Starting phenix.real_space_refine on Mon Apr 6 19:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7n_72308/04_2026/9q7n_72308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7n_72308/04_2026/9q7n_72308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q7n_72308/04_2026/9q7n_72308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7n_72308/04_2026/9q7n_72308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q7n_72308/04_2026/9q7n_72308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7n_72308/04_2026/9q7n_72308.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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 10 5.49 5 Mg 5 5.21 5 S 120 5.16 5 C 13315 2.51 5 N 3500 2.21 5 O 4060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21010 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2857 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2877 Chain: "B" Number of atoms: 2857 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2877 Chain: "C" Number of atoms: 2857 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2877 Chain: "D" Number of atoms: 2857 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2877 Chain: "E" Number of atoms: 2857 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2877 Chain: "a" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "b" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "c" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "d" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "e" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.05, per 1000 atoms: 0.38 Number of scatterers: 21010 At special positions: 0 Unit cell: (120.96, 124.2, 208.44, 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 120 16.00 P 10 15.00 Mg 5 11.99 O 4060 8.00 N 3500 7.00 C 13315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.4 seconds 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4980 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 33 sheets defined 47.5% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.749A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.800A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.729A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.740A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 removed outlier: 4.097A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.779A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.559A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.549A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.512A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.060A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.507A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.580A pdb=" N PHE A 352 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.783A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.865A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.835A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.192A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.755A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.505A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.628A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.570A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.857A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.614A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.862A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.534A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.699A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.666A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.955A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.758A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.566A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.684A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.582A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.928A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.307A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.534A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.755A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.829A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.903A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 181 through 197 removed outlier: 4.115A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.662A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.588A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.649A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.652A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) 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 347 Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.734A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.909A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 61 " --> pdb=" O ALA E 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 57 through 61' Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.525A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.560A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.580A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.788A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.638A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.591A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.671A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.617A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.544A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.506A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.792A pdb=" N ILE a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 58 through 60 No H-bonds generated for 'chain 'a' and resid 58 through 60' Processing helix chain 'a' and resid 66 through 74 Processing helix chain 'a' and resid 110 through 120 Processing helix chain 'a' and resid 120 through 128 removed outlier: 3.855A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.650A pdb=" N ASP a 142 " --> pdb=" O GLY a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 153 Processing helix chain 'b' and resid 8 through 20 removed outlier: 3.728A pdb=" N ILE b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 31 Processing helix chain 'b' and resid 58 through 60 No H-bonds generated for 'chain 'b' and resid 58 through 60' Processing helix chain 'b' and resid 66 through 74 removed outlier: 3.594A pdb=" N SER b 70 " --> pdb=" O ASP b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 110 through 128 removed outlier: 5.246A pdb=" N ASP b 122 " --> pdb=" O ALA b 118 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA b 123 " --> pdb=" O SER b 119 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 Processing helix chain 'b' and resid 146 through 153 Processing helix chain 'b' and resid 154 through 156 No H-bonds generated for 'chain 'b' and resid 154 through 156' Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.660A pdb=" N ILE c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL c 20 " --> pdb=" O ASN c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 31 Processing helix chain 'c' and resid 58 through 60 No H-bonds generated for 'chain 'c' and resid 58 through 60' Processing helix chain 'c' and resid 66 through 74 Processing helix chain 'c' and resid 110 through 128 removed outlier: 5.183A pdb=" N ASP c 122 " --> pdb=" O ALA c 118 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA c 123 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 removed outlier: 3.534A pdb=" N ASP c 142 " --> pdb=" O GLY c 139 " (cutoff:3.500A) Processing helix chain 'c' and resid 145 through 153 removed outlier: 4.253A pdb=" N LEU c 149 " --> pdb=" O ASP c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 154 through 156 No H-bonds generated for 'chain 'c' and resid 154 through 156' Processing helix chain 'd' and resid 8 through 20 removed outlier: 3.769A pdb=" N ILE d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL d 20 " --> pdb=" O ASN d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 31 Processing helix chain 'd' and resid 58 through 60 No H-bonds generated for 'chain 'd' and resid 58 through 60' Processing helix chain 'd' and resid 66 through 75 removed outlier: 3.673A pdb=" N LEU d 75 " --> pdb=" O PHE d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 128 removed outlier: 5.099A pdb=" N ASP d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE d 124 " --> pdb=" O SER d 120 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE d 128 " --> pdb=" O ILE d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 143 removed outlier: 3.600A pdb=" N ASP d 142 " --> pdb=" O GLY d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 153 Processing helix chain 'e' and resid 8 through 20 removed outlier: 3.678A pdb=" N ILE e 12 " --> pdb=" O ASN e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 25 through 31 Processing helix chain 'e' and resid 58 through 60 No H-bonds generated for 'chain 'e' and resid 58 through 60' Processing helix chain 'e' and resid 66 through 75 removed outlier: 3.616A pdb=" N LEU e 75 " --> pdb=" O PHE e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 120 through 128 removed outlier: 4.183A pdb=" N ILE e 124 " --> pdb=" O SER e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 139 through 143 removed outlier: 3.554A pdb=" N ASP e 142 " --> pdb=" O GLY e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 145 through 153 removed outlier: 4.297A pdb=" N LEU e 149 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.813A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.178A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.687A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.240A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.764A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.177A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB6, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.780A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB8, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.070A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.633A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.168A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.499A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU a 50 " --> pdb=" O LEU a 37 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.499A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU a 50 " --> pdb=" O LEU a 37 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.797A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS b 133 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.797A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.318A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU c 50 " --> pdb=" O LEU c 37 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU c 37 " --> pdb=" O GLU c 50 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ALA c 52 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N ALA c 35 " --> pdb=" O ALA c 52 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N GLN c 54 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N LYS c 33 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.318A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU c 50 " --> pdb=" O LEU c 37 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU c 37 " --> pdb=" O GLU c 50 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ALA c 52 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N ALA c 35 " --> pdb=" O ALA c 52 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N GLN c 54 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N LYS c 33 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.487A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS d 133 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.487A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.706A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU e 50 " --> pdb=" O LEU e 37 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N HIS e 133 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU e 99 " --> pdb=" O HIS e 133 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N TRP e 135 " --> pdb=" O LEU e 99 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE e 101 " --> pdb=" O TRP e 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.706A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU e 50 " --> pdb=" O LEU e 37 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) 1019 hydrogen bonds defined for protein. 2712 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: 4.25 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5762 1.34 - 1.46: 4271 1.46 - 1.58: 11187 1.58 - 1.70: 20 1.70 - 1.82: 205 Bond restraints: 21445 Sorted by residual: bond pdb=" CB MET B 190 " pdb=" CG MET B 190 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.56e+00 bond pdb=" N THR b 63 " pdb=" CA THR b 63 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.15e-02 7.56e+03 6.09e+00 bond pdb=" N THR e 63 " pdb=" CA THR e 63 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.96e+00 bond pdb=" CA THR e 63 " pdb=" C THR e 63 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.34e-02 5.57e+03 5.45e+00 bond pdb=" N ASN d 138 " pdb=" CA ASN d 138 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.83e+00 ... (remaining 21440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 28174 2.93 - 5.87: 783 5.87 - 8.80: 76 8.80 - 11.74: 21 11.74 - 14.67: 6 Bond angle restraints: 29060 Sorted by residual: angle pdb=" N ILE b 143 " pdb=" CA ILE b 143 " pdb=" C ILE b 143 " ideal model delta sigma weight residual 113.20 107.21 5.99 9.60e-01 1.09e+00 3.89e+01 angle pdb=" CA LYS D 50 " pdb=" CB LYS D 50 " pdb=" CG LYS D 50 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CB GLU B 167 " pdb=" CG GLU B 167 " pdb=" CD GLU B 167 " ideal model delta sigma weight residual 112.60 121.92 -9.32 1.70e+00 3.46e-01 3.01e+01 angle pdb=" CA GLU b 51 " pdb=" CB GLU b 51 " pdb=" CG GLU b 51 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" C ASP d 62 " pdb=" N THR d 63 " pdb=" CA THR d 63 " ideal model delta sigma weight residual 122.61 130.67 -8.06 1.56e+00 4.11e-01 2.67e+01 ... (remaining 29055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 12002 18.08 - 36.16: 853 36.16 - 54.24: 173 54.24 - 72.32: 22 72.32 - 90.40: 25 Dihedral angle restraints: 13075 sinusoidal: 5325 harmonic: 7750 Sorted by residual: dihedral pdb=" CA GLN d 136 " pdb=" C GLN d 136 " pdb=" N VAL d 137 " pdb=" CA VAL d 137 " ideal model delta harmonic sigma weight residual 180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ARG d 81 " pdb=" C ARG d 81 " pdb=" N TYR d 82 " pdb=" CA TYR d 82 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA THR E 324 " pdb=" C THR E 324 " pdb=" N MET E 325 " pdb=" CA MET E 325 " ideal model delta harmonic sigma weight residual 180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 13072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2575 0.071 - 0.142: 607 0.142 - 0.213: 70 0.213 - 0.283: 14 0.283 - 0.354: 4 Chirality restraints: 3270 Sorted by residual: chirality pdb=" CB ILE d 47 " pdb=" CA ILE d 47 " pdb=" CG1 ILE d 47 " pdb=" CG2 ILE d 47 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE e 47 " pdb=" CA ILE e 47 " pdb=" CG1 ILE e 47 " pdb=" CG2 ILE e 47 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3267 not shown) Planarity restraints: 3690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 167 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLU B 167 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU B 167 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY B 168 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 344 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C SER C 344 " -0.056 2.00e-02 2.50e+03 pdb=" O SER C 344 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE C 345 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 270 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" CD GLU E 270 " -0.055 2.00e-02 2.50e+03 pdb=" OE1 GLU E 270 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU E 270 " 0.019 2.00e-02 2.50e+03 ... (remaining 3687 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 21 2.63 - 3.20: 17088 3.20 - 3.77: 31516 3.77 - 4.33: 44830 4.33 - 4.90: 73124 Nonbonded interactions: 166579 Sorted by model distance: nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.068 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.072 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.076 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.084 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.099 2.170 ... (remaining 166574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 102 or resid 104 through 172 or resid 174 throug \ h 248 or resid 250 through 270 or resid 272 through 401)) selection = (chain 'B' and (resid 4 through 102 or resid 104 through 172 or resid 174 throug \ h 248 or resid 250 through 270 or resid 272 through 401)) selection = (chain 'C' and (resid 4 through 102 or resid 104 through 172 or resid 174 throug \ h 248 or resid 250 through 270 or resid 272 through 401)) selection = (chain 'D' and (resid 4 through 102 or resid 104 through 172 or resid 174 throug \ h 248 or resid 250 through 270 or resid 272 through 401)) selection = (chain 'E' and (resid 4 through 102 or resid 104 through 172 or resid 174 throug \ h 248 or resid 250 through 270 or resid 272 through 401)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.330 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.340 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.006 0.077 21445 Z= 0.285 Angle : 1.118 14.675 29060 Z= 0.600 Chirality : 0.061 0.354 3270 Planarity : 0.009 0.102 3690 Dihedral : 13.687 90.400 8095 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.15), residues: 2615 helix: -2.27 (0.13), residues: 940 sheet: -0.14 (0.22), residues: 510 loop : -0.35 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG c 45 TYR 0.038 0.003 TYR d 85 PHE 0.043 0.003 PHE c 71 TRP 0.029 0.003 TRP A 86 HIS 0.011 0.002 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00604 (21445) covalent geometry : angle 1.11752 (29060) hydrogen bonds : bond 0.16760 ( 976) hydrogen bonds : angle 7.33130 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8796 (mmm) cc_final: 0.8573 (mmt) REVERT: A 227 MET cc_start: 0.9293 (tpp) cc_final: 0.9071 (tpp) REVERT: C 82 MET cc_start: 0.9408 (tpt) cc_final: 0.9028 (tpt) REVERT: D 82 MET cc_start: 0.8370 (tpt) cc_final: 0.7824 (tmm) REVERT: D 176 MET cc_start: 0.9062 (mmt) cc_final: 0.8587 (mmm) REVERT: D 305 MET cc_start: 0.9161 (mmm) cc_final: 0.8756 (mmm) REVERT: D 314 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8700 (tm-30) REVERT: E 10 CYS cc_start: 0.8005 (t) cc_final: 0.7655 (t) REVERT: E 24 ASP cc_start: 0.8887 (m-30) cc_final: 0.8650 (m-30) REVERT: E 82 MET cc_start: 0.7948 (tpt) cc_final: 0.7165 (mmm) REVERT: E 119 MET cc_start: 0.9124 (mtp) cc_final: 0.8819 (ptp) REVERT: E 132 MET cc_start: 0.9261 (tmm) cc_final: 0.8919 (tmm) REVERT: E 246 GLN cc_start: 0.9367 (mt0) cc_final: 0.8853 (mp10) REVERT: E 269 MET cc_start: 0.8786 (tpt) cc_final: 0.8515 (tpp) REVERT: E 355 MET cc_start: 0.8920 (mpp) cc_final: 0.8502 (mpp) REVERT: b 115 MET cc_start: 0.9586 (tpt) cc_final: 0.8811 (tpp) REVERT: c 1 MET cc_start: 0.8633 (ttm) cc_final: 0.8359 (ttm) REVERT: d 85 TYR cc_start: 0.6655 (t80) cc_final: 0.6447 (t80) REVERT: d 115 MET cc_start: 0.9043 (tpt) cc_final: 0.8376 (tpp) REVERT: d 142 ASP cc_start: 0.8493 (m-30) cc_final: 0.8170 (m-30) REVERT: d 146 ARG cc_start: 0.7821 (ptt180) cc_final: 0.7548 (ptt180) REVERT: e 1 MET cc_start: 0.7601 (ptp) cc_final: 0.7381 (ptm) REVERT: e 89 TYR cc_start: 0.8573 (p90) cc_final: 0.8166 (p90) REVERT: e 115 MET cc_start: 0.9066 (tpt) cc_final: 0.8437 (tpp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1375 time to fit residues: 39.3157 Evaluate side-chains 133 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 258 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 162 ASN A 314 GLN C 246 GLN D 121 GLN D 162 ASN E 173 HIS A E 360 GLN d 138 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.054760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.038699 restraints weight = 316945.143| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 7.11 r_work: 0.2594 rms_B_bonded: 6.82 restraints_weight: 2.0000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21445 Z= 0.163 Angle : 0.618 9.634 29060 Z= 0.315 Chirality : 0.045 0.160 3270 Planarity : 0.004 0.053 3690 Dihedral : 5.474 48.069 2955 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 0.22 % Allowed : 4.01 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2615 helix: -0.39 (0.16), residues: 1015 sheet: -0.10 (0.22), residues: 585 loop : 0.27 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 45 TYR 0.016 0.001 TYR A 294 PHE 0.019 0.002 PHE c 71 TRP 0.013 0.001 TRP A 86 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00367 (21445) covalent geometry : angle 0.61825 (29060) hydrogen bonds : bond 0.03935 ( 976) hydrogen bonds : angle 5.04143 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9048 (tpp) cc_final: 0.8686 (tpp) REVERT: A 355 MET cc_start: 0.9430 (mmm) cc_final: 0.8931 (mmp) REVERT: C 82 MET cc_start: 0.9507 (tpt) cc_final: 0.9305 (tpt) REVERT: C 325 MET cc_start: 0.8981 (mmt) cc_final: 0.8731 (mmt) REVERT: D 82 MET cc_start: 0.8522 (tpt) cc_final: 0.8011 (tmm) REVERT: D 305 MET cc_start: 0.9252 (mmm) cc_final: 0.8817 (mmm) REVERT: E 24 ASP cc_start: 0.8789 (m-30) cc_final: 0.8508 (m-30) REVERT: E 82 MET cc_start: 0.8187 (tpt) cc_final: 0.7242 (tpp) REVERT: E 86 TRP cc_start: 0.8887 (m-10) cc_final: 0.8042 (m-90) REVERT: E 142 LEU cc_start: 0.9165 (tp) cc_final: 0.8833 (tp) REVERT: E 246 GLN cc_start: 0.9056 (mt0) cc_final: 0.8546 (mt0) REVERT: E 269 MET cc_start: 0.8821 (tpt) cc_final: 0.8501 (tpp) REVERT: E 355 MET cc_start: 0.8898 (mpp) cc_final: 0.8438 (mpp) REVERT: b 143 ILE cc_start: 0.9137 (tt) cc_final: 0.8913 (tp) REVERT: c 1 MET cc_start: 0.8807 (ttm) cc_final: 0.8494 (ttm) REVERT: c 85 TYR cc_start: 0.8756 (t80) cc_final: 0.8505 (t80) REVERT: d 68 TYR cc_start: 0.7285 (t80) cc_final: 0.6934 (t80) REVERT: d 85 TYR cc_start: 0.6403 (t80) cc_final: 0.6160 (t80) REVERT: d 115 MET cc_start: 0.9135 (tpt) cc_final: 0.8078 (tpt) REVERT: e 115 MET cc_start: 0.9114 (tpt) cc_final: 0.8494 (tpp) outliers start: 5 outliers final: 2 residues processed: 141 average time/residue: 0.1330 time to fit residues: 31.7391 Evaluate side-chains 127 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain c residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 34 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 212 optimal weight: 0.0470 chunk 148 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS B 128 ASN E 128 ASN a 133 HIS c 78 ASN d 133 HIS d 138 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.052647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.037126 restraints weight = 313057.256| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 6.89 r_work: 0.2559 rms_B_bonded: 6.72 restraints_weight: 2.0000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21445 Z= 0.186 Angle : 0.613 11.344 29060 Z= 0.308 Chirality : 0.045 0.171 3270 Planarity : 0.004 0.052 3690 Dihedral : 5.186 49.222 2955 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.26 % Allowed : 5.93 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2615 helix: 0.53 (0.17), residues: 995 sheet: -0.08 (0.22), residues: 580 loop : 0.49 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 254 TYR 0.015 0.001 TYR A 294 PHE 0.020 0.002 PHE d 71 TRP 0.013 0.001 TRP B 79 HIS 0.003 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00421 (21445) covalent geometry : angle 0.61320 (29060) hydrogen bonds : bond 0.03885 ( 976) hydrogen bonds : angle 4.73543 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9057 (tpp) cc_final: 0.8708 (tpp) REVERT: D 82 MET cc_start: 0.8575 (tpt) cc_final: 0.7987 (tmm) REVERT: D 305 MET cc_start: 0.9315 (mmm) cc_final: 0.8856 (mmm) REVERT: E 24 ASP cc_start: 0.8810 (m-30) cc_final: 0.8493 (m-30) REVERT: E 82 MET cc_start: 0.8326 (tpt) cc_final: 0.7451 (tpt) REVERT: E 86 TRP cc_start: 0.8904 (m-10) cc_final: 0.8156 (m-90) REVERT: E 246 GLN cc_start: 0.9003 (mt0) cc_final: 0.8573 (mt0) REVERT: E 269 MET cc_start: 0.8909 (tpt) cc_final: 0.8543 (tpp) REVERT: E 355 MET cc_start: 0.8865 (mpp) cc_final: 0.8385 (mpp) REVERT: b 143 ILE cc_start: 0.9129 (tt) cc_final: 0.8882 (tp) REVERT: e 89 TYR cc_start: 0.8798 (p90) cc_final: 0.8523 (p90) REVERT: e 115 MET cc_start: 0.9237 (tpt) cc_final: 0.8560 (tpp) outliers start: 6 outliers final: 2 residues processed: 130 average time/residue: 0.1341 time to fit residues: 29.6080 Evaluate side-chains 124 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain d residue 138 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 87 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 87 HIS E 173 HIS A E 353 GLN E 360 GLN d 138 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.051716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035838 restraints weight = 324930.913| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 6.94 r_work: 0.2497 rms_B_bonded: 6.65 restraints_weight: 2.0000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 21445 Z= 0.310 Angle : 0.714 10.100 29060 Z= 0.360 Chirality : 0.047 0.143 3270 Planarity : 0.004 0.052 3690 Dihedral : 5.419 50.561 2955 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.52 % Allowed : 6.80 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2615 helix: 0.78 (0.17), residues: 980 sheet: -0.27 (0.22), residues: 590 loop : 0.42 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 196 TYR 0.028 0.002 TYR d 85 PHE 0.023 0.002 PHE c 71 TRP 0.014 0.002 TRP B 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00694 (21445) covalent geometry : angle 0.71407 (29060) hydrogen bonds : bond 0.04376 ( 976) hydrogen bonds : angle 4.94124 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9061 (tpp) cc_final: 0.8731 (tpp) REVERT: D 176 MET cc_start: 0.8883 (mmm) cc_final: 0.8101 (mtt) REVERT: D 305 MET cc_start: 0.9423 (mmm) cc_final: 0.8997 (mmm) REVERT: E 24 ASP cc_start: 0.8752 (m-30) cc_final: 0.8463 (m-30) REVERT: E 82 MET cc_start: 0.8386 (tpt) cc_final: 0.7448 (mmm) REVERT: E 246 GLN cc_start: 0.8842 (mt0) cc_final: 0.8425 (mt0) REVERT: E 269 MET cc_start: 0.8956 (tpt) cc_final: 0.8549 (tpp) REVERT: E 305 MET cc_start: 0.8975 (tpp) cc_final: 0.8293 (mmm) REVERT: E 325 MET cc_start: 0.6864 (ttm) cc_final: 0.6277 (ttm) REVERT: E 355 MET cc_start: 0.8875 (mpp) cc_final: 0.8358 (mpp) REVERT: d 115 MET cc_start: 0.9304 (tpt) cc_final: 0.8506 (tpp) REVERT: d 142 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7466 (p0) REVERT: e 115 MET cc_start: 0.9262 (tpt) cc_final: 0.8370 (tpp) outliers start: 11 outliers final: 8 residues processed: 127 average time/residue: 0.1349 time to fit residues: 28.7403 Evaluate side-chains 127 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 138 ASN Chi-restraints excluded: chain d residue 142 ASP Chi-restraints excluded: chain e residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS A ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 ASN ** 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 = 0.3234 r_free = 0.3234 target = 0.052831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.037210 restraints weight = 335716.118| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 7.10 r_work: 0.2559 rms_B_bonded: 6.84 restraints_weight: 2.0000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21445 Z= 0.105 Angle : 0.554 9.310 29060 Z= 0.275 Chirality : 0.043 0.159 3270 Planarity : 0.003 0.046 3690 Dihedral : 5.097 48.506 2955 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.52 % Allowed : 7.15 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2615 helix: 0.81 (0.17), residues: 1055 sheet: -0.07 (0.22), residues: 585 loop : 0.64 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.032 0.001 TYR d 85 PHE 0.014 0.001 PHE e 103 TRP 0.014 0.001 TRP B 340 HIS 0.003 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00234 (21445) covalent geometry : angle 0.55449 (29060) hydrogen bonds : bond 0.03270 ( 976) hydrogen bonds : angle 4.52035 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.9571 (m) cc_final: 0.9367 (p) REVERT: A 176 MET cc_start: 0.9286 (mmm) cc_final: 0.8905 (tpp) REVERT: A 227 MET cc_start: 0.9018 (tpp) cc_final: 0.8696 (tpp) REVERT: C 82 MET cc_start: 0.9598 (tpt) cc_final: 0.8909 (tmm) REVERT: C 325 MET cc_start: 0.9100 (mmt) cc_final: 0.8561 (mmt) REVERT: C 355 MET cc_start: 0.9270 (mmm) cc_final: 0.8973 (mmm) REVERT: D 176 MET cc_start: 0.8808 (mmm) cc_final: 0.8016 (mtt) REVERT: D 305 MET cc_start: 0.9351 (mmm) cc_final: 0.8873 (mmm) REVERT: E 24 ASP cc_start: 0.8754 (m-30) cc_final: 0.8457 (m-30) REVERT: E 82 MET cc_start: 0.8318 (tpt) cc_final: 0.7380 (mmm) REVERT: E 119 MET cc_start: 0.9174 (ptm) cc_final: 0.8803 (ptp) REVERT: E 246 GLN cc_start: 0.8895 (mt0) cc_final: 0.8501 (mt0) REVERT: E 269 MET cc_start: 0.9001 (tpt) cc_final: 0.8579 (tpp) REVERT: E 355 MET cc_start: 0.8894 (mpp) cc_final: 0.8370 (mpp) REVERT: b 115 MET cc_start: 0.9457 (tpt) cc_final: 0.8710 (tpt) REVERT: b 143 ILE cc_start: 0.9198 (tt) cc_final: 0.8865 (tp) REVERT: d 115 MET cc_start: 0.9262 (tpt) cc_final: 0.8453 (tpp) REVERT: e 115 MET cc_start: 0.9313 (tpt) cc_final: 0.8674 (tpp) outliers start: 10 outliers final: 6 residues processed: 134 average time/residue: 0.1413 time to fit residues: 31.6416 Evaluate side-chains 131 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain d residue 124 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 105 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 ASN ** e 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 ASN ** 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 = 0.3238 r_free = 0.3238 target = 0.052962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.037358 restraints weight = 344408.267| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 7.17 r_work: 0.2559 rms_B_bonded: 6.98 restraints_weight: 2.0000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21445 Z= 0.114 Angle : 0.546 7.765 29060 Z= 0.268 Chirality : 0.043 0.150 3270 Planarity : 0.003 0.043 3690 Dihedral : 4.890 48.131 2955 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.61 % Allowed : 7.58 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2615 helix: 0.96 (0.17), residues: 1055 sheet: -0.01 (0.22), residues: 585 loop : 0.75 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 146 TYR 0.030 0.001 TYR d 85 PHE 0.013 0.001 PHE e 103 TRP 0.011 0.001 TRP B 340 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00256 (21445) covalent geometry : angle 0.54565 (29060) hydrogen bonds : bond 0.03160 ( 976) hydrogen bonds : angle 4.39005 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.9569 (m) cc_final: 0.9359 (p) REVERT: A 176 MET cc_start: 0.9264 (mmm) cc_final: 0.8892 (tpp) REVERT: A 227 MET cc_start: 0.9011 (tpp) cc_final: 0.8672 (tpp) REVERT: C 325 MET cc_start: 0.9091 (mmt) cc_final: 0.8570 (mmt) REVERT: C 355 MET cc_start: 0.9269 (mmm) cc_final: 0.8962 (mmm) REVERT: D 176 MET cc_start: 0.8795 (mmm) cc_final: 0.7996 (mtt) REVERT: D 305 MET cc_start: 0.9344 (mmm) cc_final: 0.8847 (mmm) REVERT: E 24 ASP cc_start: 0.8786 (m-30) cc_final: 0.8490 (m-30) REVERT: E 82 MET cc_start: 0.8319 (tpt) cc_final: 0.7308 (mmm) REVERT: E 119 MET cc_start: 0.9163 (ptm) cc_final: 0.8756 (ptp) REVERT: E 246 GLN cc_start: 0.8868 (mt0) cc_final: 0.8465 (mt0) REVERT: E 269 MET cc_start: 0.8994 (tpt) cc_final: 0.8577 (tpp) REVERT: E 355 MET cc_start: 0.8875 (mpp) cc_final: 0.8328 (mpp) REVERT: b 143 ILE cc_start: 0.9183 (tt) cc_final: 0.8836 (tp) REVERT: d 115 MET cc_start: 0.9270 (tpt) cc_final: 0.8443 (tpp) REVERT: e 115 MET cc_start: 0.9280 (tpt) cc_final: 0.8645 (tpp) outliers start: 11 outliers final: 9 residues processed: 140 average time/residue: 0.1348 time to fit residues: 31.8958 Evaluate side-chains 137 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 234 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS A c 138 ASN d 138 ASN ** e 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.053112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.037556 restraints weight = 323191.522| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 7.01 r_work: 0.2573 rms_B_bonded: 6.80 restraints_weight: 2.0000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21445 Z= 0.107 Angle : 0.550 13.334 29060 Z= 0.269 Chirality : 0.043 0.202 3270 Planarity : 0.003 0.042 3690 Dihedral : 4.805 47.613 2955 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.70 % Allowed : 8.15 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2615 helix: 1.03 (0.17), residues: 1055 sheet: 0.03 (0.22), residues: 585 loop : 0.84 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 146 TYR 0.027 0.001 TYR e 68 PHE 0.013 0.001 PHE e 103 TRP 0.011 0.001 TRP B 340 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00240 (21445) covalent geometry : angle 0.55044 (29060) hydrogen bonds : bond 0.03040 ( 976) hydrogen bonds : angle 4.32075 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.9568 (m) cc_final: 0.9351 (p) REVERT: A 176 MET cc_start: 0.9253 (mmm) cc_final: 0.8893 (tpp) REVERT: A 227 MET cc_start: 0.8976 (tpp) cc_final: 0.8656 (tpp) REVERT: B 355 MET cc_start: 0.9381 (mmm) cc_final: 0.9108 (mmm) REVERT: C 355 MET cc_start: 0.9248 (mmm) cc_final: 0.8931 (mmm) REVERT: D 176 MET cc_start: 0.8818 (mmm) cc_final: 0.8011 (mtt) REVERT: D 305 MET cc_start: 0.9320 (mmm) cc_final: 0.8811 (mmm) REVERT: E 24 ASP cc_start: 0.8804 (m-30) cc_final: 0.8509 (m-30) REVERT: E 82 MET cc_start: 0.8331 (tpt) cc_final: 0.7716 (mmm) REVERT: E 119 MET cc_start: 0.9098 (ptm) cc_final: 0.8745 (ptp) REVERT: E 246 GLN cc_start: 0.8868 (mt0) cc_final: 0.8462 (mt0) REVERT: E 269 MET cc_start: 0.8985 (tpt) cc_final: 0.8563 (tpp) REVERT: E 305 MET cc_start: 0.8859 (mmt) cc_final: 0.8318 (mmm) REVERT: E 355 MET cc_start: 0.8869 (mpp) cc_final: 0.8308 (mpp) REVERT: b 143 ILE cc_start: 0.9188 (tt) cc_final: 0.8834 (tp) REVERT: d 115 MET cc_start: 0.9259 (tpt) cc_final: 0.8413 (tpp) REVERT: d 142 ASP cc_start: 0.8522 (m-30) cc_final: 0.7458 (p0) REVERT: e 115 MET cc_start: 0.9273 (tpt) cc_final: 0.8686 (tpp) outliers start: 13 outliers final: 9 residues processed: 139 average time/residue: 0.1295 time to fit residues: 30.1029 Evaluate side-chains 137 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 54 optimal weight: 8.9990 chunk 230 optimal weight: 0.7980 chunk 255 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 152 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 138 ASN ** e 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 ASN ** 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 = 0.3216 r_free = 0.3216 target = 0.052230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036787 restraints weight = 317776.436| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 6.88 r_work: 0.2545 rms_B_bonded: 6.65 restraints_weight: 2.0000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21445 Z= 0.178 Angle : 0.588 9.325 29060 Z= 0.289 Chirality : 0.044 0.183 3270 Planarity : 0.004 0.044 3690 Dihedral : 4.888 49.107 2955 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.78 % Allowed : 8.10 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2615 helix: 1.01 (0.17), residues: 1055 sheet: -0.06 (0.22), residues: 590 loop : 0.88 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 254 TYR 0.028 0.001 TYR d 85 PHE 0.014 0.001 PHE e 103 TRP 0.012 0.001 TRP D 79 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00401 (21445) covalent geometry : angle 0.58827 (29060) hydrogen bonds : bond 0.03469 ( 976) hydrogen bonds : angle 4.42213 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.9566 (m) cc_final: 0.9345 (p) REVERT: A 176 MET cc_start: 0.9284 (mmm) cc_final: 0.8955 (tpp) REVERT: A 227 MET cc_start: 0.9039 (tpp) cc_final: 0.8683 (tpp) REVERT: B 355 MET cc_start: 0.9409 (mmm) cc_final: 0.9160 (mmm) REVERT: C 325 MET cc_start: 0.9099 (mmt) cc_final: 0.8543 (mmt) REVERT: D 176 MET cc_start: 0.8873 (mmm) cc_final: 0.8123 (mtt) REVERT: D 305 MET cc_start: 0.9422 (mmm) cc_final: 0.8931 (mmm) REVERT: E 24 ASP cc_start: 0.8720 (m-30) cc_final: 0.8455 (m-30) REVERT: E 82 MET cc_start: 0.8467 (tpt) cc_final: 0.7828 (mmm) REVERT: E 246 GLN cc_start: 0.8826 (mt0) cc_final: 0.8419 (mt0) REVERT: E 269 MET cc_start: 0.8989 (tpt) cc_final: 0.8578 (tpp) REVERT: E 305 MET cc_start: 0.8887 (mmt) cc_final: 0.8347 (mmm) REVERT: E 355 MET cc_start: 0.8901 (mpp) cc_final: 0.8360 (mpp) REVERT: d 115 MET cc_start: 0.9331 (tpt) cc_final: 0.8476 (tpp) REVERT: e 115 MET cc_start: 0.9295 (tpt) cc_final: 0.8680 (tpp) outliers start: 14 outliers final: 8 residues processed: 132 average time/residue: 0.1319 time to fit residues: 29.2672 Evaluate side-chains 131 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain d residue 124 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 85 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 HIS A ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 ASN e 8 ASN ** e 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.037371 restraints weight = 336898.984| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 7.15 r_work: 0.2564 rms_B_bonded: 6.96 restraints_weight: 2.0000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21445 Z= 0.113 Angle : 0.553 8.438 29060 Z= 0.269 Chirality : 0.043 0.179 3270 Planarity : 0.003 0.043 3690 Dihedral : 4.799 47.502 2955 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.74 % Allowed : 8.28 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2615 helix: 1.04 (0.17), residues: 1055 sheet: 0.10 (0.22), residues: 580 loop : 0.77 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.030 0.001 TYR d 85 PHE 0.013 0.001 PHE e 103 TRP 0.012 0.001 TRP B 340 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00254 (21445) covalent geometry : angle 0.55310 (29060) hydrogen bonds : bond 0.03070 ( 976) hydrogen bonds : angle 4.32864 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.9559 (m) cc_final: 0.9341 (p) REVERT: A 176 MET cc_start: 0.9247 (mmm) cc_final: 0.8884 (tpp) REVERT: A 227 MET cc_start: 0.8949 (tpp) cc_final: 0.8628 (tpp) REVERT: B 355 MET cc_start: 0.9381 (mmm) cc_final: 0.9125 (mmm) REVERT: C 325 MET cc_start: 0.9055 (mmt) cc_final: 0.8484 (mmt) REVERT: D 176 MET cc_start: 0.8811 (mmm) cc_final: 0.8021 (mtt) REVERT: D 305 MET cc_start: 0.9372 (mmm) cc_final: 0.8845 (mmm) REVERT: E 24 ASP cc_start: 0.8748 (m-30) cc_final: 0.8459 (m-30) REVERT: E 82 MET cc_start: 0.8342 (tpt) cc_final: 0.7324 (mmm) REVERT: E 246 GLN cc_start: 0.8858 (mt0) cc_final: 0.8503 (mt0) REVERT: E 269 MET cc_start: 0.8991 (tpt) cc_final: 0.8568 (tpp) REVERT: E 305 MET cc_start: 0.8841 (mmt) cc_final: 0.8376 (mmm) REVERT: E 355 MET cc_start: 0.8898 (mpp) cc_final: 0.8332 (mpp) REVERT: b 115 MET cc_start: 0.9363 (tpp) cc_final: 0.8949 (tpt) REVERT: b 143 ILE cc_start: 0.9186 (tt) cc_final: 0.8811 (tp) REVERT: c 115 MET cc_start: 0.8665 (tpp) cc_final: 0.8275 (tpp) REVERT: d 68 TYR cc_start: 0.8233 (t80) cc_final: 0.7814 (m-80) REVERT: d 115 MET cc_start: 0.9271 (tpt) cc_final: 0.8410 (tpp) REVERT: d 142 ASP cc_start: 0.8627 (m-30) cc_final: 0.7597 (p0) REVERT: e 115 MET cc_start: 0.9303 (tpt) cc_final: 0.8710 (tpp) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.1287 time to fit residues: 30.4555 Evaluate side-chains 136 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain d residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 259 optimal weight: 0.0010 chunk 118 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 209 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 138 ASN d 138 ASN ** e 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.038271 restraints weight = 310223.332| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 6.97 r_work: 0.2591 rms_B_bonded: 6.79 restraints_weight: 2.0000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21445 Z= 0.091 Angle : 0.541 10.734 29060 Z= 0.261 Chirality : 0.042 0.151 3270 Planarity : 0.003 0.042 3690 Dihedral : 4.638 46.643 2955 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.57 % Allowed : 8.63 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2615 helix: 1.01 (0.17), residues: 1085 sheet: 0.17 (0.23), residues: 545 loop : 0.72 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.029 0.001 TYR d 85 PHE 0.015 0.001 PHE e 15 TRP 0.013 0.001 TRP B 340 HIS 0.002 0.000 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00199 (21445) covalent geometry : angle 0.54089 (29060) hydrogen bonds : bond 0.02798 ( 976) hydrogen bonds : angle 4.22189 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5230 Ramachandran restraints generated. 2615 Oldfield, 0 Emsley, 2615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.9531 (m) cc_final: 0.9301 (p) REVERT: A 176 MET cc_start: 0.9224 (mmm) cc_final: 0.8851 (tpp) REVERT: B 355 MET cc_start: 0.9356 (mmm) cc_final: 0.9101 (mmm) REVERT: D 176 MET cc_start: 0.8769 (mmm) cc_final: 0.8006 (mtt) REVERT: D 305 MET cc_start: 0.9288 (mmm) cc_final: 0.8768 (mmm) REVERT: E 24 ASP cc_start: 0.8768 (m-30) cc_final: 0.8477 (m-30) REVERT: E 82 MET cc_start: 0.8290 (tpt) cc_final: 0.7284 (mmm) REVERT: E 246 GLN cc_start: 0.8863 (mt0) cc_final: 0.8495 (mt0) REVERT: E 269 MET cc_start: 0.8930 (tpt) cc_final: 0.8516 (tpp) REVERT: E 305 MET cc_start: 0.8783 (mmt) cc_final: 0.8477 (mmt) REVERT: E 355 MET cc_start: 0.8880 (mpp) cc_final: 0.8320 (mpp) REVERT: b 143 ILE cc_start: 0.9128 (tt) cc_final: 0.8774 (tp) REVERT: c 115 MET cc_start: 0.8659 (tpp) cc_final: 0.8277 (tpp) REVERT: d 68 TYR cc_start: 0.8187 (t80) cc_final: 0.7889 (m-80) REVERT: d 115 MET cc_start: 0.9224 (tpt) cc_final: 0.8365 (tpp) REVERT: d 142 ASP cc_start: 0.8615 (m-30) cc_final: 0.7546 (p0) REVERT: e 115 MET cc_start: 0.9285 (tpt) cc_final: 0.8764 (tpp) outliers start: 9 outliers final: 8 residues processed: 140 average time/residue: 0.1285 time to fit residues: 30.1760 Evaluate side-chains 134 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain d residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 140 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN d 136 GLN d 138 ASN ** e 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.052524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.037022 restraints weight = 303974.001| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 6.81 r_work: 0.2549 rms_B_bonded: 6.71 restraints_weight: 2.0000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21445 Z= 0.168 Angle : 0.588 8.855 29060 Z= 0.288 Chirality : 0.044 0.157 3270 Planarity : 0.003 0.043 3690 Dihedral : 4.745 48.598 2955 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.61 % Allowed : 8.67 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2615 helix: 0.98 (0.17), residues: 1085 sheet: 0.15 (0.23), residues: 545 loop : 0.69 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 81 TYR 0.025 0.001 TYR d 85 PHE 0.013 0.001 PHE e 103 TRP 0.012 0.001 TRP B 79 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00379 (21445) covalent geometry : angle 0.58789 (29060) hydrogen bonds : bond 0.03326 ( 976) hydrogen bonds : angle 4.35214 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5343.44 seconds wall clock time: 92 minutes 25.62 seconds (5545.62 seconds total)