Starting phenix.real_space_refine on Thu Sep 18 10:13:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fju_50516/09_2025/9fju_50516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fju_50516/09_2025/9fju_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_50516/09_2025/9fju_50516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fju_50516/09_2025/9fju_50516.map" model { file = "/net/cci-nas-00/data/ceres_data/9fju_50516/09_2025/9fju_50516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fju_50516/09_2025/9fju_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-2.0-5805/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: 4.22, per 1000 atoms: 0.26 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 764.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.80 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: 2.77 Time building geometry restraints manager: 1.91 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: 21757 1.92 - 3.84: 298 3.84 - 5.76: 74 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=" 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=" CB LYS E 88 " pdb=" CG LYS E 88 " pdb=" CD LYS E 88 " ideal model delta sigma weight residual 111.30 118.31 -7.01 2.30e+00 1.89e-01 9.29e+00 angle pdb=" CA MET D 44 " pdb=" CB MET D 44 " pdb=" CG MET D 44 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.44e+00 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.57: 9213 28.57 - 57.14: 526 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: 2203 0.068 - 0.136: 287 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: 2.210 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: 16.460 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- 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= 0.198 Angle : 0.658 19.132 22198 Z= 0.311 Chirality : 0.044 0.340 2498 Planarity : 0.003 0.080 2802 Dihedral : 18.807 142.847 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 aren 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 0.00406 (16310) covalent geometry : angle 0.60691 (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 : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 MET cc_start: 0.8524 (ttm) cc_final: 0.8315 (ttp) REVERT: C 223 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6615 (t80) outliers start: 3 outliers final: 1 residues processed: 163 average time/residue: 0.1103 time to fit residues: 28.9140 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 : 0.754 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.095844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074414 restraints weight = 44766.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.076994 restraints weight = 26278.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078772 restraints weight = 17983.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079970 restraints weight = 13604.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080848 restraints weight = 11121.365| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16324 Z= 0.293 Angle : 0.767 10.662 22198 Z= 0.369 Chirality : 0.051 0.351 2498 Planarity : 0.005 0.053 2802 Dihedral : 13.352 133.568 2373 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.64 % Allowed : 20.66 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 1958 helix: -0.13 (0.19), residues: 704 sheet: 0.48 (0.29), residues: 350 loop : 0.03 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 79 TYR 0.019 0.002 TYR F 80 PHE 0.019 0.002 PHE E 6 TRP 0.010 0.002 TRP F 194 HIS 0.011 0.002 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00659 (16310) covalent geometry : angle 0.75429 (22158) SS BOND : bond 0.00248 ( 2) SS BOND : angle 1.05168 ( 4) hydrogen bonds : bond 0.05465 ( 605) hydrogen bonds : angle 5.80611 ( 1581) link_BETA1-4 : bond 0.00890 ( 2) link_BETA1-4 : angle 3.83261 ( 6) link_NAG-ASN : bond 0.00615 ( 2) link_NAG-ASN : angle 6.68946 ( 6) link_TRANS : bond 0.00399 ( 8) link_TRANS : angle 1.75513 ( 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 : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8910 (mm) REVERT: B 213 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8523 (ttmm) REVERT: B 352 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7755 (t80) REVERT: C 153 MET cc_start: 0.8523 (tmm) cc_final: 0.8182 (tmm) REVERT: C 223 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7445 (t80) REVERT: D 283 MET cc_start: 0.8604 (mmp) cc_final: 0.8334 (mmt) REVERT: E 96 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8106 (mm-40) REVERT: E 166 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7938 (mpp) REVERT: E 180 GLN cc_start: 0.8181 (pt0) cc_final: 0.7952 (pm20) REVERT: F 16 MET cc_start: 0.8875 (mpp) cc_final: 0.8156 (mpp) outliers start: 79 outliers final: 51 residues processed: 233 average time/residue: 0.1119 time to fit residues: 41.2614 Evaluate side-chains 205 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 77 THR 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: 0.9980 chunk 136 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 143 optimal weight: 0.0370 chunk 34 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8062 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.099111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077907 restraints weight = 44505.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.080581 restraints weight = 25945.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082373 restraints weight = 17580.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083675 restraints weight = 13273.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084548 restraints weight = 10697.275| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16324 Z= 0.112 Angle : 0.631 10.839 22198 Z= 0.293 Chirality : 0.047 0.372 2498 Planarity : 0.003 0.044 2802 Dihedral : 11.024 133.262 2373 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.11 % Allowed : 22.36 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (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 D 147 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 0.00241 (16310) covalent geometry : angle 0.61325 (22158) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.82942 ( 4) hydrogen bonds : bond 0.04141 ( 605) hydrogen bonds : angle 5.25094 ( 1581) link_BETA1-4 : bond 0.00311 ( 2) link_BETA1-4 : angle 5.50293 ( 6) link_NAG-ASN : bond 0.00848 ( 2) link_NAG-ASN : angle 6.81356 ( 6) link_TRANS : bond 0.00265 ( 8) link_TRANS : angle 1.31628 ( 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 243 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8285 (ttmm) REVERT: C 82 MET cc_start: 0.8641 (tpt) cc_final: 0.8422 (tpt) REVERT: D 217 CYS cc_start: 0.8029 (m) cc_final: 0.7688 (m) REVERT: D 283 MET cc_start: 0.8530 (mmp) cc_final: 0.8162 (mmt) REVERT: E 166 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7885 (mpp) REVERT: F 16 MET cc_start: 0.8897 (mpp) cc_final: 0.7895 (mpp) REVERT: F 50 LYS cc_start: 0.9293 (mtpp) cc_final: 0.8946 (mtmm) REVERT: F 112 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7403 (mm-30) REVERT: F 127 GLU cc_start: 0.7615 (mp0) cc_final: 0.7411 (mp0) REVERT: F 164 MET cc_start: 0.8094 (tpp) cc_final: 0.7828 (tpp) outliers start: 53 outliers final: 35 residues processed: 228 average time/residue: 0.1101 time to fit residues: 39.5920 Evaluate side-chains 203 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS 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 338 SER Chi-restraints excluded: chain B residue 339 VAL 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 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 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: 10.0000 chunk 6 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 191 optimal weight: 0.1980 chunk 136 optimal weight: 3.9990 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: 0.1980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.098619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077149 restraints weight = 44494.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079809 restraints weight = 25984.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081638 restraints weight = 17680.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082903 restraints weight = 13330.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083789 restraints weight = 10795.925| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16324 Z= 0.134 Angle : 0.634 11.175 22198 Z= 0.292 Chirality : 0.048 0.401 2498 Planarity : 0.003 0.042 2802 Dihedral : 10.639 133.159 2373 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.58 % Allowed : 22.24 % Favored : 74.18 % 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 aren not related in a simple way. whole: 0.22 (0.19), residues: 1958 helix: 0.26 (0.20), residues: 728 sheet: 0.41 (0.29), residues: 348 loop : 0.13 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.019 0.001 TYR A 240 PHE 0.014 0.001 PHE E 6 TRP 0.010 0.001 TRP F 194 HIS 0.009 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00308 (16310) covalent geometry : angle 0.61624 (22158) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.86145 ( 4) hydrogen bonds : bond 0.03737 ( 605) hydrogen bonds : angle 5.01595 ( 1581) link_BETA1-4 : bond 0.00533 ( 2) link_BETA1-4 : angle 5.10640 ( 6) link_NAG-ASN : bond 0.00912 ( 2) link_NAG-ASN : angle 7.22541 ( 6) link_TRANS : bond 0.00158 ( 8) link_TRANS : angle 1.01924 ( 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 230 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8821 (mm) REVERT: B 213 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8234 (ttmm) REVERT: B 269 MET cc_start: 0.7775 (tpp) cc_final: 0.7421 (tpp) REVERT: D 119 MET cc_start: 0.8841 (tpp) cc_final: 0.8603 (tpp) REVERT: D 217 CYS cc_start: 0.8095 (m) cc_final: 0.7752 (m) REVERT: E 155 GLN cc_start: 0.6793 (mm110) cc_final: 0.6564 (pp30) REVERT: F 16 MET cc_start: 0.8912 (mpp) cc_final: 0.7849 (mpp) REVERT: F 50 LYS cc_start: 0.9282 (mtpp) cc_final: 0.8932 (mtmm) REVERT: F 112 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7478 (mm-30) outliers start: 61 outliers final: 43 residues processed: 216 average time/residue: 0.1155 time to fit residues: 39.5345 Evaluate side-chains 201 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 180 LEU 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 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 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 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 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 17 SER 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 F residue 216 VAL 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: 9.9990 chunk 77 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN E 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.097252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075760 restraints weight = 44714.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078346 restraints weight = 26337.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080134 restraints weight = 18056.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.081393 restraints weight = 13694.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082160 restraints weight = 11132.795| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16324 Z= 0.172 Angle : 0.664 11.332 22198 Z= 0.307 Chirality : 0.048 0.409 2498 Planarity : 0.004 0.040 2802 Dihedral : 10.400 133.547 2371 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.93 % Allowed : 22.30 % Favored : 73.77 % 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 aren not related in a simple way. whole: 0.13 (0.19), residues: 1958 helix: 0.23 (0.20), residues: 728 sheet: 0.22 (0.29), residues: 352 loop : 0.09 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.017 0.001 TYR A 240 PHE 0.013 0.001 PHE F 82 TRP 0.008 0.001 TRP C 79 HIS 0.010 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00396 (16310) covalent geometry : angle 0.64677 (22158) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.86685 ( 4) hydrogen bonds : bond 0.03883 ( 605) hydrogen bonds : angle 5.00905 ( 1581) link_BETA1-4 : bond 0.00790 ( 2) link_BETA1-4 : angle 5.06791 ( 6) link_NAG-ASN : bond 0.00936 ( 2) link_NAG-ASN : angle 7.39002 ( 6) link_TRANS : bond 0.00096 ( 8) link_TRANS : angle 0.93621 ( 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 236 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 169 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8783 (mm) REVERT: B 213 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8618 (ttmm) REVERT: D 217 CYS cc_start: 0.8171 (m) cc_final: 0.7821 (m) REVERT: F 16 MET cc_start: 0.8896 (mpp) cc_final: 0.7772 (mpp) REVERT: F 50 LYS cc_start: 0.9305 (mtpp) cc_final: 0.8949 (mtmm) REVERT: F 112 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7445 (mm-30) REVERT: F 180 GLN cc_start: 0.8691 (mt0) cc_final: 0.8433 (pt0) outliers start: 67 outliers final: 50 residues processed: 218 average time/residue: 0.1098 time to fit residues: 37.9716 Evaluate side-chains 213 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL 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 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 298 VAL Chi-restraints excluded: chain B residue 338 SER 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 194 THR 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 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 311 ASP 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 116 VAL 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 260 THR 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: 0.9990 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 160 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.097029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.075664 restraints weight = 44327.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078254 restraints weight = 25899.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080096 restraints weight = 17718.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.081349 restraints weight = 13315.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.082160 restraints weight = 10812.650| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16324 Z= 0.165 Angle : 0.661 11.356 22198 Z= 0.304 Chirality : 0.048 0.416 2498 Planarity : 0.003 0.041 2802 Dihedral : 10.212 133.642 2371 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.76 % Allowed : 22.95 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.19), residues: 1958 helix: 0.24 (0.20), residues: 730 sheet: 0.19 (0.29), residues: 352 loop : 0.09 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 147 TYR 0.014 0.001 TYR A 240 PHE 0.015 0.001 PHE F 82 TRP 0.030 0.001 TRP F 194 HIS 0.010 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00381 (16310) covalent geometry : angle 0.64387 (22158) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.81939 ( 4) hydrogen bonds : bond 0.03710 ( 605) hydrogen bonds : angle 4.92014 ( 1581) link_BETA1-4 : bond 0.00852 ( 2) link_BETA1-4 : angle 5.02614 ( 6) link_NAG-ASN : bond 0.00943 ( 2) link_NAG-ASN : angle 7.46683 ( 6) link_TRANS : bond 0.00101 ( 8) link_TRANS : angle 0.94899 ( 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 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8777 (mm) REVERT: B 213 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8663 (ttmm) REVERT: B 269 MET cc_start: 0.7829 (tpp) cc_final: 0.7442 (tpp) REVERT: C 223 PHE cc_start: 0.7944 (t80) cc_final: 0.7604 (m-80) REVERT: D 217 CYS cc_start: 0.8215 (m) cc_final: 0.7843 (m) REVERT: D 305 MET cc_start: 0.8169 (mpp) cc_final: 0.7931 (mpp) REVERT: E 77 LYS cc_start: 0.7546 (mmtt) cc_final: 0.6926 (mmtm) REVERT: F 16 MET cc_start: 0.8897 (mpp) cc_final: 0.7858 (mpp) REVERT: F 50 LYS cc_start: 0.9281 (mtpp) cc_final: 0.8940 (mtmm) outliers start: 64 outliers final: 54 residues processed: 222 average time/residue: 0.1127 time to fit residues: 40.4051 Evaluate side-chains 216 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 149 THR 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 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 123 MET Chi-restraints excluded: chain C residue 194 THR 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 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 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 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 109 PHE Chi-restraints excluded: chain F residue 115 VAL 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 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: 4.9990 chunk 130 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 110 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.096593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075538 restraints weight = 43990.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078054 restraints weight = 25868.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.079771 restraints weight = 17769.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.081032 restraints weight = 13541.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.081799 restraints weight = 10995.727| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16324 Z= 0.206 Angle : 0.701 11.468 22198 Z= 0.327 Chirality : 0.049 0.421 2498 Planarity : 0.004 0.040 2802 Dihedral : 10.177 133.839 2371 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.58 % Allowed : 23.24 % 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 aren not related in a simple way. whole: -0.04 (0.19), residues: 1958 helix: 0.12 (0.20), residues: 728 sheet: 0.09 (0.29), residues: 352 loop : -0.00 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 177 TYR 0.014 0.001 TYR F 80 PHE 0.015 0.002 PHE C 255 TRP 0.042 0.002 TRP F 194 HIS 0.012 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00475 (16310) covalent geometry : angle 0.68489 (22158) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.84169 ( 4) hydrogen bonds : bond 0.03993 ( 605) hydrogen bonds : angle 4.99597 ( 1581) link_BETA1-4 : bond 0.00774 ( 2) link_BETA1-4 : angle 4.98799 ( 6) link_NAG-ASN : bond 0.00960 ( 2) link_NAG-ASN : angle 7.57521 ( 6) link_TRANS : bond 0.00098 ( 8) link_TRANS : angle 0.93742 ( 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 249 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 171 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8812 (mm) REVERT: B 12 ASN cc_start: 0.8713 (t0) cc_final: 0.7882 (p0) REVERT: B 213 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8785 (ttmm) REVERT: B 237 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: B 269 MET cc_start: 0.7853 (tpp) cc_final: 0.7473 (tpp) REVERT: D 51 ASP cc_start: 0.7407 (p0) cc_final: 0.6972 (m-30) REVERT: D 217 CYS cc_start: 0.8292 (m) cc_final: 0.7947 (m) REVERT: D 305 MET cc_start: 0.8214 (mpp) cc_final: 0.7976 (mpp) REVERT: E 77 LYS cc_start: 0.7644 (mmtt) cc_final: 0.6967 (mmtm) REVERT: F 16 MET cc_start: 0.8909 (mpp) cc_final: 0.7890 (mpp) REVERT: F 50 LYS cc_start: 0.9256 (mtpp) cc_final: 0.8924 (mtmm) REVERT: F 180 GLN cc_start: 0.8697 (mt0) cc_final: 0.8409 (pt0) outliers start: 78 outliers final: 64 residues processed: 231 average time/residue: 0.1091 time to fit residues: 40.5343 Evaluate side-chains 230 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 163 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 219 VAL 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 120 THR 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 320 LEU 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 123 MET Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 THR 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 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 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 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 109 PHE Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 121 HIS Chi-restraints excluded: chain F residue 131 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 11 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.096236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075083 restraints weight = 43706.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077634 restraints weight = 25482.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.079408 restraints weight = 17329.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080624 restraints weight = 13057.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081493 restraints weight = 10590.554| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16324 Z= 0.172 Angle : 0.678 11.490 22198 Z= 0.316 Chirality : 0.049 0.433 2498 Planarity : 0.004 0.041 2802 Dihedral : 10.011 133.921 2371 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.46 % Allowed : 23.42 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 1958 helix: 0.15 (0.20), residues: 728 sheet: 0.04 (0.29), residues: 348 loop : -0.01 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 79 TYR 0.013 0.001 TYR D 91 PHE 0.019 0.001 PHE F 82 TRP 0.028 0.002 TRP F 194 HIS 0.012 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00398 (16310) covalent geometry : angle 0.66106 (22158) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.83934 ( 4) hydrogen bonds : bond 0.03684 ( 605) hydrogen bonds : angle 4.91554 ( 1581) link_BETA1-4 : bond 0.00716 ( 2) link_BETA1-4 : angle 4.99922 ( 6) link_NAG-ASN : bond 0.00942 ( 2) link_NAG-ASN : angle 7.62118 ( 6) link_TRANS : bond 0.00090 ( 8) link_TRANS : angle 0.96741 ( 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 245 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 12 ASN cc_start: 0.8707 (t0) cc_final: 0.8017 (p0) REVERT: B 213 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8821 (ttmm) REVERT: B 237 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: B 269 MET cc_start: 0.7871 (tpp) cc_final: 0.7510 (tpp) REVERT: C 80 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8548 (t0) REVERT: D 51 ASP cc_start: 0.7339 (p0) cc_final: 0.6913 (m-30) REVERT: D 217 CYS cc_start: 0.8300 (m) cc_final: 0.7930 (m) REVERT: D 305 MET cc_start: 0.8230 (mpp) cc_final: 0.7994 (mpp) REVERT: E 77 LYS cc_start: 0.7742 (mmtt) cc_final: 0.6988 (mmtm) REVERT: E 245 MET cc_start: 0.8267 (pmm) cc_final: 0.8038 (pmm) REVERT: F 16 MET cc_start: 0.8871 (mpp) cc_final: 0.7893 (mpp) REVERT: F 50 LYS cc_start: 0.9262 (mtpp) cc_final: 0.8903 (mtmm) REVERT: F 180 GLN cc_start: 0.8686 (mt0) cc_final: 0.8402 (pt0) outliers start: 76 outliers final: 61 residues processed: 228 average time/residue: 0.1095 time to fit residues: 40.2195 Evaluate side-chains 226 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 161 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 219 VAL 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 305 MET Chi-restraints excluded: chain B residue 320 LEU 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 80 ASP Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 MET 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 203 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 246 GLN 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 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 E residue 221 LEU 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 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 116 VAL 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 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 121 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.096568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075430 restraints weight = 43484.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077996 restraints weight = 25299.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079760 restraints weight = 17173.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.080980 restraints weight = 12961.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081847 restraints weight = 10495.702| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16324 Z= 0.151 Angle : 0.685 11.496 22198 Z= 0.316 Chirality : 0.048 0.442 2498 Planarity : 0.004 0.042 2802 Dihedral : 9.884 132.923 2370 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.11 % Allowed : 24.00 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.19), residues: 1958 helix: 0.19 (0.20), residues: 728 sheet: 0.03 (0.29), residues: 348 loop : 0.00 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 79 TYR 0.012 0.001 TYR A 240 PHE 0.027 0.001 PHE E 82 TRP 0.028 0.002 TRP F 194 HIS 0.010 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00349 (16310) covalent geometry : angle 0.66826 (22158) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.82563 ( 4) hydrogen bonds : bond 0.03538 ( 605) hydrogen bonds : angle 4.85813 ( 1581) link_BETA1-4 : bond 0.00772 ( 2) link_BETA1-4 : angle 5.00014 ( 6) link_NAG-ASN : bond 0.00920 ( 2) link_NAG-ASN : angle 7.65967 ( 6) link_TRANS : bond 0.00111 ( 8) link_TRANS : angle 0.98551 ( 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 244 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 174 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6784 (pmm) cc_final: 0.6416 (ptp) REVERT: A 293 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8847 (mm) REVERT: B 12 ASN cc_start: 0.8718 (t0) cc_final: 0.8078 (p0) REVERT: B 87 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.7930 (t-90) REVERT: B 192 ILE cc_start: 0.9074 (tp) cc_final: 0.8813 (tp) REVERT: B 213 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8822 (ttmm) REVERT: B 237 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: B 269 MET cc_start: 0.7867 (tpp) cc_final: 0.7524 (tpp) REVERT: C 80 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8539 (t0) REVERT: D 217 CYS cc_start: 0.8281 (m) cc_final: 0.7909 (m) REVERT: D 305 MET cc_start: 0.8217 (mpp) cc_final: 0.7975 (mpp) REVERT: E 77 LYS cc_start: 0.7753 (mmtt) cc_final: 0.6980 (mmtm) REVERT: E 245 MET cc_start: 0.8288 (pmm) cc_final: 0.8058 (pmm) REVERT: F 16 MET cc_start: 0.8884 (mpp) cc_final: 0.7922 (mpp) REVERT: F 36 LEU cc_start: 0.8768 (mm) cc_final: 0.8435 (mm) REVERT: F 50 LYS cc_start: 0.9276 (mtpp) cc_final: 0.8914 (mtmm) REVERT: F 180 GLN cc_start: 0.8688 (mt0) cc_final: 0.8404 (pt0) outliers start: 70 outliers final: 58 residues processed: 230 average time/residue: 0.1137 time to fit residues: 41.6762 Evaluate side-chains 228 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 165 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 219 VAL 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 120 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER 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 B residue 339 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 123 MET 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 203 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 246 GLN 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 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 E residue 221 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 116 VAL Chi-restraints excluded: chain F residue 121 HIS 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: 0.9980 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.098378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077134 restraints weight = 44220.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079776 restraints weight = 25621.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.081571 restraints weight = 17454.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082853 restraints weight = 13165.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.083729 restraints weight = 10650.414| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16324 Z= 0.112 Angle : 0.681 11.374 22198 Z= 0.310 Chirality : 0.049 0.547 2498 Planarity : 0.003 0.043 2802 Dihedral : 9.598 131.527 2370 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.99 % Allowed : 25.12 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 1958 helix: 0.26 (0.20), residues: 728 sheet: 0.09 (0.29), residues: 348 loop : 0.08 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 28 TYR 0.019 0.001 TYR F 32 PHE 0.029 0.001 PHE F 128 TRP 0.036 0.001 TRP F 194 HIS 0.007 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00256 (16310) covalent geometry : angle 0.66228 (22158) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.77091 ( 4) hydrogen bonds : bond 0.03129 ( 605) hydrogen bonds : angle 4.76515 ( 1581) link_BETA1-4 : bond 0.00826 ( 2) link_BETA1-4 : angle 5.12555 ( 6) link_NAG-ASN : bond 0.00791 ( 2) link_NAG-ASN : angle 7.93947 ( 6) link_TRANS : bond 0.00187 ( 8) link_TRANS : angle 1.02827 ( 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 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6800 (pmm) cc_final: 0.6353 (ptp) REVERT: A 293 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8942 (mm) REVERT: B 12 ASN cc_start: 0.8622 (t0) cc_final: 0.8026 (p0) REVERT: B 192 ILE cc_start: 0.9008 (tp) cc_final: 0.8762 (tp) REVERT: B 213 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8824 (ttmm) REVERT: B 237 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: B 269 MET cc_start: 0.7741 (tpp) cc_final: 0.7398 (tpp) REVERT: D 217 CYS cc_start: 0.8178 (m) cc_final: 0.7838 (m) REVERT: D 305 MET cc_start: 0.8133 (mpp) cc_final: 0.7927 (mpp) REVERT: E 77 LYS cc_start: 0.7661 (mmtt) cc_final: 0.6972 (mmtm) REVERT: E 245 MET cc_start: 0.8262 (pmm) cc_final: 0.8030 (pmm) REVERT: F 16 MET cc_start: 0.8842 (mpp) cc_final: 0.8281 (mpp) REVERT: F 36 LEU cc_start: 0.8581 (mm) cc_final: 0.8275 (mm) REVERT: F 50 LYS cc_start: 0.9276 (mtpp) cc_final: 0.8898 (mtmm) REVERT: F 180 GLN cc_start: 0.8696 (mt0) cc_final: 0.8396 (pt0) outliers start: 51 outliers final: 47 residues processed: 221 average time/residue: 0.1122 time to fit residues: 39.6507 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 : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 234 SER 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 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 320 LEU 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 203 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP 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 E residue 221 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 121 HIS 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: 5.9990 chunk 112 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 HIS ** 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 = 0.3667 r_free = 0.3667 target = 0.095760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074555 restraints weight = 44020.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077049 restraints weight = 26006.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.078777 restraints weight = 17917.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079993 restraints weight = 13624.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080812 restraints weight = 11127.430| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16324 Z= 0.237 Angle : 0.754 12.620 22198 Z= 0.351 Chirality : 0.050 0.551 2498 Planarity : 0.004 0.041 2802 Dihedral : 9.893 131.871 2370 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.76 % Allowed : 24.53 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.19), residues: 1958 helix: 0.07 (0.20), residues: 728 sheet: -0.10 (0.28), residues: 356 loop : 0.01 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 28 TYR 0.017 0.001 TYR F 32 PHE 0.031 0.002 PHE F 82 TRP 0.030 0.002 TRP F 194 HIS 0.013 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00549 (16310) covalent geometry : angle 0.73734 (22158) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.85930 ( 4) hydrogen bonds : bond 0.04044 ( 605) hydrogen bonds : angle 5.02370 ( 1581) link_BETA1-4 : bond 0.00832 ( 2) link_BETA1-4 : angle 5.00390 ( 6) link_NAG-ASN : bond 0.00846 ( 2) link_NAG-ASN : angle 8.09261 ( 6) link_TRANS : bond 0.00132 ( 8) link_TRANS : angle 0.95594 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.15 seconds wall clock time: 41 minutes 30.61 seconds (2490.61 seconds total)