Starting phenix.real_space_refine on Sat Jun 14 08:19:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjy_50517/06_2025/9fjy_50517.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjy_50517/06_2025/9fjy_50517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjy_50517/06_2025/9fjy_50517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjy_50517/06_2025/9fjy_50517.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjy_50517/06_2025/9fjy_50517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjy_50517/06_2025/9fjy_50517.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.34, per 1000 atoms: 0.65 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: 3.89 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.20 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: 5.86 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2624 1.31 - 1.44: 4354 1.44 - 1.56: 9127 1.56 - 1.69: 29 1.69 - 1.82: 176 Bond restraints: 16310 Sorted by residual: bond pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C7 NAG L 2 " pdb=" N2 NAG L 2 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C7 NAG L 1 " pdb=" N2 NAG L 1 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C7 NAG K 1 " pdb=" N2 NAG K 1 " ideal model delta sigma weight residual 1.346 1.473 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 16305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21863 2.36 - 4.72: 229 4.72 - 7.08: 55 7.08 - 9.44: 8 9.44 - 11.80: 3 Bond angle restraints: 22158 Sorted by residual: angle pdb=" CB MET F 164 " pdb=" CG MET F 164 " pdb=" SD MET F 164 " ideal model delta sigma weight residual 112.70 124.50 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 123.26 -10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CB MET B 153 " pdb=" CG MET B 153 " pdb=" SD MET B 153 " ideal model delta sigma weight residual 112.70 123.20 -10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB LYS E 126 " pdb=" CG LYS E 126 " pdb=" CD LYS E 126 " ideal model delta sigma weight residual 111.30 119.08 -7.78 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA GLU E 143 " pdb=" CB GLU E 143 " pdb=" CG GLU E 143 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 8994 24.04 - 48.08: 681 48.08 - 72.12: 105 72.12 - 96.17: 36 96.17 - 120.21: 32 Dihedral angle restraints: 9848 sinusoidal: 3984 harmonic: 5864 Sorted by residual: dihedral pdb=" CB CYS E 173 " pdb=" SG CYS E 173 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual -86.00 -149.97 63.97 1 1.00e+01 1.00e-02 5.39e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 52.07 -112.08 1 2.00e+01 2.50e-03 3.30e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 50.79 -110.78 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2244 0.074 - 0.147: 248 0.147 - 0.221: 4 0.221 - 0.294: 0 0.294 - 0.368: 2 Chirality restraints: 2498 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN E 18 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN F 18 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA HYP H 6 " pdb=" N HYP H 6 " pdb=" C HYP H 6 " pdb=" CB HYP H 6 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2495 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N TRP G 1 " -0.024 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" CA ALA G 7 " -0.021 2.00e-02 2.50e+03 pdb=" C ALA G 7 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA G 7 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TRP J 1 " -0.021 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" CA ALA J 7 " -0.018 2.00e-02 2.50e+03 pdb=" C ALA J 7 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA J 7 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 139 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CG ASP E 139 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP E 139 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP E 139 " 0.010 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 45 2.36 - 2.99: 8433 2.99 - 3.63: 24439 3.63 - 4.26: 35952 4.26 - 4.90: 58740 Nonbonded interactions: 127609 Sorted by model distance: nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.723 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.724 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.734 3.620 nonbonded pdb=" CD1 TRP G 1 " pdb=" SG CYS G 5 " model vdw 1.767 3.620 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.913 2.170 ... (remaining 127604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 1.870 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 38.430 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 16324 Z= 0.195 Angle : 0.658 22.636 22198 Z= 0.310 Chirality : 0.044 0.368 2498 Planarity : 0.003 0.027 2802 Dihedral : 18.467 120.208 6050 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.41 % Allowed : 21.30 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP B 86 HIS 0.003 0.001 HIS B 161 PHE 0.011 0.001 PHE F 118 TYR 0.010 0.001 TYR E 97 ARG 0.007 0.000 ARG C 62 Details of bonding type rmsd link_TRANS : bond 0.00707 ( 8) link_TRANS : angle 7.70652 ( 24) link_NAG-ASN : bond 0.00930 ( 2) link_NAG-ASN : angle 5.90835 ( 6) link_BETA1-4 : bond 0.00156 ( 2) link_BETA1-4 : angle 1.17775 ( 6) hydrogen bonds : bond 0.30341 ( 589) hydrogen bonds : angle 8.02258 ( 1542) SS BOND : bond 0.00059 ( 2) SS BOND : angle 1.26667 ( 4) covalent geometry : bond 0.00401 (16310) covalent geometry : angle 0.59954 (22158) *********************** 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 : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LEU cc_start: 0.8004 (tp) cc_final: 0.7234 (mp) outliers start: 7 outliers final: 4 residues processed: 186 average time/residue: 0.2285 time to fit residues: 68.5851 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 : 1.812 ------------------------------------------------------------------------------- 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 167 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.098223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076267 restraints weight = 41722.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078997 restraints weight = 25427.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080320 restraints weight = 16762.301| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 16324 Z= 0.312 Angle : 0.760 10.144 22198 Z= 0.370 Chirality : 0.051 0.361 2498 Planarity : 0.005 0.041 2802 Dihedral : 14.254 114.685 2375 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.22 % Allowed : 18.54 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1958 helix: 0.11 (0.19), residues: 704 sheet: 0.13 (0.29), residues: 350 loop : 0.19 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP G 1 HIS 0.007 0.002 HIS D 161 PHE 0.019 0.002 PHE D 31 TYR 0.017 0.002 TYR E 24 ARG 0.005 0.001 ARG C 116 Details of bonding type rmsd link_TRANS : bond 0.00175 ( 8) link_TRANS : angle 1.86437 ( 24) link_NAG-ASN : bond 0.00193 ( 2) link_NAG-ASN : angle 6.71066 ( 6) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 3.89430 ( 6) hydrogen bonds : bond 0.05323 ( 589) hydrogen bonds : angle 5.79998 ( 1542) SS BOND : bond 0.00243 ( 2) SS BOND : angle 1.14061 ( 4) covalent geometry : bond 0.00707 (16310) covalent geometry : angle 0.74709 (22158) *********************** 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 255 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 166 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 90 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8786 (m-10) REVERT: A 129 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8775 (t) REVERT: B 107 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6902 (mm-30) REVERT: B 123 MET cc_start: 0.8594 (mmm) cc_final: 0.7784 (mmm) REVERT: B 180 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8755 (tp) REVERT: C 241 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: E 156 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7912 (pp30) REVERT: E 256 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7443 (tm-30) outliers start: 89 outliers final: 41 residues processed: 237 average time/residue: 0.2119 time to fit residues: 81.9019 Evaluate side-chains 194 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 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 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 165 LEU 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 92 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** 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 ** 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 = 0.3725 r_free = 0.3725 target = 0.100579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078635 restraints weight = 40735.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.081248 restraints weight = 23273.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082928 restraints weight = 15275.698| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16324 Z= 0.123 Angle : 0.616 10.280 22198 Z= 0.286 Chirality : 0.047 0.419 2498 Planarity : 0.004 0.034 2802 Dihedral : 11.183 111.451 2370 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.58 % Allowed : 19.48 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1958 helix: 0.31 (0.20), residues: 696 sheet: 0.05 (0.28), residues: 352 loop : 0.25 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.004 0.001 HIS A 161 PHE 0.017 0.001 PHE D 352 TYR 0.015 0.001 TYR E 24 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd link_TRANS : bond 0.00228 ( 8) link_TRANS : angle 1.43448 ( 24) link_NAG-ASN : bond 0.00683 ( 2) link_NAG-ASN : angle 6.97636 ( 6) link_BETA1-4 : bond 0.00064 ( 2) link_BETA1-4 : angle 5.44159 ( 6) hydrogen bonds : bond 0.03985 ( 589) hydrogen bonds : angle 5.19003 ( 1542) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.65105 ( 4) covalent geometry : bond 0.00271 (16310) covalent geometry : angle 0.59748 (22158) *********************** 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 247 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8801 (tpt) cc_final: 0.8498 (tpt) REVERT: A 355 MET cc_start: 0.8579 (pmm) cc_final: 0.8355 (pmm) REVERT: C 205 GLU cc_start: 0.6933 (pt0) cc_final: 0.6541 (pt0) REVERT: D 119 MET cc_start: 0.7855 (ttm) cc_final: 0.7507 (tmm) REVERT: E 139 ASP cc_start: 0.8078 (t0) cc_final: 0.7861 (t0) REVERT: E 256 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7230 (tm-30) REVERT: F 6 PHE cc_start: 0.8302 (t80) cc_final: 0.7824 (t80) outliers start: 61 outliers final: 34 residues processed: 228 average time/residue: 0.2336 time to fit residues: 84.3580 Evaluate side-chains 199 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 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 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 272 CYS 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 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 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 E residue 67 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 115 VAL Chi-restraints excluded: chain F residue 158 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 192 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 134 optimal weight: 0.0970 chunk 2 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 0.0070 chunk 45 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.078169 restraints weight = 40810.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.080967 restraints weight = 22767.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082380 restraints weight = 14942.675| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16324 Z= 0.144 Angle : 0.616 10.739 22198 Z= 0.284 Chirality : 0.047 0.425 2498 Planarity : 0.003 0.035 2802 Dihedral : 10.746 114.351 2370 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.87 % Allowed : 20.13 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1958 helix: 0.43 (0.20), residues: 688 sheet: -0.05 (0.28), residues: 344 loop : 0.32 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 86 HIS 0.004 0.001 HIS A 161 PHE 0.013 0.001 PHE D 352 TYR 0.011 0.001 TYR E 24 ARG 0.002 0.000 ARG D 210 Details of bonding type rmsd link_TRANS : bond 0.00134 ( 8) link_TRANS : angle 1.08456 ( 24) link_NAG-ASN : bond 0.00688 ( 2) link_NAG-ASN : angle 7.28108 ( 6) link_BETA1-4 : bond 0.00355 ( 2) link_BETA1-4 : angle 5.23622 ( 6) hydrogen bonds : bond 0.03549 ( 589) hydrogen bonds : angle 5.00054 ( 1542) SS BOND : bond 0.00269 ( 2) SS BOND : angle 2.61471 ( 4) covalent geometry : bond 0.00330 (16310) covalent geometry : angle 0.59649 (22158) *********************** 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 234 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 1.867 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8828 (tpt) cc_final: 0.8561 (tpt) REVERT: A 90 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8736 (m-10) REVERT: A 355 MET cc_start: 0.8537 (pmm) cc_final: 0.8326 (pmm) REVERT: C 205 GLU cc_start: 0.7045 (pt0) cc_final: 0.6641 (pt0) REVERT: C 241 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: E 139 ASP cc_start: 0.8150 (t0) cc_final: 0.7911 (t0) REVERT: E 256 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7167 (tm-30) REVERT: F 166 MET cc_start: 0.6678 (ppp) cc_final: 0.6233 (ppp) outliers start: 66 outliers final: 49 residues processed: 217 average time/residue: 0.2311 time to fit residues: 80.6261 Evaluate side-chains 212 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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 142 LEU Chi-restraints excluded: chain B residue 189 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 39 ARG 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 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 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 82 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 124 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- 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** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.099190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077441 restraints weight = 41369.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079719 restraints weight = 23041.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081271 restraints weight = 15604.030| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16324 Z= 0.161 Angle : 0.625 10.976 22198 Z= 0.287 Chirality : 0.047 0.432 2498 Planarity : 0.003 0.034 2802 Dihedral : 10.554 114.510 2370 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.93 % Allowed : 19.42 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1958 helix: 0.46 (0.20), residues: 690 sheet: -0.16 (0.28), residues: 342 loop : 0.27 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 86 HIS 0.004 0.001 HIS A 161 PHE 0.012 0.001 PHE D 352 TYR 0.026 0.001 TYR F 95 ARG 0.002 0.000 ARG C 256 Details of bonding type rmsd link_TRANS : bond 0.00079 ( 8) link_TRANS : angle 0.88395 ( 24) link_NAG-ASN : bond 0.00663 ( 2) link_NAG-ASN : angle 7.46420 ( 6) link_BETA1-4 : bond 0.00533 ( 2) link_BETA1-4 : angle 5.13252 ( 6) hydrogen bonds : bond 0.03476 ( 589) hydrogen bonds : angle 4.88130 ( 1542) SS BOND : bond 0.00168 ( 2) SS BOND : angle 1.62975 ( 4) covalent geometry : bond 0.00372 (16310) covalent geometry : angle 0.60696 (22158) *********************** 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 253 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 169 time to evaluate : 1.824 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8783 (tpt) cc_final: 0.8580 (tpt) REVERT: A 90 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8894 (m-10) REVERT: B 286 ASP cc_start: 0.7839 (t0) cc_final: 0.7536 (t0) REVERT: C 153 MET cc_start: 0.7044 (mtp) cc_final: 0.6653 (ttp) REVERT: C 205 GLU cc_start: 0.7168 (pt0) cc_final: 0.6758 (pt0) REVERT: C 241 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: C 313 MET cc_start: 0.8527 (ttm) cc_final: 0.7970 (ttt) REVERT: E 139 ASP cc_start: 0.8079 (t0) cc_final: 0.7872 (t0) REVERT: E 256 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7280 (tm-30) REVERT: H 5 CYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6561 (m) REVERT: F 39 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6268 (mp0) outliers start: 84 outliers final: 64 residues processed: 236 average time/residue: 0.2432 time to fit residues: 92.5309 Evaluate side-chains 228 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 160 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 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 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 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 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 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 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 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 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 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 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 178 SER Chi-restraints excluded: chain H residue 5 CYS 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 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 106 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** F 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 = 0.3661 r_free = 0.3661 target = 0.097222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075447 restraints weight = 41281.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077768 restraints weight = 23441.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079352 restraints weight = 15951.442| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16324 Z= 0.275 Angle : 0.715 11.051 22198 Z= 0.338 Chirality : 0.050 0.420 2498 Planarity : 0.004 0.038 2802 Dihedral : 10.766 117.457 2370 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.81 % Allowed : 19.48 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1958 helix: 0.28 (0.20), residues: 688 sheet: -0.34 (0.28), residues: 340 loop : 0.08 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 158 HIS 0.005 0.001 HIS E 121 PHE 0.014 0.002 PHE D 31 TYR 0.015 0.002 TYR F 95 ARG 0.006 0.000 ARG F 187 Details of bonding type rmsd link_TRANS : bond 0.00174 ( 8) link_TRANS : angle 0.76802 ( 24) link_NAG-ASN : bond 0.00501 ( 2) link_NAG-ASN : angle 7.43727 ( 6) link_BETA1-4 : bond 0.00551 ( 2) link_BETA1-4 : angle 4.91316 ( 6) hydrogen bonds : bond 0.04165 ( 589) hydrogen bonds : angle 5.06778 ( 1542) SS BOND : bond 0.00270 ( 2) SS BOND : angle 1.52350 ( 4) covalent geometry : bond 0.00629 (16310) covalent geometry : angle 0.69970 (22158) *********************** 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 258 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 159 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 286 ASP cc_start: 0.8092 (t0) cc_final: 0.7875 (t0) REVERT: C 205 GLU cc_start: 0.7274 (pt0) cc_final: 0.6872 (pt0) REVERT: C 241 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: E 256 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7308 (tm-30) REVERT: H 5 CYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6530 (m) REVERT: F 39 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: F 126 LYS cc_start: 0.8495 (tppt) cc_final: 0.8280 (tppt) outliers start: 99 outliers final: 78 residues processed: 239 average time/residue: 0.2486 time to fit residues: 95.0136 Evaluate side-chains 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 150 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 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 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 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 236 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Chi-restraints excluded: chain F residue 196 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 113 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.099412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078024 restraints weight = 40219.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.080350 restraints weight = 22315.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081919 restraints weight = 14814.271| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16324 Z= 0.117 Angle : 0.628 11.096 22198 Z= 0.288 Chirality : 0.047 0.456 2498 Planarity : 0.004 0.042 2802 Dihedral : 10.313 116.484 2370 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.64 % Allowed : 20.72 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1958 helix: 0.54 (0.20), residues: 688 sheet: -0.22 (0.28), residues: 326 loop : 0.15 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 86 HIS 0.003 0.001 HIS D 371 PHE 0.010 0.001 PHE D 352 TYR 0.017 0.001 TYR F 95 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd link_TRANS : bond 0.00163 ( 8) link_TRANS : angle 0.94795 ( 24) link_NAG-ASN : bond 0.00724 ( 2) link_NAG-ASN : angle 7.60795 ( 6) link_BETA1-4 : bond 0.00730 ( 2) link_BETA1-4 : angle 5.12522 ( 6) hydrogen bonds : bond 0.03201 ( 589) hydrogen bonds : angle 4.76396 ( 1542) SS BOND : bond 0.00134 ( 2) SS BOND : angle 1.01689 ( 4) covalent geometry : bond 0.00264 (16310) covalent geometry : angle 0.60937 (22158) *********************** 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 247 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 168 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: B 286 ASP cc_start: 0.8035 (t0) cc_final: 0.7826 (t0) REVERT: C 205 GLU cc_start: 0.7076 (pt0) cc_final: 0.6742 (pt0) REVERT: C 241 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: E 256 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7259 (tm-30) REVERT: F 39 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5788 (mp0) REVERT: F 95 TYR cc_start: 0.8192 (t80) cc_final: 0.7874 (t80) REVERT: F 126 LYS cc_start: 0.8456 (tppt) cc_final: 0.8249 (tppt) REVERT: F 166 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6614 (tmm) outliers start: 79 outliers final: 60 residues processed: 232 average time/residue: 0.2172 time to fit residues: 82.0683 Evaluate side-chains 222 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 285 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 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 236 LEU Chi-restraints excluded: chain C residue 241 GLU 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 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 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 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 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 TRP Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 196 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 150 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 0.2980 chunk 196 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 188 optimal weight: 30.0000 chunk 60 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.098431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076661 restraints weight = 40897.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079074 restraints weight = 23241.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080611 restraints weight = 15982.432| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16324 Z= 0.204 Angle : 0.678 11.100 22198 Z= 0.315 Chirality : 0.048 0.445 2498 Planarity : 0.004 0.032 2802 Dihedral : 10.419 121.442 2370 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.64 % Allowed : 21.54 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1958 helix: 0.55 (0.20), residues: 678 sheet: -0.38 (0.28), residues: 340 loop : 0.17 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 86 HIS 0.005 0.001 HIS E 121 PHE 0.009 0.001 PHE D 31 TYR 0.017 0.001 TYR F 95 ARG 0.003 0.000 ARG E 31 Details of bonding type rmsd link_TRANS : bond 0.00096 ( 8) link_TRANS : angle 0.84307 ( 24) link_NAG-ASN : bond 0.00588 ( 2) link_NAG-ASN : angle 7.57044 ( 6) link_BETA1-4 : bond 0.00670 ( 2) link_BETA1-4 : angle 4.94180 ( 6) hydrogen bonds : bond 0.03636 ( 589) hydrogen bonds : angle 4.79688 ( 1542) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.18296 ( 4) covalent geometry : bond 0.00470 (16310) covalent geometry : angle 0.66153 (22158) *********************** 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 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 159 time to evaluate : 1.901 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.7578 (mmm) cc_final: 0.7218 (tpp) REVERT: B 286 ASP cc_start: 0.8156 (t0) cc_final: 0.7922 (t0) REVERT: C 241 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: C 283 MET cc_start: 0.8559 (mmt) cc_final: 0.8226 (mmm) REVERT: E 256 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7263 (tm-30) REVERT: F 39 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5840 (mp0) REVERT: F 166 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6614 (tmm) outliers start: 79 outliers final: 67 residues processed: 220 average time/residue: 0.2181 time to fit residues: 78.1307 Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 157 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 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 47 MET Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 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 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 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 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 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 121 HIS 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 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 128 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 69 optimal weight: 0.0060 chunk 13 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 chunk 163 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.097705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076175 restraints weight = 40400.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.078639 restraints weight = 22580.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.080061 restraints weight = 14967.671| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16324 Z= 0.227 Angle : 0.705 11.117 22198 Z= 0.328 Chirality : 0.049 0.449 2498 Planarity : 0.004 0.034 2802 Dihedral : 10.431 123.740 2370 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.05 % Allowed : 21.07 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1958 helix: 0.49 (0.20), residues: 678 sheet: -0.49 (0.27), residues: 340 loop : 0.04 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 86 HIS 0.004 0.001 HIS D 161 PHE 0.012 0.001 PHE D 31 TYR 0.017 0.001 TYR F 95 ARG 0.003 0.000 ARG C 206 Details of bonding type rmsd link_TRANS : bond 0.00112 ( 8) link_TRANS : angle 0.83936 ( 24) link_NAG-ASN : bond 0.00554 ( 2) link_NAG-ASN : angle 7.59222 ( 6) link_BETA1-4 : bond 0.00658 ( 2) link_BETA1-4 : angle 4.82224 ( 6) hydrogen bonds : bond 0.03749 ( 589) hydrogen bonds : angle 4.83424 ( 1542) SS BOND : bond 0.00227 ( 2) SS BOND : angle 1.20827 ( 4) covalent geometry : bond 0.00521 (16310) covalent geometry : angle 0.68897 (22158) *********************** 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 242 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 156 time to evaluate : 1.837 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.7575 (mmm) cc_final: 0.7255 (tpp) REVERT: B 86 TRP cc_start: 0.8934 (OUTLIER) cc_final: 0.8618 (m-10) REVERT: B 286 ASP cc_start: 0.8246 (t0) cc_final: 0.7987 (t0) REVERT: C 241 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: E 256 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7278 (tm-30) REVERT: F 39 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: F 126 LYS cc_start: 0.8493 (tppt) cc_final: 0.8275 (tppt) REVERT: F 166 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6679 (tmm) outliers start: 86 outliers final: 76 residues processed: 227 average time/residue: 0.2665 time to fit residues: 98.0366 Evaluate side-chains 234 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 154 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 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 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 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 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 121 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 157 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.097936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076025 restraints weight = 41312.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.078360 restraints weight = 23592.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079931 restraints weight = 16156.495| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16324 Z= 0.215 Angle : 0.699 11.269 22198 Z= 0.324 Chirality : 0.049 0.458 2498 Planarity : 0.004 0.036 2802 Dihedral : 10.383 125.227 2370 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.16 % Allowed : 21.13 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 1958 helix: 0.50 (0.20), residues: 678 sheet: -0.50 (0.27), residues: 340 loop : -0.01 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 86 HIS 0.004 0.001 HIS E 121 PHE 0.010 0.001 PHE D 31 TYR 0.032 0.001 TYR F 95 ARG 0.003 0.000 ARG A 256 Details of bonding type rmsd link_TRANS : bond 0.00102 ( 8) link_TRANS : angle 0.86223 ( 24) link_NAG-ASN : bond 0.00558 ( 2) link_NAG-ASN : angle 7.68926 ( 6) link_BETA1-4 : bond 0.00650 ( 2) link_BETA1-4 : angle 4.77757 ( 6) hydrogen bonds : bond 0.03674 ( 589) hydrogen bonds : angle 4.81272 ( 1542) SS BOND : bond 0.00207 ( 2) SS BOND : angle 1.23210 ( 4) covalent geometry : bond 0.00494 (16310) covalent geometry : angle 0.68238 (22158) ********************** 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 247 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 159 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.8956 (mmm) cc_final: 0.8651 (ppp) REVERT: A 305 MET cc_start: 0.7538 (mmm) cc_final: 0.7166 (tpp) REVERT: B 286 ASP cc_start: 0.8298 (t0) cc_final: 0.8052 (t0) REVERT: C 241 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: E 256 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7278 (tm-30) REVERT: H 5 CYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6415 (m) REVERT: F 39 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5899 (mp0) REVERT: F 126 LYS cc_start: 0.8525 (tppt) cc_final: 0.8294 (tppt) REVERT: F 164 MET cc_start: 0.8136 (tpp) cc_final: 0.7924 (tpp) REVERT: F 166 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6754 (tmm) outliers start: 88 outliers final: 75 residues processed: 234 average time/residue: 0.2141 time to fit residues: 82.0635 Evaluate side-chains 237 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 158 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 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 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 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 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 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 121 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR 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 68 optimal weight: 0.0270 chunk 81 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 102 optimal weight: 0.0870 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.100429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079302 restraints weight = 39924.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082053 restraints weight = 21732.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083621 restraints weight = 13808.325| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2646 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= 0.113 Angle : 0.661 11.092 22198 Z= 0.301 Chirality : 0.047 0.493 2498 Planarity : 0.004 0.033 2802 Dihedral : 9.974 122.245 2370 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.81 % Allowed : 22.59 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1958 helix: 0.69 (0.21), residues: 676 sheet: -0.33 (0.29), residues: 294 loop : 0.09 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 86 HIS 0.004 0.001 HIS B 87 PHE 0.012 0.001 PHE D 124 TYR 0.011 0.001 TYR F 95 ARG 0.002 0.000 ARG D 206 Details of bonding type rmsd link_TRANS : bond 0.00177 ( 8) link_TRANS : angle 0.98997 ( 24) link_NAG-ASN : bond 0.00723 ( 2) link_NAG-ASN : angle 7.82248 ( 6) link_BETA1-4 : bond 0.00712 ( 2) link_BETA1-4 : angle 5.01398 ( 6) hydrogen bonds : bond 0.02966 ( 589) hydrogen bonds : angle 4.57989 ( 1542) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.85145 ( 4) covalent geometry : bond 0.00258 (16310) covalent geometry : angle 0.64239 (22158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4391.68 seconds wall clock time: 78 minutes 21.01 seconds (4701.01 seconds total)