Starting phenix.real_space_refine on Thu Sep 18 10:12:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjy_50517/09_2025/9fjy_50517.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjy_50517/09_2025/9fjy_50517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjy_50517/09_2025/9fjy_50517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjy_50517/09_2025/9fjy_50517.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjy_50517/09_2025/9fjy_50517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjy_50517/09_2025/9fjy_50517.cif" } resolution = 3.79 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= 0.047 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 14 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: "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: "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: "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: 3.91, per 1000 atoms: 0.24 Number of scatterers: 15968 At special positions: 0 Unit cell: (110.88, 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: 1.61 Conformation dependent library (CDL) restraints added in 761.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 44.5% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.541A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.522A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.611A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.561A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.643A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.689A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.778A pdb=" N MET A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.839A 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: 3.660A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.986A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.513A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.500A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.587A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.603A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.762A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.842A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 4.204A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.604A pdb=" N ALA B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 175' Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.529A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.579A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.635A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.004A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix No H-bonds generated for 'chain 'B' and resid 252 through 260' Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.606A pdb=" N ILE B 282 " --> pdb=" O THR B 278 " (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: 3.510A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 306 removed outlier: 3.995A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 306' 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 355 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 81 through 93 removed outlier: 3.510A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.822A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.503A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.691A pdb=" N MET C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.962A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.749A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix No H-bonds generated for 'chain 'C' and resid 252 through 260' Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.619A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) 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 355 removed outlier: 3.632A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.526A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.569A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 371' Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.813A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.516A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.965A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.674A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.532A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.604A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.591A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.670A 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: 3.697A pdb=" N PHE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.569A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.617A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.548A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.534A pdb=" N SER D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.003A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 removed outlier: 4.337A pdb=" N ASN E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.529A pdb=" N ALA E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 4.046A pdb=" N TYR E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 158 removed outlier: 4.203A pdb=" N ASN E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 152 " --> pdb=" O TYR E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.878A pdb=" N SER E 223 " --> pdb=" O SER E 219 " (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 18 removed outlier: 3.780A pdb=" N MET F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 removed outlier: 3.609A pdb=" N ARG F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 139 through 158 removed outlier: 3.614A pdb=" N GLU F 143 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR F 148 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP F 158 " --> pdb=" O VAL F 154 " (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: 3.611A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.734A 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: 4.006A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.104A 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 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.510A pdb=" N GLY B 20 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.931A 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: 3.621A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB3, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.856A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C 133 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.727A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 68 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.756A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.276A 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: 3.640A pdb=" N PHE D 31 " --> pdb=" O CYS D 17 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ALA D 135 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.930A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.630A 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 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.602A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.602A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 297 " --> pdb=" O LYS D 328 " (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: 3.605A pdb=" N GLU E 256 " --> pdb=" O ALA E 231 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 96 removed outlier: 6.796A pdb=" N VAL E 91 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER E 119 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP E 93 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE E 128 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU E 127 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N MET E 164 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA E 129 " --> pdb=" O MET E 164 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET E 166 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL E 131 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASP E 168 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU E 133 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL E 216 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.720A pdb=" N LEU F 36 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 256 " --> pdb=" O ALA F 231 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 90 through 96 removed outlier: 5.956A pdb=" N VAL F 91 " --> pdb=" O SER F 119 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER F 119 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP F 93 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA F 114 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 132 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL F 116 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE F 130 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N MET F 164 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA F 129 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET F 166 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL F 131 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP F 168 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU F 133 " --> pdb=" O ASP F 168 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU F 165 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 167 " --> pdb=" O ARG F 213 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1542 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: 2.63 Time building geometry restraints manager: 1.97 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: 2624 1.31 - 1.44: 4354 1.44 - 1.56: 9127 1.56 - 1.69: 29 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 1.474 -0.128 2.00e-02 2.50e+03 4.10e+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 4.09e+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 1.473 -0.127 2.00e-02 2.50e+03 4.01e+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 3.25e+01 ... (remaining 16305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21863 2.36 - 4.72: 229 4.72 - 7.08: 55 7.08 - 9.44: 8 9.44 - 11.80: 3 Bond angle restraints: 22158 Sorted by residual: angle pdb=" CB MET F 164 " pdb=" CG MET F 164 " pdb=" SD MET F 164 " ideal model delta sigma weight residual 112.70 124.50 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 123.26 -10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CB MET B 153 " pdb=" CG MET B 153 " pdb=" SD MET B 153 " ideal model delta sigma weight residual 112.70 123.20 -10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB LYS E 126 " pdb=" CG LYS E 126 " pdb=" CD LYS E 126 " ideal model delta sigma weight residual 111.30 119.08 -7.78 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA GLU E 143 " pdb=" CB GLU E 143 " pdb=" CG GLU E 143 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 8994 24.04 - 48.08: 681 48.08 - 72.12: 105 72.12 - 96.17: 36 96.17 - 120.21: 32 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 -149.97 63.97 1 1.00e+01 1.00e-02 5.39e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 52.07 -112.08 1 2.00e+01 2.50e-03 3.30e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 50.79 -110.78 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2244 0.074 - 0.147: 248 0.147 - 0.221: 4 0.221 - 0.294: 0 0.294 - 0.368: 2 Chirality restraints: 2498 Sorted by residual: 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 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+00 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 2.90e+00 chirality pdb=" CA HYP H 6 " pdb=" N HYP H 6 " pdb=" C HYP H 6 " pdb=" CB HYP H 6 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2495 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N TRP G 1 " -0.024 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" CA ALA G 7 " -0.021 2.00e-02 2.50e+03 pdb=" C ALA G 7 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA G 7 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TRP J 1 " -0.021 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" CA ALA J 7 " -0.018 2.00e-02 2.50e+03 pdb=" C ALA J 7 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA J 7 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 139 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CG ASP E 139 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP E 139 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP E 139 " 0.010 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 45 2.36 - 2.99: 8433 2.99 - 3.63: 24439 3.63 - 4.26: 35952 4.26 - 4.90: 58740 Nonbonded interactions: 127609 Sorted by model distance: nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.723 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.724 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.734 3.620 nonbonded pdb=" CD1 TRP G 1 " pdb=" SG CYS G 5 " model vdw 1.767 3.620 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.913 2.170 ... (remaining 127604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 0.128 16324 Z= 0.195 Angle : 0.658 22.636 22198 Z= 0.310 Chirality : 0.044 0.368 2498 Planarity : 0.003 0.027 2802 Dihedral : 18.467 120.208 6050 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.41 % Allowed : 21.30 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.26 (0.19), residues: 1958 helix: 0.13 (0.20), residues: 664 sheet: 0.35 (0.29), residues: 350 loop : 0.33 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 62 TYR 0.010 0.001 TYR E 97 PHE 0.011 0.001 PHE F 118 TRP 0.014 0.001 TRP B 86 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00401 (16310) covalent geometry : angle 0.59954 (22158) SS BOND : bond 0.00059 ( 2) SS BOND : angle 1.26667 ( 4) hydrogen bonds : bond 0.30341 ( 589) hydrogen bonds : angle 8.02258 ( 1542) link_BETA1-4 : bond 0.00156 ( 2) link_BETA1-4 : angle 1.17775 ( 6) link_NAG-ASN : bond 0.00930 ( 2) link_NAG-ASN : angle 5.90835 ( 6) link_TRANS : bond 0.00707 ( 8) link_TRANS : angle 7.70652 ( 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 188 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LEU cc_start: 0.8004 (tp) cc_final: 0.7273 (mp) outliers start: 7 outliers final: 4 residues processed: 186 average time/residue: 0.0967 time to fit residues: 29.3038 Evaluate side-chains 175 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain I 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: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.098393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076679 restraints weight = 40781.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.079254 restraints weight = 23370.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080805 restraints weight = 15025.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081426 restraints weight = 11127.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081766 restraints weight = 10161.242| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16324 Z= 0.281 Angle : 0.736 10.036 22198 Z= 0.356 Chirality : 0.050 0.368 2498 Planarity : 0.005 0.040 2802 Dihedral : 14.240 114.510 2375 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.81 % Allowed : 18.60 % Favored : 76.58 % 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: 0.11 (0.19), residues: 716 sheet: 0.20 (0.29), residues: 348 loop : 0.20 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 187 TYR 0.016 0.002 TYR E 24 PHE 0.019 0.002 PHE D 352 TRP 0.015 0.002 TRP B 86 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00640 (16310) covalent geometry : angle 0.72271 (22158) SS BOND : bond 0.00235 ( 2) SS BOND : angle 1.12095 ( 4) hydrogen bonds : bond 0.05381 ( 589) hydrogen bonds : angle 5.77866 ( 1542) link_BETA1-4 : bond 0.00460 ( 2) link_BETA1-4 : angle 3.77607 ( 6) link_NAG-ASN : bond 0.00257 ( 2) link_NAG-ASN : angle 6.65373 ( 6) link_TRANS : bond 0.00171 ( 8) link_TRANS : angle 1.91965 ( 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 251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 169 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 129 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8695 (t) REVERT: B 107 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: B 123 MET cc_start: 0.8603 (mmm) cc_final: 0.7845 (mmm) REVERT: B 180 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8732 (tp) REVERT: B 185 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8289 (tt) REVERT: C 241 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6801 (tm-30) REVERT: E 256 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7452 (tm-30) outliers start: 82 outliers final: 41 residues processed: 232 average time/residue: 0.0924 time to fit residues: 35.5332 Evaluate side-chains 196 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 158 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 178 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.097884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.075565 restraints weight = 41777.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078227 restraints weight = 24556.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079815 restraints weight = 15848.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.080240 restraints weight = 11593.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080696 restraints weight = 10832.733| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16324 Z= 0.220 Angle : 0.665 10.176 22198 Z= 0.315 Chirality : 0.048 0.407 2498 Planarity : 0.004 0.038 2802 Dihedral : 11.526 113.759 2370 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.28 % Allowed : 18.96 % Favored : 75.76 % 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: 0.06 (0.19), residues: 1958 helix: 0.17 (0.20), residues: 704 sheet: -0.04 (0.28), residues: 348 loop : 0.17 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 187 TYR 0.014 0.001 TYR E 24 PHE 0.018 0.001 PHE D 352 TRP 0.014 0.001 TRP E 158 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00502 (16310) covalent geometry : angle 0.64841 (22158) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.82973 ( 4) hydrogen bonds : bond 0.04538 ( 589) hydrogen bonds : angle 5.31496 ( 1542) link_BETA1-4 : bond 0.00095 ( 2) link_BETA1-4 : angle 5.21276 ( 6) link_NAG-ASN : bond 0.00536 ( 2) link_NAG-ASN : angle 6.86763 ( 6) link_TRANS : bond 0.00131 ( 8) link_TRANS : angle 1.38216 ( 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 260 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 170 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8842 (tpt) cc_final: 0.8515 (tpt) REVERT: A 90 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8859 (m-10) REVERT: A 153 MET cc_start: 0.8479 (ttt) cc_final: 0.8247 (ttt) REVERT: B 12 ASN cc_start: 0.8494 (t0) cc_final: 0.8196 (m-40) REVERT: B 185 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8183 (tt) REVERT: C 241 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: E 153 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8716 (m-30) REVERT: E 256 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7330 (tm-30) REVERT: H 5 CYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6718 (m) outliers start: 90 outliers final: 48 residues processed: 235 average time/residue: 0.0989 time to fit residues: 37.6549 Evaluate side-chains 209 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 38 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 175 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 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 = 0.3705 r_free = 0.3705 target = 0.099707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.078047 restraints weight = 41260.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.080352 restraints weight = 22778.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081826 restraints weight = 15498.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082747 restraints weight = 11326.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.083147 restraints weight = 10015.412| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16324 Z= 0.127 Angle : 0.615 10.659 22198 Z= 0.284 Chirality : 0.047 0.424 2498 Planarity : 0.004 0.035 2802 Dihedral : 10.814 112.052 2370 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.75 % Allowed : 19.89 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.19), residues: 1958 helix: 0.42 (0.20), residues: 688 sheet: -0.13 (0.28), residues: 342 loop : 0.27 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.012 0.001 TYR E 24 PHE 0.014 0.001 PHE D 352 TRP 0.023 0.002 TRP B 86 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00286 (16310) covalent geometry : angle 0.59523 (22158) SS BOND : bond 0.00273 ( 2) SS BOND : angle 2.67327 ( 4) hydrogen bonds : bond 0.03538 ( 589) hydrogen bonds : angle 4.99346 ( 1542) link_BETA1-4 : bond 0.00309 ( 2) link_BETA1-4 : angle 5.25599 ( 6) link_NAG-ASN : bond 0.00715 ( 2) link_NAG-ASN : angle 7.23219 ( 6) link_TRANS : bond 0.00165 ( 8) link_TRANS : angle 1.12151 ( 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 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 176 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8819 (tpt) cc_final: 0.8509 (tpt) REVERT: A 90 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8826 (m-10) REVERT: B 185 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8002 (tt) REVERT: B 286 ASP cc_start: 0.7627 (t0) cc_final: 0.7396 (t0) REVERT: C 241 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: D 119 MET cc_start: 0.7905 (ttm) cc_final: 0.7531 (tmm) REVERT: E 256 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7200 (tm-30) REVERT: H 5 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6610 (m) REVERT: F 39 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5853 (mp0) outliers start: 81 outliers final: 58 residues processed: 236 average time/residue: 0.0969 time to fit residues: 36.9008 Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 179 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.098793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077105 restraints weight = 40436.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.079845 restraints weight = 22900.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.081421 restraints weight = 14445.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082000 restraints weight = 10598.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082378 restraints weight = 9753.471| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16324 Z= 0.164 Angle : 0.633 10.893 22198 Z= 0.293 Chirality : 0.047 0.428 2498 Planarity : 0.004 0.033 2802 Dihedral : 10.695 115.159 2370 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.46 % Allowed : 19.66 % Favored : 74.88 % 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: 0.25 (0.19), residues: 1958 helix: 0.45 (0.20), residues: 690 sheet: -0.18 (0.28), residues: 338 loop : 0.28 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.011 0.001 TYR E 95 PHE 0.011 0.001 PHE D 352 TRP 0.018 0.001 TRP B 86 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00377 (16310) covalent geometry : angle 0.61442 (22158) SS BOND : bond 0.00345 ( 2) SS BOND : angle 1.86896 ( 4) hydrogen bonds : bond 0.03542 ( 589) hydrogen bonds : angle 4.92504 ( 1542) link_BETA1-4 : bond 0.00555 ( 2) link_BETA1-4 : angle 5.14843 ( 6) link_NAG-ASN : bond 0.00657 ( 2) link_NAG-ASN : angle 7.38222 ( 6) link_TRANS : bond 0.00071 ( 8) link_TRANS : angle 0.91059 ( 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 259 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 166 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8794 (tpt) cc_final: 0.8543 (tpt) REVERT: A 90 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8920 (m-10) REVERT: B 185 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8030 (tt) REVERT: B 286 ASP cc_start: 0.7811 (t0) cc_final: 0.7559 (t0) REVERT: C 241 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: E 256 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7258 (tm-30) REVERT: H 5 CYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6600 (m) outliers start: 93 outliers final: 69 residues processed: 238 average time/residue: 0.0976 time to fit residues: 37.7169 Evaluate side-chains 234 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Chi-restraints excluded: chain F residue 196 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 160 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.096809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075117 restraints weight = 40613.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077773 restraints weight = 23300.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079179 restraints weight = 15054.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079938 restraints weight = 11058.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080265 restraints weight = 10131.000| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16324 Z= 0.260 Angle : 0.703 10.937 22198 Z= 0.332 Chirality : 0.049 0.422 2498 Planarity : 0.004 0.038 2802 Dihedral : 10.805 117.162 2370 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.10 % Allowed : 20.19 % Favored : 73.71 % 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: -0.01 (0.19), residues: 1958 helix: 0.28 (0.20), residues: 690 sheet: -0.38 (0.28), residues: 340 loop : 0.10 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 187 TYR 0.013 0.001 TYR E 95 PHE 0.012 0.002 PHE D 31 TRP 0.033 0.002 TRP B 86 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd covalent geometry : bond 0.00599 (16310) covalent geometry : angle 0.68691 (22158) SS BOND : bond 0.00300 ( 2) SS BOND : angle 1.70965 ( 4) hydrogen bonds : bond 0.04063 ( 589) hydrogen bonds : angle 5.05670 ( 1542) link_BETA1-4 : bond 0.00616 ( 2) link_BETA1-4 : angle 4.91114 ( 6) link_NAG-ASN : bond 0.00532 ( 2) link_NAG-ASN : angle 7.41649 ( 6) link_TRANS : bond 0.00159 ( 8) link_TRANS : angle 0.78452 ( 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 267 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 163 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8802 (tpt) cc_final: 0.8570 (tpt) REVERT: B 185 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8179 (tt) REVERT: B 286 ASP cc_start: 0.8035 (t0) cc_final: 0.7827 (t0) REVERT: C 241 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: D 227 MET cc_start: 0.8938 (mmt) cc_final: 0.8717 (mmm) REVERT: E 256 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7303 (tm-30) REVERT: H 5 CYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6503 (m) REVERT: F 39 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6002 (mp0) outliers start: 104 outliers final: 81 residues processed: 250 average time/residue: 0.1002 time to fit residues: 40.6384 Evaluate side-chains 235 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 150 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 196 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 0.0570 chunk 196 optimal weight: 20.0000 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 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 = 0.3697 r_free = 0.3697 target = 0.099208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077427 restraints weight = 40509.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.080117 restraints weight = 23777.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081302 restraints weight = 15008.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081719 restraints weight = 12285.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081814 restraints weight = 10912.752| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16324 Z= 0.130 Angle : 0.634 10.978 22198 Z= 0.292 Chirality : 0.047 0.451 2498 Planarity : 0.003 0.033 2802 Dihedral : 10.432 116.076 2370 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 5.11 % Allowed : 21.36 % Favored : 73.53 % 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: 0.23 (0.19), residues: 1958 helix: 0.50 (0.20), residues: 690 sheet: -0.20 (0.28), residues: 322 loop : 0.20 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.013 0.001 TYR E 97 PHE 0.010 0.001 PHE D 352 TRP 0.039 0.002 TRP B 86 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00297 (16310) covalent geometry : angle 0.61603 (22158) SS BOND : bond 0.00166 ( 2) SS BOND : angle 1.09900 ( 4) hydrogen bonds : bond 0.03304 ( 589) hydrogen bonds : angle 4.80400 ( 1542) link_BETA1-4 : bond 0.00705 ( 2) link_BETA1-4 : angle 5.10781 ( 6) link_NAG-ASN : bond 0.00732 ( 2) link_NAG-ASN : angle 7.55106 ( 6) link_TRANS : bond 0.00126 ( 8) link_TRANS : angle 0.92473 ( 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 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 170 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: B 185 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8160 (tt) REVERT: B 286 ASP cc_start: 0.8049 (t0) cc_final: 0.7847 (t0) REVERT: C 241 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: E 160 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6534 (tt) REVERT: E 256 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7245 (tm-30) REVERT: H 5 CYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6544 (m) REVERT: F 39 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5966 (mp0) outliers start: 87 outliers final: 68 residues processed: 241 average time/residue: 0.0949 time to fit residues: 37.6749 Evaluate side-chains 235 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 162 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 196 ILE 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: 1.9990 chunk 161 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 4 optimal weight: 0.0030 chunk 91 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 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 = 0.3690 r_free = 0.3690 target = 0.098795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076995 restraints weight = 41041.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079380 restraints weight = 23381.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080973 restraints weight = 15493.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081637 restraints weight = 11230.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082058 restraints weight = 10202.397| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2362 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= 0.155 Angle : 0.655 11.037 22198 Z= 0.300 Chirality : 0.048 0.453 2498 Planarity : 0.003 0.032 2802 Dihedral : 10.354 119.458 2370 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.22 % Allowed : 21.48 % 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: 0.24 (0.19), residues: 1958 helix: 0.52 (0.20), residues: 690 sheet: -0.21 (0.28), residues: 322 loop : 0.20 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.038 0.001 TYR F 95 PHE 0.008 0.001 PHE D 352 TRP 0.042 0.002 TRP B 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00360 (16310) covalent geometry : angle 0.63710 (22158) SS BOND : bond 0.00179 ( 2) SS BOND : angle 1.12302 ( 4) hydrogen bonds : bond 0.03333 ( 589) hydrogen bonds : angle 4.74560 ( 1542) link_BETA1-4 : bond 0.00718 ( 2) link_BETA1-4 : angle 5.03774 ( 6) link_NAG-ASN : bond 0.00658 ( 2) link_NAG-ASN : angle 7.59308 ( 6) link_TRANS : bond 0.00100 ( 8) link_TRANS : angle 0.88548 ( 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 260 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 171 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: B 185 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8105 (tt) REVERT: B 286 ASP cc_start: 0.8081 (t0) cc_final: 0.7867 (t0) REVERT: C 241 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: E 160 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6491 (tt) REVERT: E 256 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7262 (tm-30) REVERT: H 5 CYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6443 (m) REVERT: F 39 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: F 166 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6585 (tmm) outliers start: 89 outliers final: 74 residues processed: 242 average time/residue: 0.0999 time to fit residues: 39.9014 Evaluate side-chains 247 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 167 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 196 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 121 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 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 = 0.3700 r_free = 0.3700 target = 0.099363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077341 restraints weight = 41011.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.080147 restraints weight = 23423.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081478 restraints weight = 15467.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.082299 restraints weight = 11175.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082578 restraints weight = 10243.913| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16324 Z= 0.142 Angle : 0.657 11.043 22198 Z= 0.300 Chirality : 0.047 0.464 2498 Planarity : 0.003 0.033 2802 Dihedral : 10.211 120.478 2370 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.16 % Allowed : 21.60 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.19), residues: 1958 helix: 0.63 (0.21), residues: 678 sheet: -0.25 (0.28), residues: 324 loop : 0.24 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.012 0.001 TYR E 97 PHE 0.009 0.001 PHE D 223 TRP 0.045 0.002 TRP B 86 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00330 (16310) covalent geometry : angle 0.63898 (22158) SS BOND : bond 0.00151 ( 2) SS BOND : angle 1.03057 ( 4) hydrogen bonds : bond 0.03175 ( 589) hydrogen bonds : angle 4.69206 ( 1542) link_BETA1-4 : bond 0.00788 ( 2) link_BETA1-4 : angle 5.01317 ( 6) link_NAG-ASN : bond 0.00683 ( 2) link_NAG-ASN : angle 7.65589 ( 6) link_TRANS : bond 0.00114 ( 8) link_TRANS : angle 0.90637 ( 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 264 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 176 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8128 (tt) REVERT: B 286 ASP cc_start: 0.8105 (t0) cc_final: 0.7897 (t0) REVERT: C 153 MET cc_start: 0.7189 (mtp) cc_final: 0.6890 (mtt) REVERT: C 241 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: E 160 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6479 (tt) REVERT: E 256 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7249 (tm-30) REVERT: H 5 CYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6342 (m) REVERT: F 39 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5786 (mp0) REVERT: F 166 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6486 (tmm) outliers start: 88 outliers final: 74 residues processed: 247 average time/residue: 0.0959 time to fit residues: 38.8857 Evaluate side-chains 251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 171 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 196 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 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 = 0.3716 r_free = 0.3716 target = 0.100353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079117 restraints weight = 40074.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081692 restraints weight = 21975.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.083031 restraints weight = 14292.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084222 restraints weight = 10673.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.084363 restraints weight = 9194.204| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16324 Z= 0.116 Angle : 0.659 11.050 22198 Z= 0.300 Chirality : 0.047 0.478 2498 Planarity : 0.003 0.034 2802 Dihedral : 9.987 120.579 2370 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.11 % Allowed : 22.77 % Favored : 73.12 % 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: 0.33 (0.19), residues: 1958 helix: 0.70 (0.21), residues: 676 sheet: -0.30 (0.28), residues: 328 loop : 0.23 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.033 0.001 TYR F 95 PHE 0.013 0.001 PHE D 223 TRP 0.042 0.002 TRP B 86 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00269 (16310) covalent geometry : angle 0.64115 (22158) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.88935 ( 4) hydrogen bonds : bond 0.02910 ( 589) hydrogen bonds : angle 4.59751 ( 1542) link_BETA1-4 : bond 0.00701 ( 2) link_BETA1-4 : angle 5.06122 ( 6) link_NAG-ASN : bond 0.00737 ( 2) link_NAG-ASN : angle 7.73515 ( 6) link_TRANS : bond 0.00160 ( 8) link_TRANS : angle 0.94756 ( 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 250 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 ASP cc_start: 0.8180 (t0) cc_final: 0.7980 (t0) REVERT: C 153 MET cc_start: 0.7106 (mtp) cc_final: 0.6797 (mtt) REVERT: C 241 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6737 (tm-30) REVERT: E 160 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6404 (tt) REVERT: E 256 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7209 (tm-30) REVERT: F 39 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.5687 (mp0) REVERT: F 166 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6585 (tmm) outliers start: 70 outliers final: 61 residues processed: 237 average time/residue: 0.1021 time to fit residues: 39.1150 Evaluate side-chains 236 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 171 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 196 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 53 optimal weight: 0.0770 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 169 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 175 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 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 = 0.3726 r_free = 0.3726 target = 0.100940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079234 restraints weight = 40662.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.081705 restraints weight = 23806.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083357 restraints weight = 15377.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.083607 restraints weight = 12341.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083748 restraints weight = 10745.872| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16324 Z= 0.111 Angle : 0.658 12.381 22198 Z= 0.297 Chirality : 0.047 0.485 2498 Planarity : 0.003 0.033 2802 Dihedral : 9.855 121.039 2370 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.23 % Allowed : 22.71 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.19), residues: 1958 helix: 0.70 (0.21), residues: 676 sheet: -0.39 (0.29), residues: 302 loop : 0.23 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.009 0.001 TYR F 95 PHE 0.013 0.001 PHE D 223 TRP 0.021 0.002 TRP B 86 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00257 (16310) covalent geometry : angle 0.64006 (22158) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.84171 ( 4) hydrogen bonds : bond 0.02869 ( 589) hydrogen bonds : angle 4.56556 ( 1542) link_BETA1-4 : bond 0.00720 ( 2) link_BETA1-4 : angle 5.06384 ( 6) link_NAG-ASN : bond 0.00738 ( 2) link_NAG-ASN : angle 7.77578 ( 6) link_TRANS : bond 0.00171 ( 8) link_TRANS : angle 0.94867 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.77 seconds wall clock time: 38 minutes 33.50 seconds (2313.50 seconds total)