: 0.8230 (mtt) REVERT: D 325 MET cc_start: 0.7120 (mtp) cc_final: 0.6825 (mtt) REVERT: D 337 TYR cc_start: 0.8796 (m-80) cc_final: 0.8548 (m-80) REVERT: E 178 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7890 (tp) REVERT: E 222 ASP cc_start: 0.7346 (p0) cc_final: 0.7088 (p0) REVERT: F 203 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7779 (m) outliers start: 79 outliers final: 57 residues processed: 249 average time/residue: 0.2528 time to fit residues: 104.1409 Evaluate side-chains 251 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 52 optimal weight: 0.2980 chunk 214 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18344 Z= 0.251 Angle : 0.598 8.468 24911 Z= 0.275 Chirality : 0.047 0.243 2776 Planarity : 0.004 0.039 3156 Dihedral : 10.011 124.268 2620 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.91 % Allowed : 26.85 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.19), residues: 2196 helix: 0.81 (0.18), residues: 948 sheet: -0.29 (0.30), residues: 312 loop : 0.39 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 340 HIS 0.004 0.001 HIS E 254 PHE 0.014 0.001 PHE F 255 TYR 0.007 0.001 TYR E 143 ARG 0.002 0.000 ARG E 116 *********************** 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 264 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 190 time to evaluate : 2.158 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8085 (t80) REVERT: B 107 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: B 203 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7939 (m) REVERT: B 225 ASN cc_start: 0.8972 (t0) cc_final: 0.8268 (t0) REVERT: C 16 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8058 (mp) REVERT: C 132 MET cc_start: 0.9015 (tmm) cc_final: 0.8681 (ttp) REVERT: C 225 ASN cc_start: 0.8893 (t0) cc_final: 0.8517 (t0) REVERT: D 44 MET cc_start: 0.8516 (mmm) cc_final: 0.8263 (mmm) REVERT: D 227 MET cc_start: 0.8197 (mmm) cc_final: 0.7773 (tpp) REVERT: D 325 MET cc_start: 0.7098 (mtp) cc_final: 0.6824 (mtt) REVERT: E 178 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7886 (tp) REVERT: E 222 ASP cc_start: 0.7313 (p0) cc_final: 0.7059 (p0) REVERT: F 203 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7789 (m) REVERT: F 283 MET cc_start: 0.8341 (mmm) cc_final: 0.8060 (mmt) outliers start: 74 outliers final: 55 residues processed: 243 average time/residue: 0.2407 time to fit residues: 97.4981 Evaluate side-chains 251 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 190 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 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 107 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.003 0.029 18344 Z= 0.219 Angle : 0.590 8.420 24911 Z= 0.271 Chirality : 0.046 0.242 2776 Planarity : 0.004 0.039 3156 Dihedral : 9.791 123.309 2620 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.75 % Allowed : 26.85 % 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: 0.61 (0.19), residues: 2196 helix: 0.85 (0.18), residues: 948 sheet: -0.33 (0.30), residues: 312 loop : 0.41 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 340 HIS 0.003 0.001 HIS A 254 PHE 0.014 0.001 PHE F 255 TYR 0.008 0.001 TYR B 337 ARG 0.002 0.000 ARG E 116 *********************** 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 267 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 196 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 203 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7886 (m) REVERT: B 225 ASN cc_start: 0.8972 (t0) cc_final: 0.8275 (t0) REVERT: C 16 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8044 (mp) REVERT: C 132 MET cc_start: 0.8992 (tmm) cc_final: 0.8645 (ttp) REVERT: C 225 ASN cc_start: 0.8915 (t0) cc_final: 0.8524 (t0) REVERT: D 41 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: D 44 MET cc_start: 0.8517 (mmm) cc_final: 0.8153 (mtt) REVERT: D 227 MET cc_start: 0.8194 (mmm) cc_final: 0.7762 (tpp) REVERT: D 325 MET cc_start: 0.7186 (mtp) cc_final: 0.6961 (mtt) REVERT: E 178 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7880 (tp) REVERT: E 222 ASP cc_start: 0.7240 (p0) cc_final: 0.6992 (p0) REVERT: F 203 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7772 (m) outliers start: 71 outliers final: 58 residues processed: 247 average time/residue: 0.2426 time to fit residues: 99.6429 Evaluate side-chains 256 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 192 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 201 VAL Chi-restraints excluded: chain A residue 363 ASP 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 120 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain 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 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18344 Z= 0.244 Angle : 0.597 8.353 24911 Z= 0.274 Chirality : 0.046 0.245 2776 Planarity : 0.004 0.039 3156 Dihedral : 9.605 124.604 2620 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.96 % Allowed : 26.48 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.19), residues: 2196 helix: 0.83 (0.18), residues: 948 sheet: -0.49 (0.29), residues: 318 loop : 0.43 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 340 HIS 0.004 0.001 HIS E 254 PHE 0.014 0.001 PHE F 255 TYR 0.007 0.001 TYR B 337 ARG 0.002 0.000 ARG A 177 *********************** 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 270 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 195 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8122 (t80) REVERT: B 203 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7932 (m) REVERT: B 225 ASN cc_start: 0.8977 (t0) cc_final: 0.8285 (t0) REVERT: C 16 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 132 MET cc_start: 0.9029 (tmm) cc_final: 0.8811 (ttp) REVERT: D 41 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: D 44 MET cc_start: 0.8535 (mmm) cc_final: 0.8327 (mmm) REVERT: D 227 MET cc_start: 0.8197 (mmm) cc_final: 0.7757 (tpp) REVERT: D 325 MET cc_start: 0.7141 (mtp) cc_final: 0.6930 (mtt) REVERT: E 178 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7890 (tp) REVERT: E 222 ASP cc_start: 0.7225 (p0) cc_final: 0.6984 (p0) REVERT: F 123 MET cc_start: 0.7751 (ttp) cc_final: 0.7523 (ttm) REVERT: F 203 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7788 (m) outliers start: 75 outliers final: 60 residues processed: 249 average time/residue: 0.2437 time to fit residues: 100.9782 Evaluate side-chains 256 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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 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 120 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE 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 D residue 16 LEU Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 338 SER 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 180 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.2980 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 0.0570 chunk 199 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18344 Z= 0.164 Angle : 0.570 7.783 24911 Z= 0.261 Chirality : 0.045 0.239 2776 Planarity : 0.004 0.041 3156 Dihedral : 9.139 118.701 2620 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.38 % Allowed : 27.01 % 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: 0.67 (0.19), residues: 2196 helix: 0.92 (0.18), residues: 948 sheet: -0.34 (0.27), residues: 378 loop : 0.51 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS A 254 PHE 0.014 0.001 PHE F 255 TYR 0.007 0.001 TYR B 337 ARG 0.002 0.000 ARG A 177 *********************** 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 263 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 1.995 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8744 (tpt) cc_final: 0.8469 (tpt) REVERT: A 124 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8040 (t80) REVERT: B 203 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7823 (m) REVERT: B 225 ASN cc_start: 0.8904 (t0) cc_final: 0.8245 (t0) REVERT: B 299 MET cc_start: 0.8857 (mmm) cc_final: 0.8609 (mmm) REVERT: C 132 MET cc_start: 0.8948 (tmm) cc_final: 0.8713 (ttp) REVERT: D 41 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: D 44 MET cc_start: 0.8401 (mmm) cc_final: 0.8036 (mtt) REVERT: D 227 MET cc_start: 0.8180 (mmm) cc_final: 0.7740 (tpp) REVERT: E 178 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7805 (tp) REVERT: E 222 ASP cc_start: 0.7153 (p0) cc_final: 0.6913 (p0) REVERT: F 123 MET cc_start: 0.7680 (ttp) cc_final: 0.7456 (ttm) REVERT: F 203 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7685 (m) REVERT: F 270 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8043 (tp30) outliers start: 64 outliers final: 54 residues processed: 247 average time/residue: 0.2409 time to fit residues: 99.5477 Evaluate side-chains 254 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 1.960 ------------------------------------------------------------------------------- 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 A residue 344 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE 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 D residue 16 LEU Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 338 SER 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 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 221 optimal weight: 0.0070 chunk 203 optimal weight: 0.7980 chunk 176 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18344 Z= 0.194 Angle : 0.577 7.927 24911 Z= 0.264 Chirality : 0.046 0.241 2776 Planarity : 0.004 0.040 3156 Dihedral : 8.875 116.881 2620 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.38 % Allowed : 26.90 % Favored : 69.71 % 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: 0.66 (0.19), residues: 2196 helix: 0.92 (0.18), residues: 948 sheet: -0.36 (0.27), residues: 378 loop : 0.51 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS A 254 PHE 0.014 0.001 PHE F 255 TYR 0.010 0.001 TYR B 337 ARG 0.002 0.000 ARG E 116 ********************** 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 257 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 193 time to evaluate : 2.160 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8748 (tpt) cc_final: 0.8471 (tpt) REVERT: A 124 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8044 (t80) REVERT: B 203 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7860 (m) REVERT: B 225 ASN cc_start: 0.8899 (t0) cc_final: 0.8322 (t0) REVERT: B 299 MET cc_start: 0.8862 (mmm) cc_final: 0.8639 (mmm) REVERT: C 132 MET cc_start: 0.8966 (tmm) cc_final: 0.8736 (ttp) REVERT: D 41 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: D 44 MET cc_start: 0.8410 (mmm) cc_final: 0.8033 (mtt) REVERT: D 227 MET cc_start: 0.8182 (mmm) cc_final: 0.7742 (tpp) REVERT: E 178 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7800 (tp) REVERT: E 222 ASP cc_start: 0.7148 (p0) cc_final: 0.6917 (p0) REVERT: E 363 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: F 123 MET cc_start: 0.7715 (ttp) cc_final: 0.7475 (ttm) REVERT: F 203 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7731 (m) REVERT: F 270 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8016 (tp30) outliers start: 64 outliers final: 57 residues processed: 241 average time/residue: 0.2385 time to fit residues: 96.6310 Evaluate side-chains 255 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 201 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 PHE 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 338 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 338 SER 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 325 MET Chi-restraints excluded: chain F residue 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 1.9990 chunk 187 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 chunk 26 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.105625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.091636 restraints weight = 24252.932| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.36 r_work: 0.2984 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18344 Z= 0.145 Angle : 0.562 7.772 24911 Z= 0.256 Chirality : 0.045 0.236 2776 Planarity : 0.004 0.040 3156 Dihedral : 8.521 112.991 2620 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.12 % Allowed : 27.06 % Favored : 69.82 % 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: 0.72 (0.19), residues: 2196 helix: 0.98 (0.18), residues: 948 sheet: -0.37 (0.27), residues: 378 loop : 0.55 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS A 254 PHE 0.014 0.001 PHE F 255 TYR 0.010 0.001 TYR B 337 ARG 0.002 0.000 ARG E 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.42 seconds wall clock time: 65 minutes 22.62 seconds (3922.62 seconds total)