Starting phenix.real_space_refine on Sun Aug 24 07:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duu_47179/08_2025/9duu_47179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duu_47179/08_2025/9duu_47179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9duu_47179/08_2025/9duu_47179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duu_47179/08_2025/9duu_47179_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9duu_47179/08_2025/9duu_47179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duu_47179/08_2025/9duu_47179.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.148 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 3020 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 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17953 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 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: 3.89, per 1000 atoms: 0.22 Number of scatterers: 17953 At special positions: 0 Unit cell: (79.328, 100.64, 224.96, 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 3020 7.00 C 11327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP M 1 " - " ALA M 7 " " DTH M 4 " - " ALA M 3 " " TRP N 1 " - " ALA N 7 " " DTH N 4 " - " ALA N 3 " " TRP O 1 " - " ALA O 7 " " DTH O 4 " - " ALA O 3 " " TRP P 1 " - " ALA P 7 " " DTH P 4 " - " ALA P 3 " " TRP Q 1 " - " ALA Q 7 " " DTH Q 4 " - " ALA Q 3 " " TRP R 1 " - " ALA R 7 " " DTH R 4 " - " ALA R 3 " " TRP S 1 " - " ALA S 7 " " DTH S 4 " - " ALA S 3 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 744.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH M 4 " pdb=" CB DTH N 4 " pdb=" CB DTH O 4 " pdb=" CB DTH P 4 " pdb=" CB DTH Q 4 " pdb=" CB DTH R 4 " pdb=" CB DTH S 4 " Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 36 sheets defined 46.3% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 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: 3.655A 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 193 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.525A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.638A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.684A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (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: 3.666A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.535A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.644A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.612A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) 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 252 through 257 Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.567A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.527A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.536A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.520A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.729A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 181 through 193 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: 3.613A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.569A 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 258 through 263 removed outlier: 4.318A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.765A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.142A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.546A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) 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 351 through 355 removed outlier: 3.683A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 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 removed outlier: 3.655A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.298A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.896A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.867A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.529A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) 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 removed outlier: 3.528A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.799A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 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 removed outlier: 3.693A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) 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 252 through 257 Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.536A 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 288 through 295 removed outlier: 4.510A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.866A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (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 removed outlier: 3.516A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.896A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 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 Processing helix chain 'F' and resid 137 through 146 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 removed outlier: 3.583A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) No H-bonds generated for '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 295 removed outlier: 3.758A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.575A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (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 351 through 355 removed outlier: 3.700A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.323A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.086A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.126A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.463A 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 31 removed outlier: 4.300A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.096A 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: 5.744A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.489A 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 31 removed outlier: 4.423A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.118A 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 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.020A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.307A 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 31 removed outlier: 4.133A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.910A 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 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 5.973A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.113A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.531A pdb=" N HIS E 161 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.233A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.800A pdb=" N THR F 160 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 5.860A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 821 hydrogen bonds defined for protein. 2154 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: 2.64 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2971 1.27 - 1.40: 4394 1.40 - 1.54: 10583 1.54 - 1.67: 167 1.67 - 1.81: 229 Bond restraints: 18344 Sorted by residual: bond pdb=" C LYS F 238 " pdb=" O LYS F 238 " ideal model delta sigma weight residual 1.234 1.135 0.099 1.25e-02 6.40e+03 6.23e+01 bond pdb=" C LYS B 238 " pdb=" O LYS B 238 " ideal model delta sigma weight residual 1.234 1.135 0.099 1.28e-02 6.10e+03 6.03e+01 bond pdb=" C LYS C 238 " pdb=" O LYS C 238 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.28e-02 6.10e+03 5.27e+01 bond pdb=" C LYS D 238 " pdb=" O LYS D 238 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.30e-02 5.92e+03 3.79e+01 bond pdb=" C LYS A 238 " pdb=" O LYS A 238 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.25e-02 6.40e+03 3.04e+01 ... (remaining 18339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 24210 2.12 - 4.23: 548 4.23 - 6.35: 107 6.35 - 8.46: 23 8.46 - 10.58: 17 Bond angle restraints: 24905 Sorted by residual: angle pdb=" N LYS D 238 " pdb=" CA LYS D 238 " pdb=" CB LYS D 238 " ideal model delta sigma weight residual 111.08 102.59 8.49 1.71e+00 3.42e-01 2.47e+01 angle pdb=" C HYP N 6 " pdb=" N ALA N 7 " pdb=" CA ALA N 7 " ideal model delta sigma weight residual 121.70 113.20 8.50 1.80e+00 3.09e-01 2.23e+01 angle pdb=" C HYP S 6 " pdb=" N ALA S 7 " pdb=" CA ALA S 7 " ideal model delta sigma weight residual 121.70 113.22 8.48 1.80e+00 3.09e-01 2.22e+01 angle pdb=" C HYP Q 6 " pdb=" N ALA Q 7 " pdb=" CA ALA Q 7 " ideal model delta sigma weight residual 121.70 113.26 8.44 1.80e+00 3.09e-01 2.20e+01 angle pdb=" C HYP M 6 " pdb=" N ALA M 7 " pdb=" CA ALA M 7 " ideal model delta sigma weight residual 121.70 113.30 8.40 1.80e+00 3.09e-01 2.18e+01 ... (remaining 24900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 9916 24.12 - 48.25: 1004 48.25 - 72.37: 117 72.37 - 96.49: 18 96.49 - 120.62: 5 Dihedral angle restraints: 11060 sinusoidal: 4495 harmonic: 6565 Sorted by residual: 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 60.61 -120.62 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 55.47 -115.47 1 2.00e+01 2.50e-03 3.43e+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 54.29 -114.29 1 2.00e+01 2.50e-03 3.39e+01 ... (remaining 11057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2198 0.048 - 0.096: 397 0.096 - 0.144: 169 0.144 - 0.192: 10 0.192 - 0.240: 2 Chirality restraints: 2776 Sorted by residual: chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 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 9.27e-01 chirality pdb=" CA CYS R 5 " pdb=" N CYS R 5 " pdb=" C CYS R 5 " pdb=" CB CYS R 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 2773 not shown) Planarity restraints: 3170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 237 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU D 237 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU D 237 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS D 238 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 237 " 0.012 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C GLU C 237 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU C 237 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 238 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 237 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLU A 237 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU A 237 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 238 " 0.012 2.00e-02 2.50e+03 ... (remaining 3167 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 97 2.38 - 3.01: 9806 3.01 - 3.64: 26491 3.64 - 4.27: 40851 4.27 - 4.90: 71403 Nonbonded interactions: 148648 Sorted by model distance: nonbonded pdb=" CD1 TRP S 1 " pdb=" SG CYS S 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP N 1 " pdb=" SG CYS N 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP M 1 " pdb=" SG CYS M 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 ... (remaining 148643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.650 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.005 0.101 18358 Z= 0.274 Angle : 0.771 10.576 24947 Z= 0.391 Chirality : 0.045 0.240 2776 Planarity : 0.004 0.048 3156 Dihedral : 17.764 120.617 6818 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.37 % Favored : 95.36 % Rotamer: Outliers : 0.85 % Allowed : 29.70 % Favored : 69.45 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.19), residues: 2196 helix: 1.20 (0.18), residues: 930 sheet: 0.10 (0.34), residues: 282 loop : -0.04 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.009 0.001 TYR E 279 PHE 0.007 0.001 PHE B 200 TRP 0.012 0.002 TRP Q 1 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00511 (18344) covalent geometry : angle 0.75614 (24905) hydrogen bonds : bond 0.20464 ( 809) hydrogen bonds : angle 7.32226 ( 2154) link_TRANS : bond 0.00345 ( 14) link_TRANS : angle 3.71896 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 215 average time/residue: 0.1010 time to fit residues: 35.6857 Evaluate side-chains 209 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain M residue 5 CYS Chi-restraints excluded: chain N residue 5 CYS Chi-restraints excluded: chain O residue 5 CYS Chi-restraints excluded: chain P residue 5 CYS Chi-restraints excluded: chain Q residue 5 CYS Chi-restraints excluded: chain R residue 5 CYS Chi-restraints excluded: chain S residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.2980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.100636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.090231 restraints weight = 22020.898| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.18 r_work: 0.2775 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18358 Z= 0.144 Angle : 0.596 6.590 24947 Z= 0.283 Chirality : 0.046 0.194 2776 Planarity : 0.004 0.032 3156 Dihedral : 9.289 118.392 2636 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.05 % Favored : 94.67 % Rotamer: Outliers : 3.28 % Allowed : 26.22 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.19), residues: 2196 helix: 1.10 (0.18), residues: 948 sheet: 0.12 (0.29), residues: 354 loop : 0.12 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.008 0.001 TYR A 198 PHE 0.007 0.001 PHE D 255 TRP 0.020 0.002 TRP Q 1 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00340 (18344) covalent geometry : angle 0.59624 (24905) hydrogen bonds : bond 0.03386 ( 809) hydrogen bonds : angle 5.41987 ( 2154) link_TRANS : bond 0.00300 ( 14) link_TRANS : angle 0.68161 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.6565 (t80) REVERT: B 99 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: C 72 GLU cc_start: 0.8007 (pm20) cc_final: 0.7545 (pt0) REVERT: E 364 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7534 (mt-10) outliers start: 62 outliers final: 26 residues processed: 245 average time/residue: 0.0992 time to fit residues: 40.3532 Evaluate side-chains 223 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 125 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 174 optimal weight: 0.0020 chunk 168 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.089160 restraints weight = 22409.454| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.19 r_work: 0.2753 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18358 Z= 0.129 Angle : 0.567 6.425 24947 Z= 0.266 Chirality : 0.045 0.219 2776 Planarity : 0.003 0.032 3156 Dihedral : 8.663 116.731 2621 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.08 % Rotamer: Outliers : 2.64 % Allowed : 25.63 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.19), residues: 2196 helix: 1.14 (0.18), residues: 948 sheet: 0.04 (0.29), residues: 354 loop : 0.16 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 290 TYR 0.007 0.001 TYR A 198 PHE 0.007 0.001 PHE E 255 TRP 0.012 0.002 TRP E 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00306 (18344) covalent geometry : angle 0.56708 (24905) hydrogen bonds : bond 0.03052 ( 809) hydrogen bonds : angle 5.13744 ( 2154) link_TRANS : bond 0.00146 ( 14) link_TRANS : angle 0.59656 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 124 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.6794 (t80) REVERT: B 82 MET cc_start: 0.8905 (tpt) cc_final: 0.8463 (tpt) REVERT: B 99 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: C 72 GLU cc_start: 0.8068 (pm20) cc_final: 0.7795 (pt0) REVERT: C 82 MET cc_start: 0.8486 (mmm) cc_final: 0.8240 (tpt) REVERT: C 132 MET cc_start: 0.8559 (ttp) cc_final: 0.8093 (ttp) REVERT: C 283 MET cc_start: 0.7474 (ttm) cc_final: 0.7273 (mmt) outliers start: 50 outliers final: 28 residues processed: 233 average time/residue: 0.1029 time to fit residues: 39.2400 Evaluate side-chains 225 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 179 optimal weight: 0.0980 chunk 87 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.097466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.086598 restraints weight = 22312.150| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.21 r_work: 0.2706 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18358 Z= 0.166 Angle : 0.593 6.574 24947 Z= 0.280 Chirality : 0.047 0.234 2776 Planarity : 0.004 0.033 3156 Dihedral : 8.442 115.804 2621 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.24 % Favored : 94.49 % Rotamer: Outliers : 3.38 % Allowed : 25.21 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.19), residues: 2196 helix: 1.11 (0.18), residues: 942 sheet: -0.18 (0.28), residues: 366 loop : 0.16 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 372 TYR 0.013 0.001 TYR D 279 PHE 0.007 0.001 PHE A 255 TRP 0.013 0.002 TRP B 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00402 (18344) covalent geometry : angle 0.59344 (24905) hydrogen bonds : bond 0.03111 ( 809) hydrogen bonds : angle 4.98338 ( 2154) link_TRANS : bond 0.00205 ( 14) link_TRANS : angle 0.55708 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 194 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 124 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7050 (t80) REVERT: B 99 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: C 82 MET cc_start: 0.8545 (mmm) cc_final: 0.8322 (tpt) REVERT: C 132 MET cc_start: 0.8687 (ttp) cc_final: 0.8060 (ttt) REVERT: C 283 MET cc_start: 0.7639 (ttm) cc_final: 0.7428 (mmt) REVERT: D 132 MET cc_start: 0.8926 (tmm) cc_final: 0.8542 (ttp) REVERT: D 283 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6552 (ttm) REVERT: E 115 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8240 (t0) outliers start: 64 outliers final: 36 residues processed: 242 average time/residue: 0.0973 time to fit residues: 38.8227 Evaluate side-chains 224 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 12 ASN C 12 ASN D 12 ASN D 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.095176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.084340 restraints weight = 22381.104| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.21 r_work: 0.2679 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18358 Z= 0.197 Angle : 0.616 7.210 24947 Z= 0.291 Chirality : 0.048 0.247 2776 Planarity : 0.004 0.032 3156 Dihedral : 8.495 117.035 2621 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.33 % Favored : 94.40 % Rotamer: Outliers : 3.81 % Allowed : 25.00 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.19), residues: 2196 helix: 0.99 (0.18), residues: 942 sheet: -0.46 (0.26), residues: 378 loop : 0.06 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 372 TYR 0.008 0.001 TYR D 279 PHE 0.008 0.001 PHE C 255 TRP 0.014 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00482 (18344) covalent geometry : angle 0.61581 (24905) hydrogen bonds : bond 0.03198 ( 809) hydrogen bonds : angle 4.97493 ( 2154) link_TRANS : bond 0.00227 ( 14) link_TRANS : angle 0.58745 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.6993 (t80) REVERT: B 99 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: C 132 MET cc_start: 0.8770 (ttp) cc_final: 0.8164 (ttt) REVERT: D 283 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7194 (ttm) REVERT: E 115 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8291 (t0) REVERT: E 346 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8289 (tp) outliers start: 72 outliers final: 45 residues processed: 245 average time/residue: 0.0938 time to fit residues: 37.3659 Evaluate side-chains 238 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.094005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.083277 restraints weight = 22431.303| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 1.20 r_work: 0.2659 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18358 Z= 0.229 Angle : 0.642 7.521 24947 Z= 0.304 Chirality : 0.049 0.253 2776 Planarity : 0.004 0.034 3156 Dihedral : 8.568 117.346 2621 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.60 % Favored : 94.13 % Rotamer: Outliers : 4.02 % Allowed : 24.63 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.18), residues: 2196 helix: 0.89 (0.18), residues: 942 sheet: -0.63 (0.26), residues: 366 loop : -0.03 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.010 0.001 TYR A 133 PHE 0.008 0.001 PHE C 255 TRP 0.015 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00562 (18344) covalent geometry : angle 0.64167 (24905) hydrogen bonds : bond 0.03357 ( 809) hydrogen bonds : angle 4.99255 ( 2154) link_TRANS : bond 0.00275 ( 14) link_TRANS : angle 0.66206 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 188 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7012 (t80) REVERT: B 99 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: D 132 MET cc_start: 0.9000 (tmm) cc_final: 0.8513 (ttp) REVERT: D 283 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6999 (mtt) REVERT: E 115 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8345 (t0) REVERT: E 346 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8300 (tp) outliers start: 76 outliers final: 54 residues processed: 245 average time/residue: 0.0977 time to fit residues: 39.5034 Evaluate side-chains 243 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 89 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 193 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135683 restraints weight = 20052.277| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.37 r_work: 0.2685 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18358 Z= 0.150 Angle : 0.588 6.676 24947 Z= 0.276 Chirality : 0.047 0.248 2776 Planarity : 0.004 0.035 3156 Dihedral : 8.493 118.397 2621 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.74 % Favored : 94.99 % Rotamer: Outliers : 3.86 % Allowed : 24.63 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 2196 helix: 1.04 (0.18), residues: 942 sheet: -0.61 (0.26), residues: 378 loop : -0.00 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 290 TYR 0.008 0.001 TYR A 133 PHE 0.007 0.001 PHE E 255 TRP 0.014 0.002 TRP F 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00366 (18344) covalent geometry : angle 0.58824 (24905) hydrogen bonds : bond 0.02895 ( 809) hydrogen bonds : angle 4.87490 ( 2154) link_TRANS : bond 0.00168 ( 14) link_TRANS : angle 0.50412 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 196 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.6894 (t80) REVERT: B 99 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: D 132 MET cc_start: 0.8981 (tmm) cc_final: 0.8454 (ttp) REVERT: D 283 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7007 (mtt) REVERT: E 95 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8298 (ttm110) REVERT: E 115 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8316 (t0) REVERT: E 346 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8290 (tp) outliers start: 73 outliers final: 47 residues processed: 249 average time/residue: 0.0966 time to fit residues: 40.0435 Evaluate side-chains 238 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 197 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136285 restraints weight = 19966.965| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.36 r_work: 0.2677 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18358 Z= 0.141 Angle : 0.580 6.596 24947 Z= 0.272 Chirality : 0.046 0.245 2776 Planarity : 0.004 0.035 3156 Dihedral : 8.401 117.183 2621 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.15 % Favored : 94.58 % Rotamer: Outliers : 3.75 % Allowed : 24.47 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 2196 helix: 1.11 (0.18), residues: 942 sheet: -0.57 (0.26), residues: 378 loop : 0.03 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 290 TYR 0.009 0.001 TYR A 133 PHE 0.008 0.001 PHE E 255 TRP 0.014 0.002 TRP F 340 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00342 (18344) covalent geometry : angle 0.58031 (24905) hydrogen bonds : bond 0.02826 ( 809) hydrogen bonds : angle 4.81577 ( 2154) link_TRANS : bond 0.00157 ( 14) link_TRANS : angle 0.49501 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8028 (ttp) cc_final: 0.7646 (ttp) REVERT: A 124 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.6888 (t80) REVERT: B 99 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: D 132 MET cc_start: 0.9017 (tmm) cc_final: 0.8508 (ttp) REVERT: D 283 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7037 (mtt) REVERT: E 115 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8321 (t0) REVERT: E 132 MET cc_start: 0.8808 (ttp) cc_final: 0.8090 (tmm) REVERT: E 346 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8273 (tp) outliers start: 71 outliers final: 54 residues processed: 247 average time/residue: 0.0985 time to fit residues: 40.0191 Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 25 optimal weight: 0.5980 chunk 123 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 221 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138798 restraints weight = 19851.432| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.37 r_work: 0.2704 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18358 Z= 0.110 Angle : 0.558 6.712 24947 Z= 0.260 Chirality : 0.045 0.241 2776 Planarity : 0.003 0.035 3156 Dihedral : 8.258 115.828 2621 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.08 % Rotamer: Outliers : 3.22 % Allowed : 25.00 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.19), residues: 2196 helix: 1.23 (0.18), residues: 942 sheet: -0.51 (0.26), residues: 378 loop : 0.11 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 95 TYR 0.008 0.001 TYR A 133 PHE 0.007 0.001 PHE A 255 TRP 0.013 0.002 TRP E 340 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00261 (18344) covalent geometry : angle 0.55791 (24905) hydrogen bonds : bond 0.02596 ( 809) hydrogen bonds : angle 4.73056 ( 2154) link_TRANS : bond 0.00109 ( 14) link_TRANS : angle 0.38266 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7839 (ttp) cc_final: 0.7437 (ttp) REVERT: A 124 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.6800 (t80) REVERT: B 99 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: C 361 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7478 (mt-10) REVERT: D 30 VAL cc_start: 0.9387 (t) cc_final: 0.9186 (p) REVERT: D 132 MET cc_start: 0.9020 (tmm) cc_final: 0.8512 (ttp) REVERT: E 132 MET cc_start: 0.8819 (ttp) cc_final: 0.8085 (tmm) REVERT: E 346 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8241 (tp) outliers start: 61 outliers final: 49 residues processed: 247 average time/residue: 0.0968 time to fit residues: 39.6087 Evaluate side-chains 249 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 198 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 204 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.087225 restraints weight = 21930.958| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.17 r_work: 0.2705 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18358 Z= 0.136 Angle : 0.573 6.514 24947 Z= 0.267 Chirality : 0.046 0.243 2776 Planarity : 0.004 0.035 3156 Dihedral : 8.212 113.551 2621 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.01 % Favored : 94.72 % Rotamer: Outliers : 3.22 % Allowed : 24.95 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.19), residues: 2196 helix: 1.19 (0.18), residues: 942 sheet: -0.53 (0.26), residues: 378 loop : 0.11 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 95 TYR 0.010 0.001 TYR D 279 PHE 0.007 0.001 PHE A 255 TRP 0.013 0.002 TRP F 340 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00328 (18344) covalent geometry : angle 0.57352 (24905) hydrogen bonds : bond 0.02750 ( 809) hydrogen bonds : angle 4.71724 ( 2154) link_TRANS : bond 0.00139 ( 14) link_TRANS : angle 0.44517 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 197 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.6818 (t80) REVERT: B 99 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: C 361 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7472 (mt-10) REVERT: D 132 MET cc_start: 0.9012 (tmm) cc_final: 0.8532 (ttp) REVERT: E 143 TYR cc_start: 0.8350 (m-80) cc_final: 0.8064 (m-80) REVERT: E 346 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8140 (tp) outliers start: 61 outliers final: 52 residues processed: 245 average time/residue: 0.1041 time to fit residues: 42.2846 Evaluate side-chains 251 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 38 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 131 optimal weight: 0.0770 chunk 206 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.097868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.087114 restraints weight = 22124.181| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.20 r_work: 0.2711 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18358 Z= 0.125 Angle : 0.567 6.495 24947 Z= 0.264 Chirality : 0.046 0.242 2776 Planarity : 0.003 0.035 3156 Dihedral : 8.166 113.214 2621 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 3.17 % Allowed : 25.05 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 2196 helix: 1.23 (0.18), residues: 942 sheet: -0.48 (0.26), residues: 378 loop : 0.14 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 95 TYR 0.011 0.001 TYR D 279 PHE 0.007 0.001 PHE A 255 TRP 0.013 0.002 TRP F 340 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00300 (18344) covalent geometry : angle 0.56726 (24905) hydrogen bonds : bond 0.02667 ( 809) hydrogen bonds : angle 4.69645 ( 2154) link_TRANS : bond 0.00130 ( 14) link_TRANS : angle 0.41399 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2984.66 seconds wall clock time: 52 minutes 18.77 seconds (3138.77 seconds total)