Starting phenix.real_space_refine on Sun May 3 21:20:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjy_50517/05_2026/9fjy_50517.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjy_50517/05_2026/9fjy_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fjy_50517/05_2026/9fjy_50517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjy_50517/05_2026/9fjy_50517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fjy_50517/05_2026/9fjy_50517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjy_50517/05_2026/9fjy_50517.map" } 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-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15968 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1990 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain breaks: 1 Chain: "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: 3.66, per 1000 atoms: 0.23 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: 1.22 Conformation dependent library (CDL) restraints added in 670.9 milliseconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 27 sheets defined 44.5% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 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: 2.19 Time building geometry restraints manager: 1.52 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: 21855 2.36 - 4.72: 236 4.72 - 7.08: 56 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=" C EEP J 2 " pdb=" CA EEP J 2 " pdb=" CB EEP J 2 " ideal model delta sigma weight residual 110.50 105.40 5.10 1.50e+00 4.44e-01 1.16e+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 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 8991 24.04 - 48.08: 684 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: 2246 0.074 - 0.147: 246 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: 2.010 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.500 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- 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= 0.200 Angle : 0.663 22.636 22198 Z= 0.315 Chirality : 0.044 0.368 2498 Planarity : 0.003 0.027 2802 Dihedral : 18.468 120.208 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 are 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 0.00411 (16310) covalent geometry : angle 0.60503 (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 : 0.445 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: 0.0994 time to fit residues: 30.1878 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 : 0.567 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.098714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076473 restraints weight = 41568.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079189 restraints weight = 24736.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.080703 restraints weight = 15852.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.081395 restraints weight = 11915.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081670 restraints weight = 11085.139| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1501 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= 0.286 Angle : 0.742 9.990 22198 Z= 0.358 Chirality : 0.050 0.387 2498 Planarity : 0.005 0.040 2802 Dihedral : 14.093 114.667 2375 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.05 % Allowed : 18.49 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1958 helix: 0.03 (0.19), residues: 716 sheet: 0.17 (0.29), residues: 348 loop : 0.18 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 187 TYR 0.017 0.002 TYR E 24 PHE 0.019 0.002 PHE D 352 TRP 0.014 0.002 TRP B 86 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00647 (16310) covalent geometry : angle 0.72851 (22158) SS BOND : bond 0.00231 ( 2) SS BOND : angle 1.16080 ( 4) hydrogen bonds : bond 0.04972 ( 589) hydrogen bonds : angle 5.72681 ( 1542) link_BETA1-4 : bond 0.00374 ( 2) link_BETA1-4 : angle 3.83124 ( 6) link_NAG-ASN : bond 0.00209 ( 2) link_NAG-ASN : angle 6.77319 ( 6) link_TRANS : bond 0.00249 ( 8) link_TRANS : angle 2.00232 ( 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 253 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 167 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 90 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8786 (m-10) REVERT: A 129 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8727 (t) REVERT: B 107 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: B 123 MET cc_start: 0.8593 (mmm) cc_final: 0.7849 (mmm) REVERT: B 180 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8752 (tp) REVERT: B 185 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8294 (tt) REVERT: C 241 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: E 156 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7887 (pp30) REVERT: E 256 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7463 (tm-30) outliers start: 86 outliers final: 42 residues processed: 233 average time/residue: 0.0928 time to fit residues: 35.9114 Evaluate side-chains 198 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 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 303 THR 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 E residue 156 GLN Chi-restraints excluded: chain E residue 192 PHE 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: 2.9990 chunk 82 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS E 180 GLN ** 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 = 0.3687 r_free = 0.3687 target = 0.098603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076432 restraints weight = 41558.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079137 restraints weight = 24140.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080672 restraints weight = 15365.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081545 restraints weight = 11335.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081869 restraints weight = 10369.867| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16324 Z= 0.185 Angle : 0.643 10.293 22198 Z= 0.303 Chirality : 0.048 0.413 2498 Planarity : 0.004 0.036 2802 Dihedral : 11.567 113.379 2370 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.64 % Allowed : 19.48 % Favored : 75.88 % 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 are not related in a simple way. whole: 0.11 (0.19), residues: 1958 helix: 0.21 (0.20), residues: 704 sheet: -0.01 (0.28), residues: 348 loop : 0.20 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.014 0.001 TYR E 24 PHE 0.017 0.001 PHE D 352 TRP 0.013 0.001 TRP D 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00422 (16310) covalent geometry : angle 0.62588 (22158) SS BOND : bond 0.00178 ( 2) SS BOND : angle 0.73107 ( 4) hydrogen bonds : bond 0.04376 ( 589) hydrogen bonds : angle 5.27000 ( 1542) link_BETA1-4 : bond 0.00045 ( 2) link_BETA1-4 : angle 5.24041 ( 6) link_NAG-ASN : bond 0.00580 ( 2) link_NAG-ASN : angle 6.88813 ( 6) link_TRANS : bond 0.00153 ( 8) link_TRANS : angle 1.30638 ( 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 251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8838 (tpt) cc_final: 0.8509 (tpt) REVERT: B 12 ASN cc_start: 0.8485 (t0) cc_final: 0.8191 (m-40) REVERT: B 185 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8174 (tt) REVERT: C 241 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: E 139 ASP cc_start: 0.8198 (t0) cc_final: 0.7996 (t0) REVERT: E 153 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8727 (m-30) REVERT: E 256 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7318 (tm-30) outliers start: 79 outliers final: 42 residues processed: 230 average time/residue: 0.0933 time to fit residues: 34.9574 Evaluate side-chains 202 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU 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 89 THR Chi-restraints excluded: chain B residue 107 GLU 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 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 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 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 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: 9.9990 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** C 137 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079129 restraints weight = 41132.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.081620 restraints weight = 23318.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.083052 restraints weight = 16236.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083884 restraints weight = 11058.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.084192 restraints weight = 9875.297| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16324 Z= 0.109 Angle : 0.602 10.782 22198 Z= 0.277 Chirality : 0.047 0.432 2498 Planarity : 0.003 0.034 2802 Dihedral : 10.723 111.264 2370 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.17 % Allowed : 20.01 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 1958 helix: 0.45 (0.21), residues: 686 sheet: -0.07 (0.28), residues: 354 loop : 0.30 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 312 TYR 0.012 0.001 TYR E 24 PHE 0.013 0.001 PHE D 352 TRP 0.025 0.001 TRP B 86 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00241 (16310) covalent geometry : angle 0.58225 (22158) SS BOND : bond 0.00317 ( 2) SS BOND : angle 2.23740 ( 4) hydrogen bonds : bond 0.03265 ( 589) hydrogen bonds : angle 4.91232 ( 1542) link_BETA1-4 : bond 0.00481 ( 2) link_BETA1-4 : angle 5.31295 ( 6) link_NAG-ASN : bond 0.00775 ( 2) link_NAG-ASN : angle 7.37286 ( 6) link_TRANS : bond 0.00184 ( 8) link_TRANS : angle 1.01271 ( 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 252 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8794 (tpt) cc_final: 0.8527 (tpt) REVERT: A 90 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8723 (m-10) REVERT: B 185 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8101 (tt) REVERT: C 241 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: D 119 MET cc_start: 0.7817 (ttm) cc_final: 0.7491 (tmm) REVERT: E 157 LYS cc_start: 0.8858 (tptp) cc_final: 0.8651 (tptp) REVERT: E 256 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7158 (tm-30) REVERT: F 6 PHE cc_start: 0.8410 (t80) cc_final: 0.7956 (t80) REVERT: F 39 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5987 (mp0) REVERT: F 166 MET cc_start: 0.6609 (ppp) cc_final: 0.6126 (ppp) outliers start: 71 outliers final: 51 residues processed: 236 average time/residue: 0.1017 time to fit residues: 38.6779 Evaluate side-chains 222 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain B residue 142 LEU 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 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 132 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 GLU 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 54 VAL 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 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 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: 2.9990 chunk 77 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 188 optimal weight: 30.0000 chunk 156 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 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 156 GLN F 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.097431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075188 restraints weight = 41519.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.077743 restraints weight = 24339.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.079378 restraints weight = 15914.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.079721 restraints weight = 11673.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.080132 restraints weight = 10784.073| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16324 Z= 0.253 Angle : 0.687 10.939 22198 Z= 0.325 Chirality : 0.049 0.419 2498 Planarity : 0.004 0.034 2802 Dihedral : 10.914 117.195 2370 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.69 % Allowed : 19.54 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.19), residues: 1958 helix: 0.35 (0.20), residues: 692 sheet: -0.26 (0.28), residues: 340 loop : 0.20 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 9 TYR 0.013 0.001 TYR E 95 PHE 0.012 0.001 PHE D 31 TRP 0.024 0.002 TRP B 86 HIS 0.005 0.001 HIS E 121 Details of bonding type rmsd covalent geometry : bond 0.00578 (16310) covalent geometry : angle 0.67110 (22158) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.75199 ( 4) hydrogen bonds : bond 0.04041 ( 589) hydrogen bonds : angle 5.03929 ( 1542) link_BETA1-4 : bond 0.00506 ( 2) link_BETA1-4 : angle 5.00104 ( 6) link_NAG-ASN : bond 0.00547 ( 2) link_NAG-ASN : angle 7.39117 ( 6) link_TRANS : bond 0.00141 ( 8) link_TRANS : angle 0.76259 ( 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 262 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 165 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8795 (tpt) cc_final: 0.8556 (tpt) REVERT: A 90 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8980 (m-10) REVERT: B 123 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7595 (tpp) REVERT: B 185 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8229 (tt) REVERT: B 286 ASP cc_start: 0.7953 (t0) cc_final: 0.7686 (t0) REVERT: C 241 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: E 256 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7298 (tm-30) outliers start: 97 outliers final: 70 residues processed: 240 average time/residue: 0.0952 time to fit residues: 37.1596 Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 153 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 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 123 MET 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 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 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 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 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 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 149 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 SER 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: 6.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 152 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 180 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 = 0.3694 r_free = 0.3694 target = 0.098948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077326 restraints weight = 40275.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.080084 restraints weight = 22788.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081448 restraints weight = 14479.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.082456 restraints weight = 10840.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082713 restraints weight = 9777.390| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2166 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= 0.150 Angle : 0.621 11.001 22198 Z= 0.288 Chirality : 0.047 0.442 2498 Planarity : 0.004 0.034 2802 Dihedral : 10.563 115.124 2370 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.58 % Allowed : 20.19 % Favored : 74.24 % 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 are not related in a simple way. whole: 0.28 (0.19), residues: 1958 helix: 0.54 (0.20), residues: 690 sheet: -0.23 (0.28), residues: 338 loop : 0.26 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 187 TYR 0.010 0.001 TYR E 95 PHE 0.011 0.001 PHE D 352 TRP 0.041 0.002 TRP B 86 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00344 (16310) covalent geometry : angle 0.60286 (22158) SS BOND : bond 0.00275 ( 2) SS BOND : angle 1.38984 ( 4) hydrogen bonds : bond 0.03353 ( 589) hydrogen bonds : angle 4.84887 ( 1542) link_BETA1-4 : bond 0.00665 ( 2) link_BETA1-4 : angle 5.07588 ( 6) link_NAG-ASN : bond 0.00703 ( 2) link_NAG-ASN : angle 7.53865 ( 6) link_TRANS : bond 0.00102 ( 8) link_TRANS : angle 0.85956 ( 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 261 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 166 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 TRP cc_start: 0.8906 (OUTLIER) cc_final: 0.8601 (m-10) REVERT: B 185 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8143 (tt) REVERT: B 286 ASP cc_start: 0.7906 (t0) cc_final: 0.7679 (t0) REVERT: C 241 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: E 256 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7273 (tm-30) REVERT: F 39 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5890 (mp0) outliers start: 95 outliers final: 71 residues processed: 241 average time/residue: 0.0946 time to fit residues: 36.9745 Evaluate side-chains 237 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 162 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 16 MET 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 107 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 134 VAL 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 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 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 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 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 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 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 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 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 192 PHE 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: 3.9990 chunk 130 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 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 = 0.3677 r_free = 0.3677 target = 0.098082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076156 restraints weight = 40944.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078438 restraints weight = 23413.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079968 restraints weight = 15842.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.081065 restraints weight = 11517.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.081291 restraints weight = 10385.040| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16324 Z= 0.197 Angle : 0.659 11.062 22198 Z= 0.307 Chirality : 0.048 0.435 2498 Planarity : 0.004 0.036 2802 Dihedral : 10.558 117.852 2370 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.87 % Allowed : 20.66 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1958 helix: 0.58 (0.21), residues: 678 sheet: -0.36 (0.28), residues: 340 loop : 0.19 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.032 0.001 TYR F 95 PHE 0.009 0.001 PHE D 352 TRP 0.043 0.002 TRP B 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00452 (16310) covalent geometry : angle 0.64178 (22158) SS BOND : bond 0.00194 ( 2) SS BOND : angle 1.24770 ( 4) hydrogen bonds : bond 0.03601 ( 589) hydrogen bonds : angle 4.85012 ( 1542) link_BETA1-4 : bond 0.00707 ( 2) link_BETA1-4 : angle 4.98049 ( 6) link_NAG-ASN : bond 0.00609 ( 2) link_NAG-ASN : angle 7.50848 ( 6) link_TRANS : bond 0.00085 ( 8) link_TRANS : angle 0.81018 ( 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 264 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 164 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: B 185 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8179 (tt) REVERT: C 241 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: E 256 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 39 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5920 (mp0) REVERT: F 166 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6524 (tmm) outliers start: 100 outliers final: 84 residues processed: 245 average time/residue: 0.0908 time to fit residues: 36.4606 Evaluate side-chains 247 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 158 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 16 MET 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 123 MET 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 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 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 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 43 VAL Chi-restraints excluded: chain D residue 54 VAL 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 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 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 149 ASP Chi-restraints excluded: chain E residue 165 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 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 Chi-restraints excluded: chain F residue 214 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 11 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 180 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.099131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077463 restraints weight = 40343.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.080340 restraints weight = 22786.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081882 restraints weight = 14156.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082354 restraints weight = 10454.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082873 restraints weight = 9748.868| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2360 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= 0.137 Angle : 0.644 11.068 22198 Z= 0.297 Chirality : 0.047 0.450 2498 Planarity : 0.003 0.035 2802 Dihedral : 10.343 117.860 2370 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.58 % Allowed : 21.24 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1958 helix: 0.68 (0.21), residues: 678 sheet: -0.36 (0.28), residues: 340 loop : 0.26 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.020 0.001 TYR F 95 PHE 0.009 0.001 PHE D 352 TRP 0.050 0.002 TRP B 86 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00317 (16310) covalent geometry : angle 0.62615 (22158) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.03412 ( 4) hydrogen bonds : bond 0.03215 ( 589) hydrogen bonds : angle 4.73543 ( 1542) link_BETA1-4 : bond 0.00714 ( 2) link_BETA1-4 : angle 5.06318 ( 6) link_NAG-ASN : bond 0.00686 ( 2) link_NAG-ASN : angle 7.58361 ( 6) link_TRANS : bond 0.00118 ( 8) link_TRANS : angle 0.88599 ( 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 270 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 175 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8108 (tt) REVERT: C 241 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: E 256 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7246 (tm-30) REVERT: F 39 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: F 95 TYR cc_start: 0.8155 (t80) cc_final: 0.7896 (t80) REVERT: F 166 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6516 (tmm) outliers start: 95 outliers final: 78 residues processed: 252 average time/residue: 0.0947 time to fit residues: 39.1934 Evaluate side-chains 247 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 165 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 30 VAL 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 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 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 132 MET 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 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 43 VAL 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 149 THR 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 303 THR 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 149 ASP Chi-restraints excluded: chain E residue 156 GLN 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 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 Chi-restraints excluded: chain F residue 214 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 121 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 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 = 0.3683 r_free = 0.3683 target = 0.098454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076951 restraints weight = 40433.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079281 restraints weight = 22745.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080823 restraints weight = 15224.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081589 restraints weight = 10944.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.081800 restraints weight = 9776.798| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16324 Z= 0.175 Angle : 0.672 11.101 22198 Z= 0.312 Chirality : 0.048 0.449 2498 Planarity : 0.004 0.033 2802 Dihedral : 10.349 120.339 2370 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.22 % Allowed : 22.01 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1958 helix: 0.67 (0.21), residues: 678 sheet: -0.38 (0.28), residues: 340 loop : 0.23 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.019 0.001 TYR F 95 PHE 0.008 0.001 PHE D 352 TRP 0.038 0.002 TRP B 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00405 (16310) covalent geometry : angle 0.65542 (22158) SS BOND : bond 0.00187 ( 2) SS BOND : angle 1.08563 ( 4) hydrogen bonds : bond 0.03329 ( 589) hydrogen bonds : angle 4.73543 ( 1542) link_BETA1-4 : bond 0.00675 ( 2) link_BETA1-4 : angle 4.97250 ( 6) link_NAG-ASN : bond 0.00650 ( 2) link_NAG-ASN : angle 7.58469 ( 6) link_TRANS : bond 0.00085 ( 8) link_TRANS : angle 0.83899 ( 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 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 168 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.7570 (mmm) cc_final: 0.7236 (tpp) REVERT: B 185 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8165 (tt) REVERT: C 241 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: E 256 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7251 (tm-30) REVERT: F 39 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5885 (mp0) REVERT: F 95 TYR cc_start: 0.8152 (t80) cc_final: 0.7898 (t80) REVERT: F 166 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6634 (tmm) outliers start: 89 outliers final: 80 residues processed: 241 average time/residue: 0.0938 time to fit residues: 36.8422 Evaluate side-chains 251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 167 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 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 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 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 132 MET 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 370 VAL 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 64 ILE 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 159 VAL 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 303 THR 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 149 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 195 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 46 VAL 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: 0.0010 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.100997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.079853 restraints weight = 39981.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081959 restraints weight = 22114.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083679 restraints weight = 15008.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084657 restraints weight = 10517.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.085043 restraints weight = 9270.116| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2500 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= 0.109 Angle : 0.653 11.047 22198 Z= 0.299 Chirality : 0.047 0.481 2498 Planarity : 0.003 0.033 2802 Dihedral : 9.941 118.490 2370 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.28 % Allowed : 22.77 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1958 helix: 0.80 (0.21), residues: 676 sheet: -0.27 (0.28), residues: 328 loop : 0.22 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.012 0.001 TYR F 95 PHE 0.008 0.001 PHE D 352 TRP 0.034 0.002 TRP B 86 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00251 (16310) covalent geometry : angle 0.63424 (22158) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.81732 ( 4) hydrogen bonds : bond 0.02790 ( 589) hydrogen bonds : angle 4.56779 ( 1542) link_BETA1-4 : bond 0.00767 ( 2) link_BETA1-4 : angle 5.09732 ( 6) link_NAG-ASN : bond 0.00776 ( 2) link_NAG-ASN : angle 7.72990 ( 6) link_TRANS : bond 0.00188 ( 8) link_TRANS : angle 0.96978 ( 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 259 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 186 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8894 (mmm) cc_final: 0.8685 (ppp) REVERT: E 256 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7202 (tm-30) REVERT: F 39 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: F 95 TYR cc_start: 0.8154 (t80) cc_final: 0.7883 (t80) REVERT: F 166 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6678 (tmm) outliers start: 73 outliers final: 61 residues processed: 247 average time/residue: 0.1056 time to fit residues: 42.4816 Evaluate side-chains 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 175 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 219 VAL 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 134 VAL 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 25 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL 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 201 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 267 LEU 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 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 303 THR 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 156 GLN Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 46 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 Chi-restraints excluded: chain F residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.100616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078842 restraints weight = 40735.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081396 restraints weight = 23769.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082769 restraints weight = 15224.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.083084 restraints weight = 12420.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083946 restraints weight = 11088.084| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2539 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= 0.126 Angle : 0.658 11.094 22198 Z= 0.300 Chirality : 0.047 0.474 2498 Planarity : 0.003 0.033 2802 Dihedral : 9.961 121.338 2370 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.99 % Allowed : 22.77 % 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 are not related in a simple way. whole: 0.36 (0.19), residues: 1958 helix: 0.76 (0.21), residues: 678 sheet: -0.32 (0.28), residues: 332 loop : 0.24 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.015 0.001 TYR F 95 PHE 0.009 0.001 PHE D 223 TRP 0.030 0.002 TRP B 86 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00293 (16310) covalent geometry : angle 0.64048 (22158) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.89730 ( 4) hydrogen bonds : bond 0.02896 ( 589) hydrogen bonds : angle 4.55738 ( 1542) link_BETA1-4 : bond 0.00715 ( 2) link_BETA1-4 : angle 5.05993 ( 6) link_NAG-ASN : bond 0.00721 ( 2) link_NAG-ASN : angle 7.71420 ( 6) link_TRANS : bond 0.00137 ( 8) link_TRANS : angle 0.90465 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.99 seconds wall clock time: 38 minutes 30.26 seconds (2310.26 seconds total)