Starting phenix.real_space_refine on Sun May 3 21:23:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fju_50516/05_2026/9fju_50516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fju_50516/05_2026/9fju_50516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fju_50516/05_2026/9fju_50516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fju_50516/05_2026/9fju_50516.map" model { file = "/net/cci-nas-00/data/ceres_data/9fju_50516/05_2026/9fju_50516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fju_50516/05_2026/9fju_50516.cif" } resolution = 3.84 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= 0.046 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 8 5.21 5 S 104 5.16 5 C 10084 2.51 5 N 2666 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15968 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 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: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 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: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 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: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 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: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1990 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain breaks: 1 Chain: "F" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1990 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain breaks: 1 Chain: "G" 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: "G" 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: "H" 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: "H" 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: "I" 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: "I" 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: "J" 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: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.53, per 1000 atoms: 0.28 Number of scatterers: 15968 At special positions: 0 Unit cell: (108.24, 80.08, 190.08, 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 104 16.00 P 12 15.00 Mg 8 11.99 O 3094 8.00 N 2666 7.00 C 10084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 173 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 173 " - pdb=" SG CYS F 209 " distance=2.03 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 BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG K 1 " - " ASN E 18 " " NAG L 1 " - " ASN F 18 " TRANS " TRP G 1 " - " ALA G 7 " " DTH G 4 " - " ALA G 3 " " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 838.3 milliseconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 27 sheets defined 44.4% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.879A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.807A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.921A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.766A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.684A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.626A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.858A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.778A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 4.325A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 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 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.526A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.936A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.879A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 4.298A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.675A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.677A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.805A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.644A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.575A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.799A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 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 349 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.509A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.527A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.855A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.798A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.839A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.787A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.776A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.917A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 removed outlier: 3.502A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.626A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.744A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.816A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.847A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.765A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.524A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.598A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.631A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.973A pdb=" N MET D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.735A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.543A pdb=" N PHE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 removed outlier: 3.530A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.609A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.536A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.561A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.117A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 removed outlier: 4.365A pdb=" N ASN E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 31 removed outlier: 3.890A pdb=" N ARG E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.534A pdb=" N GLY E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 139 through 158 removed outlier: 4.347A pdb=" N GLU E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.905A pdb=" N SER E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.956A pdb=" N SER E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 Processing helix chain 'E' and resid 242 through 250 Processing helix chain 'F' and resid 12 through 17 removed outlier: 4.039A pdb=" N MET F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.740A pdb=" N VAL F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 54 removed outlier: 3.675A pdb=" N GLY F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 155 removed outlier: 3.743A pdb=" N ASN F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR F 148 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN F 155 " --> pdb=" O TYR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 184 Processing helix chain 'F' and resid 218 through 225 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 242 through 250 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.693A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.744A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) 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 131 through 132 removed outlier: 3.942A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 357 " --> pdb=" O MET A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.676A pdb=" N LEU A 176 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 154 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.527A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.599A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.832A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) 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 176 through 178 removed outlier: 4.370A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.626A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.512A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 133 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.092A pdb=" N VAL E 67 " --> pdb=" O VAL C 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.711A pdb=" N LEU C 176 " --> pdb=" O THR C 162 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.473A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.730A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 66 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.505A pdb=" N ILE D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.547A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 165 through 166 removed outlier: 3.688A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.775A pdb=" N VAL E 255 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 256 " --> pdb=" O ALA E 231 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 231 " --> pdb=" O GLU E 256 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 89 through 95 removed outlier: 3.653A pdb=" N SER E 90 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS E 117 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR E 94 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL E 115 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE E 128 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N MET E 164 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA E 129 " --> pdb=" O MET E 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 193 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.611A pdb=" N LEU F 83 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN F 38 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE F 8 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL F 40 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR F 10 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU F 256 " --> pdb=" O ALA F 231 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 231 " --> pdb=" O GLU F 256 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 89 through 96 removed outlier: 6.569A pdb=" N VAL F 91 " --> pdb=" O SER F 119 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER F 119 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP F 93 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA F 114 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA F 132 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 116 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 128 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N MET F 164 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA F 129 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET F 166 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 131 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP F 168 " --> pdb=" O VAL F 131 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1581 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: 2.83 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2625 1.31 - 1.43: 4350 1.43 - 1.56: 9127 1.56 - 1.69: 32 1.69 - 1.82: 176 Bond restraints: 16310 Sorted by residual: bond pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 1.346 1.475 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C7 NAG L 2 " pdb=" N2 NAG L 2 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C7 NAG L 1 " pdb=" N2 NAG L 1 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C7 NAG K 1 " pdb=" N2 NAG K 1 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.28e+01 ... (remaining 16305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 21749 1.92 - 3.84: 299 3.84 - 5.76: 81 5.76 - 7.68: 24 7.68 - 9.60: 5 Bond angle restraints: 22158 Sorted by residual: angle pdb=" N ILE D 289 " pdb=" CA ILE D 289 " pdb=" C ILE D 289 " ideal model delta sigma weight residual 112.83 109.47 3.36 9.90e-01 1.02e+00 1.15e+01 angle pdb=" C EEP H 2 " pdb=" CA EEP H 2 " pdb=" CB EEP H 2 " ideal model delta sigma weight residual 110.50 105.54 4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" CB MET D 44 " pdb=" CG MET D 44 " pdb=" SD MET D 44 " ideal model delta sigma weight residual 112.70 122.30 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" N GLY B 150 " pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 110.96 114.70 -3.74 1.19e+00 7.06e-01 9.87e+00 angle pdb=" C EEP I 2 " pdb=" CA EEP I 2 " pdb=" CB EEP I 2 " ideal model delta sigma weight residual 110.50 105.80 4.70 1.50e+00 4.44e-01 9.82e+00 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.57: 9211 28.57 - 57.14: 528 57.14 - 85.71: 54 85.71 - 114.28: 51 114.28 - 142.85: 4 Dihedral angle restraints: 9848 sinusoidal: 3984 harmonic: 5864 Sorted by residual: dihedral pdb=" CB CYS E 173 " pdb=" SG CYS E 173 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual -86.00 -161.59 75.59 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 157.15 142.85 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" CA TRP I 1 " pdb=" N TRP I 1 " pdb=" C ALA I 7 " pdb=" CA ALA I 7 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2205 0.068 - 0.136: 285 0.136 - 0.204: 6 0.204 - 0.272: 0 0.272 - 0.340: 2 Chirality restraints: 2498 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN F 18 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN E 18 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA HYP I 6 " pdb=" N HYP I 6 " pdb=" C HYP I 6 " pdb=" CB HYP I 6 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 2495 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N TRP G 1 " -0.036 2.00e-02 2.50e+03 6.22e-02 3.86e+01 pdb=" CA ALA G 7 " -0.031 2.00e-02 2.50e+03 pdb=" C ALA G 7 " 0.107 2.00e-02 2.50e+03 pdb=" O ALA G 7 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TRP J 1 " 0.022 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" CA ALA J 7 " 0.019 2.00e-02 2.50e+03 pdb=" C ALA J 7 " -0.066 2.00e-02 2.50e+03 pdb=" O ALA J 7 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TRP H 1 " 0.021 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" CA ALA H 7 " 0.018 2.00e-02 2.50e+03 pdb=" C ALA H 7 " -0.064 2.00e-02 2.50e+03 pdb=" O ALA H 7 " 0.024 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 43 2.34 - 2.98: 8174 2.98 - 3.62: 24423 3.62 - 4.26: 36266 4.26 - 4.90: 59227 Nonbonded interactions: 128133 Sorted by model distance: nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.705 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.727 3.620 nonbonded pdb=" CD1 TRP G 1 " pdb=" SG CYS G 5 " model vdw 1.727 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.730 3.620 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.976 2.170 ... (remaining 128128 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' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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 group one per residue 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.580 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.004 0.129 16324 Z= 0.203 Angle : 0.664 19.132 22198 Z= 0.316 Chirality : 0.044 0.340 2498 Planarity : 0.003 0.080 2802 Dihedral : 18.821 142.847 6050 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.18 % Allowed : 22.18 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1958 helix: -0.20 (0.20), residues: 674 sheet: 0.46 (0.29), residues: 374 loop : 0.40 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 95 TYR 0.011 0.001 TYR E 63 PHE 0.026 0.001 PHE C 255 TRP 0.016 0.001 TRP F 194 HIS 0.007 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00416 (16310) covalent geometry : angle 0.61302 (22158) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.79574 ( 4) hydrogen bonds : bond 0.31045 ( 605) hydrogen bonds : angle 8.05070 ( 1581) link_BETA1-4 : bond 0.00232 ( 2) link_BETA1-4 : angle 0.77683 ( 6) link_NAG-ASN : bond 0.01037 ( 2) link_NAG-ASN : angle 5.75031 ( 6) link_TRANS : bond 0.01340 ( 8) link_TRANS : angle 7.23200 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 MET cc_start: 0.8525 (ttm) cc_final: 0.8315 (ttp) REVERT: C 223 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6614 (t80) outliers start: 3 outliers final: 1 residues processed: 163 average time/residue: 0.1095 time to fit residues: 28.7956 Evaluate side-chains 156 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 59 GLN C 371 HIS E 155 GLN F 134 HIS F 252 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.095895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074361 restraints weight = 44824.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076935 restraints weight = 26512.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078704 restraints weight = 18215.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079950 restraints weight = 13814.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080798 restraints weight = 11274.649| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 16324 Z= 0.291 Angle : 0.759 10.838 22198 Z= 0.367 Chirality : 0.050 0.324 2498 Planarity : 0.005 0.057 2802 Dihedral : 13.533 133.645 2373 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.64 % Allowed : 20.42 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1958 helix: -0.12 (0.19), residues: 704 sheet: 0.49 (0.29), residues: 350 loop : 0.04 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 79 TYR 0.019 0.002 TYR F 80 PHE 0.023 0.002 PHE E 6 TRP 0.010 0.002 TRP C 356 HIS 0.011 0.002 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00664 (16310) covalent geometry : angle 0.74676 (22158) SS BOND : bond 0.00238 ( 2) SS BOND : angle 1.02205 ( 4) hydrogen bonds : bond 0.05777 ( 605) hydrogen bonds : angle 5.83255 ( 1581) link_BETA1-4 : bond 0.00333 ( 2) link_BETA1-4 : angle 3.63787 ( 6) link_NAG-ASN : bond 0.00723 ( 2) link_NAG-ASN : angle 6.63861 ( 6) link_TRANS : bond 0.00411 ( 8) link_TRANS : angle 1.82387 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 173 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8912 (mm) REVERT: B 213 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8503 (ttmm) REVERT: B 352 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7741 (t80) REVERT: C 153 MET cc_start: 0.8519 (tmm) cc_final: 0.8175 (tmm) REVERT: C 223 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7450 (t80) REVERT: D 283 MET cc_start: 0.8598 (mmp) cc_final: 0.8326 (mmt) REVERT: E 96 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8104 (mm-40) REVERT: E 166 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7932 (mpp) REVERT: E 180 GLN cc_start: 0.8180 (pt0) cc_final: 0.7947 (pm20) REVERT: F 16 MET cc_start: 0.8868 (mpp) cc_final: 0.8148 (mpp) outliers start: 79 outliers final: 49 residues processed: 233 average time/residue: 0.1057 time to fit residues: 39.5506 Evaluate side-chains 202 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 148 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 178 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 143 optimal weight: 0.0980 chunk 34 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 GLN F 170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.099299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078144 restraints weight = 44468.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080828 restraints weight = 25855.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082655 restraints weight = 17498.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083828 restraints weight = 13177.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.084802 restraints weight = 10731.891| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16324 Z= 0.110 Angle : 0.631 10.708 22198 Z= 0.293 Chirality : 0.047 0.373 2498 Planarity : 0.003 0.043 2802 Dihedral : 11.140 133.100 2373 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.29 % Allowed : 21.95 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1958 helix: 0.08 (0.19), residues: 742 sheet: 0.34 (0.30), residues: 338 loop : 0.19 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 79 TYR 0.029 0.001 TYR A 240 PHE 0.018 0.001 PHE E 6 TRP 0.014 0.001 TRP F 194 HIS 0.006 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00232 (16310) covalent geometry : angle 0.61373 (22158) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.82751 ( 4) hydrogen bonds : bond 0.04123 ( 605) hydrogen bonds : angle 5.24823 ( 1581) link_BETA1-4 : bond 0.00653 ( 2) link_BETA1-4 : angle 5.48504 ( 6) link_NAG-ASN : bond 0.00860 ( 2) link_NAG-ASN : angle 6.81946 ( 6) link_TRANS : bond 0.00322 ( 8) link_TRANS : angle 1.31973 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: C 82 MET cc_start: 0.8637 (tpt) cc_final: 0.8416 (tpt) REVERT: D 217 CYS cc_start: 0.8028 (m) cc_final: 0.7660 (m) REVERT: D 283 MET cc_start: 0.8515 (mmp) cc_final: 0.8161 (mmt) REVERT: E 155 GLN cc_start: 0.6842 (mm110) cc_final: 0.6534 (pp30) REVERT: E 166 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7873 (mpp) REVERT: F 16 MET cc_start: 0.8899 (mpp) cc_final: 0.8162 (mpp) REVERT: F 50 LYS cc_start: 0.9294 (mtpp) cc_final: 0.8942 (mtmm) REVERT: F 112 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7419 (mm-30) REVERT: F 127 GLU cc_start: 0.7582 (mp0) cc_final: 0.7373 (mp0) REVERT: F 164 MET cc_start: 0.8118 (tpp) cc_final: 0.7875 (tpp) outliers start: 56 outliers final: 38 residues processed: 230 average time/residue: 0.1072 time to fit residues: 39.1439 Evaluate side-chains 203 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN F 134 HIS F 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073820 restraints weight = 44694.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076289 restraints weight = 26413.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078037 restraints weight = 18240.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079255 restraints weight = 13855.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080073 restraints weight = 11338.482| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16324 Z= 0.284 Angle : 0.753 11.435 22198 Z= 0.358 Chirality : 0.051 0.395 2498 Planarity : 0.004 0.044 2802 Dihedral : 11.246 135.644 2373 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.99 % Allowed : 22.07 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1958 helix: -0.03 (0.19), residues: 728 sheet: 0.21 (0.29), residues: 358 loop : -0.02 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 177 TYR 0.022 0.002 TYR A 240 PHE 0.020 0.002 PHE C 127 TRP 0.011 0.002 TRP E 181 HIS 0.013 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00651 (16310) covalent geometry : angle 0.73888 (22158) SS BOND : bond 0.00235 ( 2) SS BOND : angle 1.09515 ( 4) hydrogen bonds : bond 0.04887 ( 605) hydrogen bonds : angle 5.38003 ( 1581) link_BETA1-4 : bond 0.00683 ( 2) link_BETA1-4 : angle 4.95659 ( 6) link_NAG-ASN : bond 0.00931 ( 2) link_NAG-ASN : angle 7.31468 ( 6) link_TRANS : bond 0.00186 ( 8) link_TRANS : angle 0.87405 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 163 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8768 (mm) REVERT: B 213 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8372 (ttmm) REVERT: B 352 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7893 (t80) REVERT: C 176 LEU cc_start: 0.8833 (mp) cc_final: 0.8631 (mp) REVERT: F 16 MET cc_start: 0.8967 (mpp) cc_final: 0.8071 (mpp) REVERT: F 112 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7656 (mm-30) REVERT: F 180 GLN cc_start: 0.8692 (mt0) cc_final: 0.8470 (pt0) outliers start: 85 outliers final: 63 residues processed: 231 average time/residue: 0.0989 time to fit residues: 36.7853 Evaluate side-chains 219 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 153 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 121 HIS Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 179 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.097925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076454 restraints weight = 44517.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079100 restraints weight = 26048.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.080916 restraints weight = 17761.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082130 restraints weight = 13411.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083045 restraints weight = 10936.904| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16324 Z= 0.124 Angle : 0.649 11.184 22198 Z= 0.300 Chirality : 0.048 0.407 2498 Planarity : 0.004 0.043 2802 Dihedral : 10.632 134.433 2371 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.17 % Allowed : 23.83 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1958 helix: 0.20 (0.20), residues: 728 sheet: 0.26 (0.29), residues: 348 loop : 0.01 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 213 TYR 0.016 0.001 TYR A 240 PHE 0.016 0.001 PHE F 82 TRP 0.032 0.001 TRP F 194 HIS 0.009 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00280 (16310) covalent geometry : angle 0.63241 (22158) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.86094 ( 4) hydrogen bonds : bond 0.03653 ( 605) hydrogen bonds : angle 4.98285 ( 1581) link_BETA1-4 : bond 0.00678 ( 2) link_BETA1-4 : angle 5.05776 ( 6) link_NAG-ASN : bond 0.00920 ( 2) link_NAG-ASN : angle 7.28815 ( 6) link_TRANS : bond 0.00161 ( 8) link_TRANS : angle 0.98155 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8511 (mmp) cc_final: 0.8295 (tpp) REVERT: A 293 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8747 (mm) REVERT: B 213 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8671 (ttmm) REVERT: D 82 MET cc_start: 0.8477 (tpt) cc_final: 0.8192 (tpt) REVERT: D 217 CYS cc_start: 0.8148 (m) cc_final: 0.7814 (m) REVERT: E 96 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7562 (tm-30) REVERT: F 16 MET cc_start: 0.8916 (mpp) cc_final: 0.7808 (mpp) REVERT: F 50 LYS cc_start: 0.9286 (mtpp) cc_final: 0.8932 (mtmm) REVERT: F 112 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7482 (mm-30) outliers start: 54 outliers final: 42 residues processed: 210 average time/residue: 0.1059 time to fit residues: 35.1305 Evaluate side-chains 202 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 152 optimal weight: 0.0870 chunk 181 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 97 optimal weight: 0.0060 overall best weight: 1.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.097969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076566 restraints weight = 44180.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079194 restraints weight = 25804.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081007 restraints weight = 17609.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082259 restraints weight = 13311.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083147 restraints weight = 10808.722| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16324 Z= 0.122 Angle : 0.643 11.319 22198 Z= 0.296 Chirality : 0.048 0.415 2498 Planarity : 0.003 0.042 2802 Dihedral : 10.385 133.359 2371 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.76 % Allowed : 23.18 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.19), residues: 1958 helix: 0.24 (0.20), residues: 730 sheet: 0.32 (0.29), residues: 348 loop : 0.06 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 79 TYR 0.017 0.001 TYR F 95 PHE 0.014 0.001 PHE C 255 TRP 0.043 0.001 TRP F 194 HIS 0.008 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00279 (16310) covalent geometry : angle 0.62528 (22158) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.77798 ( 4) hydrogen bonds : bond 0.03434 ( 605) hydrogen bonds : angle 4.85358 ( 1581) link_BETA1-4 : bond 0.00663 ( 2) link_BETA1-4 : angle 5.06604 ( 6) link_NAG-ASN : bond 0.00918 ( 2) link_NAG-ASN : angle 7.42807 ( 6) link_TRANS : bond 0.00152 ( 8) link_TRANS : angle 0.97664 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8742 (mm) REVERT: B 213 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8640 (ttmm) REVERT: B 269 MET cc_start: 0.7794 (tpp) cc_final: 0.7453 (tpp) REVERT: C 119 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8032 (ttt) REVERT: D 82 MET cc_start: 0.8428 (tpt) cc_final: 0.8154 (tpt) REVERT: D 217 CYS cc_start: 0.8151 (m) cc_final: 0.7799 (m) REVERT: E 156 GLN cc_start: 0.8443 (pp30) cc_final: 0.7963 (pp30) REVERT: F 16 MET cc_start: 0.8909 (mpp) cc_final: 0.7838 (mpp) REVERT: F 50 LYS cc_start: 0.9284 (mtpp) cc_final: 0.8931 (mtmm) REVERT: F 112 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7510 (mm-30) REVERT: F 180 GLN cc_start: 0.8685 (mt0) cc_final: 0.8439 (pt0) outliers start: 64 outliers final: 50 residues processed: 221 average time/residue: 0.0992 time to fit residues: 35.4598 Evaluate side-chains 214 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.095273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074050 restraints weight = 44143.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076532 restraints weight = 26059.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.078252 restraints weight = 18051.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079473 restraints weight = 13780.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080337 restraints weight = 11274.415| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16324 Z= 0.258 Angle : 0.740 11.735 22198 Z= 0.348 Chirality : 0.050 0.425 2498 Planarity : 0.004 0.038 2802 Dihedral : 10.540 133.964 2371 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.75 % Allowed : 23.06 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 1958 helix: 0.07 (0.19), residues: 728 sheet: 0.04 (0.29), residues: 356 loop : -0.09 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 177 TYR 0.018 0.002 TYR F 80 PHE 0.022 0.002 PHE C 255 TRP 0.041 0.002 TRP F 194 HIS 0.015 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00593 (16310) covalent geometry : angle 0.72404 (22158) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.92034 ( 4) hydrogen bonds : bond 0.04355 ( 605) hydrogen bonds : angle 5.09584 ( 1581) link_BETA1-4 : bond 0.00594 ( 2) link_BETA1-4 : angle 4.99466 ( 6) link_NAG-ASN : bond 0.00959 ( 2) link_NAG-ASN : angle 7.67127 ( 6) link_TRANS : bond 0.00139 ( 8) link_TRANS : angle 0.92041 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 171 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8792 (mm) REVERT: B 12 ASN cc_start: 0.8733 (t0) cc_final: 0.7953 (p0) REVERT: B 87 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.8030 (t-90) REVERT: B 213 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8847 (ttmm) REVERT: B 237 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: B 269 MET cc_start: 0.7877 (tpp) cc_final: 0.7528 (tpp) REVERT: D 51 ASP cc_start: 0.7502 (p0) cc_final: 0.7002 (m-30) REVERT: D 82 MET cc_start: 0.8458 (tpt) cc_final: 0.8224 (tpt) REVERT: D 217 CYS cc_start: 0.8353 (m) cc_final: 0.8042 (m) REVERT: D 305 MET cc_start: 0.8195 (mpp) cc_final: 0.7941 (mpp) REVERT: E 35 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8800 (m) REVERT: E 51 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8533 (tp) REVERT: E 77 LYS cc_start: 0.7658 (mmtt) cc_final: 0.6872 (mmtm) REVERT: F 16 MET cc_start: 0.8920 (mpp) cc_final: 0.7928 (mpp) REVERT: F 50 LYS cc_start: 0.9258 (mtpp) cc_final: 0.8917 (mtmm) REVERT: F 112 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7548 (mm-30) REVERT: F 133 LEU cc_start: 0.7548 (tp) cc_final: 0.7342 (tt) outliers start: 81 outliers final: 56 residues processed: 235 average time/residue: 0.0980 time to fit residues: 37.3471 Evaluate side-chains 219 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 157 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 121 HIS Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 11 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 143 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.097337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075828 restraints weight = 44464.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078447 restraints weight = 26027.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080258 restraints weight = 17780.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081496 restraints weight = 13472.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082393 restraints weight = 10983.091| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16324 Z= 0.129 Angle : 0.673 11.725 22198 Z= 0.310 Chirality : 0.048 0.481 2498 Planarity : 0.003 0.041 2802 Dihedral : 10.163 133.893 2371 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.76 % Allowed : 23.88 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1958 helix: 0.24 (0.20), residues: 728 sheet: 0.13 (0.29), residues: 348 loop : -0.05 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 254 TYR 0.011 0.001 TYR A 240 PHE 0.012 0.001 PHE E 82 TRP 0.034 0.001 TRP F 194 HIS 0.011 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00298 (16310) covalent geometry : angle 0.65477 (22158) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.82413 ( 4) hydrogen bonds : bond 0.03463 ( 605) hydrogen bonds : angle 4.84833 ( 1581) link_BETA1-4 : bond 0.00826 ( 2) link_BETA1-4 : angle 5.02006 ( 6) link_NAG-ASN : bond 0.00801 ( 2) link_NAG-ASN : angle 7.82330 ( 6) link_TRANS : bond 0.00147 ( 8) link_TRANS : angle 0.98106 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8802 (mm) REVERT: B 12 ASN cc_start: 0.8710 (t0) cc_final: 0.7938 (p0) REVERT: B 192 ILE cc_start: 0.9108 (tp) cc_final: 0.8848 (tp) REVERT: B 213 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8894 (ttmm) REVERT: B 237 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: B 269 MET cc_start: 0.7912 (tpp) cc_final: 0.7581 (tpp) REVERT: C 119 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.8049 (ttt) REVERT: D 82 MET cc_start: 0.8351 (tpt) cc_final: 0.8138 (tpt) REVERT: D 217 CYS cc_start: 0.8465 (m) cc_final: 0.8147 (m) REVERT: D 305 MET cc_start: 0.8208 (mpp) cc_final: 0.7937 (mpp) REVERT: E 51 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8511 (tp) REVERT: E 77 LYS cc_start: 0.7696 (mmtt) cc_final: 0.6931 (mmtm) REVERT: E 156 GLN cc_start: 0.8569 (pp30) cc_final: 0.8130 (pp30) REVERT: F 16 MET cc_start: 0.8869 (mpp) cc_final: 0.7884 (mpp) REVERT: F 36 LEU cc_start: 0.8783 (mm) cc_final: 0.8474 (mm) REVERT: F 50 LYS cc_start: 0.9268 (mtpp) cc_final: 0.8899 (mtmm) REVERT: F 133 LEU cc_start: 0.7523 (tp) cc_final: 0.7288 (tt) REVERT: F 166 MET cc_start: 0.7810 (tpt) cc_final: 0.7552 (tpp) REVERT: F 180 GLN cc_start: 0.8680 (mt0) cc_final: 0.8447 (pt0) outliers start: 64 outliers final: 50 residues processed: 222 average time/residue: 0.1037 time to fit residues: 36.6881 Evaluate side-chains 218 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 121 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077109 restraints weight = 44128.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079770 restraints weight = 25724.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081605 restraints weight = 17525.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082846 restraints weight = 13216.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.083652 restraints weight = 10764.419| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16324 Z= 0.111 Angle : 0.665 11.884 22198 Z= 0.304 Chirality : 0.048 0.520 2498 Planarity : 0.003 0.043 2802 Dihedral : 9.880 131.599 2370 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.11 % Allowed : 24.53 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.19), residues: 1958 helix: 0.33 (0.20), residues: 728 sheet: 0.18 (0.29), residues: 348 loop : 0.03 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 28 TYR 0.012 0.001 TYR A 240 PHE 0.026 0.001 PHE E 82 TRP 0.034 0.001 TRP F 194 HIS 0.008 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00252 (16310) covalent geometry : angle 0.64582 (22158) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.74744 ( 4) hydrogen bonds : bond 0.03098 ( 605) hydrogen bonds : angle 4.73896 ( 1581) link_BETA1-4 : bond 0.00766 ( 2) link_BETA1-4 : angle 5.14523 ( 6) link_NAG-ASN : bond 0.00779 ( 2) link_NAG-ASN : angle 8.06192 ( 6) link_TRANS : bond 0.00179 ( 8) link_TRANS : angle 1.01838 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8846 (mm) REVERT: B 12 ASN cc_start: 0.8664 (t0) cc_final: 0.7981 (p0) REVERT: B 192 ILE cc_start: 0.9019 (tp) cc_final: 0.8768 (tp) REVERT: B 213 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8837 (ttmm) REVERT: B 237 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: D 217 CYS cc_start: 0.8481 (m) cc_final: 0.8154 (m) REVERT: D 305 MET cc_start: 0.8182 (mpp) cc_final: 0.7970 (mpp) REVERT: E 51 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8495 (tp) REVERT: E 77 LYS cc_start: 0.7624 (mmtt) cc_final: 0.6918 (mmtm) REVERT: E 156 GLN cc_start: 0.8482 (pp30) cc_final: 0.8134 (pp30) REVERT: E 245 MET cc_start: 0.8201 (pmm) cc_final: 0.7961 (pmm) REVERT: F 16 MET cc_start: 0.8828 (mpp) cc_final: 0.7882 (mpp) REVERT: F 36 LEU cc_start: 0.8571 (mm) cc_final: 0.8288 (mm) REVERT: F 50 LYS cc_start: 0.9267 (mtpp) cc_final: 0.8909 (mtmm) REVERT: F 133 LEU cc_start: 0.7516 (tp) cc_final: 0.7291 (tt) REVERT: F 180 GLN cc_start: 0.8691 (mt0) cc_final: 0.8455 (pt0) outliers start: 53 outliers final: 46 residues processed: 222 average time/residue: 0.1024 time to fit residues: 36.7315 Evaluate side-chains 220 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 59 GLN E 44 HIS ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.095980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074669 restraints weight = 45114.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077175 restraints weight = 27127.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.078886 restraints weight = 18865.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080046 restraints weight = 14495.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080910 restraints weight = 11943.939| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16324 Z= 0.235 Angle : 0.747 12.456 22198 Z= 0.348 Chirality : 0.051 0.532 2498 Planarity : 0.004 0.041 2802 Dihedral : 10.130 131.547 2370 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.93 % Allowed : 25.23 % 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 are not related in a simple way. whole: -0.09 (0.19), residues: 1958 helix: 0.13 (0.20), residues: 728 sheet: -0.05 (0.28), residues: 356 loop : -0.03 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 28 TYR 0.015 0.001 TYR F 32 PHE 0.028 0.002 PHE C 255 TRP 0.037 0.002 TRP F 194 HIS 0.012 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00545 (16310) covalent geometry : angle 0.72976 (22158) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.85639 ( 4) hydrogen bonds : bond 0.04040 ( 605) hydrogen bonds : angle 4.99192 ( 1581) link_BETA1-4 : bond 0.00752 ( 2) link_BETA1-4 : angle 5.07198 ( 6) link_NAG-ASN : bond 0.00820 ( 2) link_NAG-ASN : angle 8.20748 ( 6) link_TRANS : bond 0.00121 ( 8) link_TRANS : angle 0.91430 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8831 (mm) REVERT: B 12 ASN cc_start: 0.8774 (t0) cc_final: 0.8150 (p0) REVERT: B 192 ILE cc_start: 0.9174 (tp) cc_final: 0.8917 (tp) REVERT: B 213 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8975 (ttmm) REVERT: B 237 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: D 217 CYS cc_start: 0.8555 (m) cc_final: 0.8251 (m) REVERT: D 305 MET cc_start: 0.8173 (mpp) cc_final: 0.7890 (mpp) REVERT: E 51 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8599 (tp) REVERT: E 77 LYS cc_start: 0.7616 (mmtt) cc_final: 0.6830 (mmtm) REVERT: E 245 MET cc_start: 0.8314 (pmm) cc_final: 0.8007 (pmm) REVERT: F 16 MET cc_start: 0.8871 (mpp) cc_final: 0.7897 (mpp) REVERT: F 36 LEU cc_start: 0.8593 (mm) cc_final: 0.8222 (mm) REVERT: F 50 LYS cc_start: 0.9271 (mtpp) cc_final: 0.8905 (mtmm) REVERT: F 133 LEU cc_start: 0.7532 (tp) cc_final: 0.7294 (tt) REVERT: F 180 GLN cc_start: 0.8681 (mt0) cc_final: 0.8449 (pt0) outliers start: 50 outliers final: 43 residues processed: 207 average time/residue: 0.1014 time to fit residues: 34.0332 Evaluate side-chains 213 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 169 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077123 restraints weight = 43995.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079804 restraints weight = 25696.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081631 restraints weight = 17480.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082880 restraints weight = 13221.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.083769 restraints weight = 10742.700| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16324 Z= 0.107 Angle : 0.689 12.734 22198 Z= 0.314 Chirality : 0.049 0.530 2498 Planarity : 0.003 0.043 2802 Dihedral : 9.807 131.526 2370 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.35 % Allowed : 26.12 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1958 helix: 0.33 (0.20), residues: 728 sheet: 0.12 (0.29), residues: 348 loop : 0.02 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 28 TYR 0.019 0.001 TYR F 32 PHE 0.027 0.001 PHE C 255 TRP 0.037 0.002 TRP F 194 HIS 0.008 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00238 (16310) covalent geometry : angle 0.67045 (22158) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.79367 ( 4) hydrogen bonds : bond 0.03073 ( 605) hydrogen bonds : angle 4.73501 ( 1581) link_BETA1-4 : bond 0.00714 ( 2) link_BETA1-4 : angle 5.17218 ( 6) link_NAG-ASN : bond 0.00755 ( 2) link_NAG-ASN : angle 8.18052 ( 6) link_TRANS : bond 0.00198 ( 8) link_TRANS : angle 1.03084 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.95 seconds wall clock time: 39 minutes 54.82 seconds (2394.82 seconds total)