Starting phenix.real_space_refine on Tue Apr 7 03:39:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y9j_72703/04_2026/9y9j_72703.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y9j_72703/04_2026/9y9j_72703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y9j_72703/04_2026/9y9j_72703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y9j_72703/04_2026/9y9j_72703.map" model { file = "/net/cci-nas-00/data/ceres_data/9y9j_72703/04_2026/9y9j_72703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y9j_72703/04_2026/9y9j_72703.cif" } resolution = 3.58 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= 0.007 sd= 0.022 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 134 5.16 5 C 15112 2.51 5 N 3982 2.21 5 O 4575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 23818 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2846 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: 2891 Chain: "D" Number of atoms: 2846 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: 2891 Chain: "E" Number of atoms: 2839 Number of conformers: 1 Conformer: "" 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 Chain: "W" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1372 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "X" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1372 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} 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: 7.10, per 1000 atoms: 0.30 Number of scatterers: 23818 At special positions: 0 Unit cell: (115.56, 127.44, 234.36, 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 134 16.00 P 10 15.00 Mg 5 11.99 O 4575 8.00 N 3982 7.00 C 15112 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: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 35 sheets defined 52.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.586A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 61' Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.883A 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 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.602A 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: 3.771A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.632A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.627A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 4.047A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 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: 4.094A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.270A 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 347 Processing helix chain 'A' and resid 349 through 356 removed outlier: 4.427A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.643A pdb=" N LYS B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.826A 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 removed outlier: 3.557A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.569A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.999A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.706A 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 252 through 257 removed outlier: 3.616A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.507A 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 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 4.135A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.262A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.535A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 349 through 356 removed outlier: 4.407A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.644A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 4.035A 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 112 through 126 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.627A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.804A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.682A 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: 3.679A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.693A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.520A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 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 295 removed outlier: 4.063A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.351A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 349 through 356 removed outlier: 4.392A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.673A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.820A 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 removed outlier: 3.613A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.636A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.929A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 3.599A 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 255 Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.617A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.602A pdb=" N PHE D 266 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 4.034A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.529A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 349 through 356 removed outlier: 3.532A pdb=" N PHE D 352 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.683A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS E 61 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.528A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.887A 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 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.642A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.748A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.809A 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 256 removed outlier: 3.583A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.697A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 3.517A pdb=" N PHE E 266 " --> pdb=" O GLN E 263 " (cutoff:3.500A) 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: 4.218A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.218A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 349 through 356 removed outlier: 4.379A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'W' and resid 41 through 52 Processing helix chain 'W' and resid 53 through 66 Processing helix chain 'W' and resid 67 through 93 removed outlier: 3.573A pdb=" N LYS W 71 " --> pdb=" O GLY W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 122 Proline residue: W 107 - end of helix removed outlier: 3.609A pdb=" N ASN W 122 " --> pdb=" O PHE W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 137 through 144 removed outlier: 4.167A pdb=" N VAL W 144 " --> pdb=" O LEU W 141 " (cutoff:3.500A) Processing helix chain 'W' and resid 149 through 173 removed outlier: 4.001A pdb=" N TYR W 164 " --> pdb=" O ALA W 160 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG W 167 " --> pdb=" O PHE W 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 201 removed outlier: 4.000A pdb=" N VAL W 180 " --> pdb=" O ASP W 176 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP W 190 " --> pdb=" O TYR W 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 52 Processing helix chain 'X' and resid 53 through 66 Processing helix chain 'X' and resid 67 through 93 Processing helix chain 'X' and resid 97 through 122 Proline residue: X 107 - end of helix removed outlier: 3.606A pdb=" N ASN X 122 " --> pdb=" O PHE X 118 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 136 Processing helix chain 'X' and resid 137 through 144 removed outlier: 4.126A pdb=" N VAL X 144 " --> pdb=" O LEU X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 173 removed outlier: 3.940A pdb=" N TYR X 153 " --> pdb=" O LYS X 149 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG X 167 " --> pdb=" O PHE X 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS X 173 " --> pdb=" O LEU X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 201 removed outlier: 3.965A pdb=" N VAL X 180 " --> pdb=" O ASP X 176 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP X 190 " --> pdb=" O TYR X 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.793A 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 128 removed outlier: 4.981A pdb=" N ASP a 122 " --> pdb=" O ALA a 118 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.514A 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 'a' and resid 154 through 156 No H-bonds generated for 'chain 'a' and resid 154 through 156' Processing helix chain 'b' and resid 8 through 20 removed outlier: 3.832A 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 Processing helix chain 'b' and resid 110 through 120 Processing helix chain 'b' and resid 120 through 128 removed outlier: 4.062A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.551A pdb=" N ASP b 142 " --> pdb=" O GLY b 139 " (cutoff:3.500A) 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: 3.832A pdb=" N ILE c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 3.581A 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 120 Processing helix chain 'c' and resid 120 through 128 removed outlier: 3.971A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 removed outlier: 3.642A pdb=" N ASP c 142 " --> pdb=" O GLY c 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE c 143 " --> pdb=" O LEU c 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 139 through 143' Processing helix chain 'c' and resid 146 through 153 Processing helix chain 'd' and resid 8 through 20 removed outlier: 3.830A pdb=" N ILE d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) removed outlier: 3.556A 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 74 Processing helix chain 'd' and resid 110 through 128 removed outlier: 5.108A pdb=" N ASP d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE d 124 " --> pdb=" O SER d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 143 removed outlier: 3.587A 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 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'e' and resid 8 through 20 removed outlier: 3.819A pdb=" N ILE e 12 " --> pdb=" O ASN e 8 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL e 20 " --> pdb=" O ASN e 16 " (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 74 Processing helix chain 'e' and resid 110 through 128 removed outlier: 5.075A pdb=" N ASP e 122 " --> pdb=" O ALA e 118 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA e 123 " --> pdb=" O SER e 119 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE e 124 " --> pdb=" O SER e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 139 through 143 removed outlier: 3.593A pdb=" N ASP e 142 " --> pdb=" O GLY e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 145 through 153 removed outlier: 4.195A pdb=" N LEU e 149 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 156 No H-bonds generated for 'chain 'e' and resid 154 through 156' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.747A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (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: 6.539A 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: 3.773A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.801A pdb=" N TYR B 53 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.175A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.820A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.262A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.726A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 7.501A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.909A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.267A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.466A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU a 50 " --> pdb=" O LEU a 37 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.466A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU a 50 " --> pdb=" O LEU a 37 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.516A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL b 49 " --> pdb=" O LEU b 40 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU b 40 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLU b 51 " --> pdb=" O PHE b 38 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N PHE b 38 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N LYS b 53 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL b 36 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE b 55 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N HIS b 133 " --> pdb=" O GLU b 97 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU b 99 " --> pdb=" O HIS b 133 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TRP b 135 " --> pdb=" O LEU b 99 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE b 101 " --> pdb=" O TRP b 135 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.516A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL b 49 " --> pdb=" O LEU b 40 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU b 40 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLU b 51 " --> pdb=" O PHE b 38 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N PHE b 38 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N LYS b 53 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL b 36 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE b 55 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.547A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.547A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.588A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU d 50 " --> pdb=" O LEU d 37 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS d 133 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.588A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU d 50 " --> pdb=" O LEU d 37 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.585A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU e 50 " --> pdb=" O LEU e 37 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 11.107A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS e 133 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.585A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU e 50 " --> pdb=" O LEU e 37 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 11.107A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3285 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: 4.68 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7507 1.34 - 1.46: 4572 1.46 - 1.58: 11975 1.58 - 1.70: 15 1.70 - 1.81: 231 Bond restraints: 24300 Sorted by residual: bond pdb=" N LYS X 149 " pdb=" CA LYS X 149 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.41e-02 5.03e+03 8.13e+00 bond pdb=" N THR d 63 " pdb=" CA THR d 63 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.15e-02 7.56e+03 6.74e+00 bond pdb=" N THR a 63 " pdb=" CA THR a 63 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.15e-02 7.56e+03 6.64e+00 bond pdb=" N THR c 63 " pdb=" CA THR c 63 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.15e-02 7.56e+03 6.59e+00 bond pdb=" N THR e 63 " pdb=" CA THR e 63 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.15e-02 7.56e+03 6.29e+00 ... (remaining 24295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 31351 2.01 - 4.02: 1304 4.02 - 6.03: 180 6.03 - 8.04: 42 8.04 - 10.05: 14 Bond angle restraints: 32891 Sorted by residual: angle pdb=" N PRO W 150 " pdb=" CA PRO W 150 " pdb=" C PRO W 150 " ideal model delta sigma weight residual 113.57 105.34 8.23 1.31e+00 5.83e-01 3.95e+01 angle pdb=" C PRO A 264 " pdb=" N SER A 265 " pdb=" CA SER A 265 " ideal model delta sigma weight residual 120.63 130.68 -10.05 1.61e+00 3.86e-01 3.90e+01 angle pdb=" C ARG A 335 " pdb=" N LYS A 336 " pdb=" CA LYS A 336 " ideal model delta sigma weight residual 121.19 131.08 -9.89 1.59e+00 3.96e-01 3.87e+01 angle pdb=" C GLU A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C GLY A 268 " pdb=" N MET A 269 " pdb=" CA MET A 269 " ideal model delta sigma weight residual 122.82 129.75 -6.93 1.42e+00 4.96e-01 2.38e+01 ... (remaining 32886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 13549 17.39 - 34.78: 938 34.78 - 52.17: 190 52.17 - 69.56: 46 69.56 - 86.96: 35 Dihedral angle restraints: 14758 sinusoidal: 6010 harmonic: 8748 Sorted by residual: dihedral pdb=" CA LYS A 61 " pdb=" C LYS A 61 " pdb=" N ARG A 62 " pdb=" CA ARG A 62 " ideal model delta harmonic sigma weight residual 180.00 146.10 33.90 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA LYS B 61 " pdb=" C LYS B 61 " pdb=" N ARG B 62 " pdb=" CA ARG B 62 " ideal model delta harmonic sigma weight residual 180.00 148.03 31.97 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA MET B 47 " pdb=" C MET B 47 " pdb=" N GLY B 48 " pdb=" CA GLY B 48 " ideal model delta harmonic sigma weight residual -180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 14755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3044 0.072 - 0.144: 569 0.144 - 0.215: 51 0.215 - 0.287: 18 0.287 - 0.359: 2 Chirality restraints: 3684 Sorted by residual: chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA VAL W 144 " pdb=" N VAL W 144 " pdb=" C VAL W 144 " pdb=" CB VAL W 144 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE D 287 " pdb=" CA ILE D 287 " pdb=" CG1 ILE D 287 " pdb=" CG2 ILE D 287 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3681 not shown) Planarity restraints: 4175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO B 243 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP W 143 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C TRP W 143 " -0.060 2.00e-02 2.50e+03 pdb=" O TRP W 143 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL W 144 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA X 41 " -0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO X 42 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO X 42 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO X 42 " -0.044 5.00e-02 4.00e+02 ... (remaining 4172 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 41 2.66 - 3.22: 19878 3.22 - 3.78: 35642 3.78 - 4.34: 50643 4.34 - 4.90: 82320 Nonbonded interactions: 188524 Sorted by model distance: nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.096 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.100 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.103 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.107 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.116 2.170 ... (remaining 188519 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 39 or resid 50 through 172 or resid 174 through \ 401)) selection = (chain 'B' and (resid 4 through 39 or resid 50 through 172 or resid 174 through \ 401)) selection = (chain 'C' and (resid 4 through 172 or resid 174 through 401)) selection = (chain 'D' and (resid 4 through 172 or resid 174 through 401)) selection = (chain 'E' and (resid 4 through 172 or resid 174 through 401)) } ncs_group { reference = chain 'W' selection = chain 'X' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 28.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.680 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.005 0.056 24300 Z= 0.252 Angle : 0.936 10.054 32891 Z= 0.521 Chirality : 0.057 0.359 3684 Planarity : 0.008 0.088 4175 Dihedral : 13.529 86.955 9126 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.61 % Favored : 96.12 % Rotamer: Outliers : 0.23 % Allowed : 0.04 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.90 (0.14), residues: 2965 helix: -2.09 (0.11), residues: 1235 sheet: -0.59 (0.22), residues: 521 loop : -0.33 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 147 TYR 0.020 0.002 TYR D 218 PHE 0.042 0.002 PHE A 90 TRP 0.024 0.002 TRP D 86 HIS 0.010 0.002 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00473 (24300) covalent geometry : angle 0.93589 (32891) hydrogen bonds : bond 0.16415 ( 1181) hydrogen bonds : angle 6.78741 ( 3285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 233 time to evaluate : 0.892 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8792 (t-90) cc_final: 0.8467 (t-170) REVERT: A 44 MET cc_start: 0.6112 (mtt) cc_final: 0.5747 (mtp) REVERT: A 82 MET cc_start: 0.8930 (tpt) cc_final: 0.8577 (tpp) REVERT: A 119 MET cc_start: 0.9390 (ttm) cc_final: 0.9038 (mtt) REVERT: A 123 MET cc_start: 0.9303 (mmp) cc_final: 0.9078 (mmm) REVERT: A 313 MET cc_start: 0.9534 (mmm) cc_final: 0.9258 (tpp) REVERT: B 82 MET cc_start: 0.9191 (tpt) cc_final: 0.8656 (tpp) REVERT: B 123 MET cc_start: 0.9237 (mmp) cc_final: 0.8981 (mmm) REVERT: C 82 MET cc_start: 0.8950 (tpt) cc_final: 0.7976 (mmm) REVERT: C 227 MET cc_start: 0.8848 (mmm) cc_final: 0.8497 (mmt) REVERT: C 313 MET cc_start: 0.8995 (mmm) cc_final: 0.8592 (tpp) REVERT: D 82 MET cc_start: 0.9209 (tpt) cc_final: 0.8776 (tmm) REVERT: D 283 MET cc_start: 0.9063 (mmm) cc_final: 0.8380 (mpp) REVERT: D 305 MET cc_start: 0.9111 (mmm) cc_final: 0.8836 (tpp) REVERT: D 313 MET cc_start: 0.8693 (mmm) cc_final: 0.8156 (tpt) REVERT: E 354 GLN cc_start: 0.8769 (pm20) cc_final: 0.8324 (pm20) REVERT: W 47 PHE cc_start: 0.8886 (t80) cc_final: 0.8646 (t80) REVERT: W 75 MET cc_start: 0.9402 (mtt) cc_final: 0.9014 (mmp) REVERT: W 144 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8495 (m) REVERT: W 157 MET cc_start: 0.9080 (mmp) cc_final: 0.8197 (tpp) REVERT: W 158 ASN cc_start: 0.9465 (t0) cc_final: 0.9109 (m-40) REVERT: X 129 ASN cc_start: 0.9363 (m-40) cc_final: 0.9128 (p0) REVERT: a 1 MET cc_start: 0.7570 (ttp) cc_final: 0.7006 (tpt) REVERT: a 115 MET cc_start: 0.9074 (tpt) cc_final: 0.8819 (mmm) REVERT: b 115 MET cc_start: 0.9124 (tpt) cc_final: 0.8633 (tpp) REVERT: c 80 CYS cc_start: 0.8606 (m) cc_final: 0.7709 (t) REVERT: c 115 MET cc_start: 0.8737 (tpt) cc_final: 0.8333 (tpp) REVERT: e 115 MET cc_start: 0.8853 (tpt) cc_final: 0.8248 (tpp) outliers start: 5 outliers final: 1 residues processed: 237 average time/residue: 0.1593 time to fit residues: 59.2874 Evaluate side-chains 150 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain X residue 149 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 49 GLN B 101 HIS B 162 ASN B 314 GLN D 128 ASN D 246 GLN D 354 GLN E 87 HIS E 101 HIS E 128 ASN E 246 GLN W 139 GLN W 166 ASN ** W 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 94 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.034750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.025764 restraints weight = 278829.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.026768 restraints weight = 120940.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.027427 restraints weight = 71361.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.027871 restraints weight = 49960.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.028172 restraints weight = 38964.448| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 24300 Z= 0.347 Angle : 0.761 12.268 32891 Z= 0.393 Chirality : 0.047 0.185 3684 Planarity : 0.006 0.064 4175 Dihedral : 5.731 58.084 3314 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.02 % Favored : 95.85 % Rotamer: Outliers : 0.54 % Allowed : 4.34 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 2965 helix: 0.18 (0.14), residues: 1267 sheet: -0.51 (0.22), residues: 524 loop : 0.15 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 206 TYR 0.024 0.002 TYR D 188 PHE 0.024 0.002 PHE c 38 TRP 0.024 0.002 TRP W 143 HIS 0.007 0.002 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00762 (24300) covalent geometry : angle 0.76140 (32891) hydrogen bonds : bond 0.04882 ( 1181) hydrogen bonds : angle 4.91712 ( 3285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 1.060 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 40 HIS cc_start: 0.8787 (t-90) cc_final: 0.8507 (t70) REVERT: A 44 MET cc_start: 0.5973 (mtt) cc_final: 0.5705 (mtt) REVERT: A 119 MET cc_start: 0.9402 (ttm) cc_final: 0.8975 (mtt) REVERT: A 123 MET cc_start: 0.9364 (mmp) cc_final: 0.9086 (mmm) REVERT: A 227 MET cc_start: 0.9505 (mtp) cc_final: 0.9254 (mtp) REVERT: A 299 MET cc_start: 0.8008 (mpp) cc_final: 0.7470 (pmm) REVERT: A 313 MET cc_start: 0.9589 (mmm) cc_final: 0.9285 (tpp) REVERT: B 82 MET cc_start: 0.9189 (tpt) cc_final: 0.8903 (tpt) REVERT: C 82 MET cc_start: 0.9183 (tpt) cc_final: 0.8304 (tmm) REVERT: C 227 MET cc_start: 0.8984 (mmm) cc_final: 0.8636 (mmt) REVERT: D 82 MET cc_start: 0.9289 (tpt) cc_final: 0.9004 (tmm) REVERT: D 123 MET cc_start: 0.9084 (tpp) cc_final: 0.8795 (tpp) REVERT: W 47 PHE cc_start: 0.8874 (t80) cc_final: 0.8640 (t80) REVERT: W 58 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8370 (t80) REVERT: W 75 MET cc_start: 0.9455 (mtt) cc_final: 0.9125 (mmp) REVERT: W 158 ASN cc_start: 0.9632 (t0) cc_final: 0.9268 (m-40) REVERT: X 146 MET cc_start: 0.8189 (mmp) cc_final: 0.7989 (mmm) REVERT: a 115 MET cc_start: 0.9236 (tpt) cc_final: 0.8950 (mmm) REVERT: b 115 MET cc_start: 0.9310 (tpt) cc_final: 0.8927 (tpp) REVERT: c 80 CYS cc_start: 0.8453 (m) cc_final: 0.7698 (t) REVERT: c 115 MET cc_start: 0.8833 (tpt) cc_final: 0.8509 (tpp) REVERT: e 46 GLN cc_start: 0.9104 (mt0) cc_final: 0.8742 (tt0) REVERT: e 115 MET cc_start: 0.8895 (tpt) cc_final: 0.8488 (tpp) outliers start: 14 outliers final: 8 residues processed: 172 average time/residue: 0.1520 time to fit residues: 43.2208 Evaluate side-chains 149 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain W residue 58 TYR Chi-restraints excluded: chain W residue 99 ASN Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 33 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 233 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 128 ASN D 59 GLN W 92 GLN ** W 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.035073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.026263 restraints weight = 245987.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.027239 restraints weight = 110809.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.027887 restraints weight = 66576.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.028323 restraints weight = 47042.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028610 restraints weight = 36944.562| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24300 Z= 0.172 Angle : 0.598 10.495 32891 Z= 0.303 Chirality : 0.043 0.197 3684 Planarity : 0.005 0.066 4175 Dihedral : 5.306 56.167 3309 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 0.50 % Allowed : 5.77 % Favored : 93.73 % 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: 0.48 (0.16), residues: 2965 helix: 0.86 (0.15), residues: 1270 sheet: -0.42 (0.23), residues: 524 loop : 0.30 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 146 TYR 0.012 0.001 TYR B 91 PHE 0.014 0.001 PHE c 38 TRP 0.013 0.001 TRP W 143 HIS 0.007 0.001 HIS X 179 Details of bonding type rmsd covalent geometry : bond 0.00380 (24300) covalent geometry : angle 0.59753 (32891) hydrogen bonds : bond 0.03870 ( 1181) hydrogen bonds : angle 4.53342 ( 3285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8790 (t-90) cc_final: 0.8374 (t-170) REVERT: A 44 MET cc_start: 0.6000 (mtt) cc_final: 0.5739 (mtt) REVERT: A 119 MET cc_start: 0.9411 (ttm) cc_final: 0.8974 (mtt) REVERT: A 123 MET cc_start: 0.9361 (mmp) cc_final: 0.9081 (mmm) REVERT: A 227 MET cc_start: 0.9534 (mtp) cc_final: 0.9294 (mtp) REVERT: A 283 MET cc_start: 0.8904 (tpp) cc_final: 0.8678 (tpp) REVERT: A 299 MET cc_start: 0.8100 (mpp) cc_final: 0.7593 (pmm) REVERT: A 313 MET cc_start: 0.9590 (mmm) cc_final: 0.9252 (tpp) REVERT: B 82 MET cc_start: 0.9202 (tpt) cc_final: 0.8918 (mmm) REVERT: C 82 MET cc_start: 0.9123 (tpt) cc_final: 0.8324 (tmm) REVERT: D 236 LEU cc_start: 0.9244 (mp) cc_final: 0.8966 (tt) REVERT: W 75 MET cc_start: 0.9384 (mtt) cc_final: 0.9126 (mmp) REVERT: W 158 ASN cc_start: 0.9624 (t0) cc_final: 0.9323 (t0) REVERT: X 162 MET cc_start: 0.9189 (mtp) cc_final: 0.8913 (ptp) REVERT: a 48 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8682 (mm) REVERT: b 115 MET cc_start: 0.9256 (tpt) cc_final: 0.8837 (tpp) REVERT: c 68 TYR cc_start: 0.8310 (t80) cc_final: 0.8014 (t80) REVERT: c 80 CYS cc_start: 0.8449 (m) cc_final: 0.7673 (t) REVERT: c 115 MET cc_start: 0.8795 (tpt) cc_final: 0.8469 (tpt) REVERT: e 46 GLN cc_start: 0.9113 (mt0) cc_final: 0.8773 (tt0) REVERT: e 115 MET cc_start: 0.8870 (tpt) cc_final: 0.8428 (tpp) outliers start: 13 outliers final: 9 residues processed: 152 average time/residue: 0.1488 time to fit residues: 37.7748 Evaluate side-chains 148 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain W residue 99 ASN Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain d residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 86 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 133 optimal weight: 0.0670 chunk 286 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** W 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 133 HIS e 26 GLN 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 = 0.035200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.026294 restraints weight = 270925.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.027317 restraints weight = 117001.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.027991 restraints weight = 68723.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028456 restraints weight = 47784.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.028724 restraints weight = 36895.662| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24300 Z= 0.142 Angle : 0.564 10.613 32891 Z= 0.282 Chirality : 0.043 0.216 3684 Planarity : 0.004 0.066 4175 Dihedral : 5.044 53.219 3309 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.15 % Rotamer: Outliers : 0.85 % Allowed : 5.69 % Favored : 93.46 % 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: 0.80 (0.16), residues: 2965 helix: 1.19 (0.15), residues: 1280 sheet: -0.31 (0.23), residues: 524 loop : 0.40 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 146 TYR 0.010 0.001 TYR B 91 PHE 0.021 0.001 PHE X 47 TRP 0.028 0.001 TRP X 207 HIS 0.007 0.001 HIS X 72 Details of bonding type rmsd covalent geometry : bond 0.00315 (24300) covalent geometry : angle 0.56354 (32891) hydrogen bonds : bond 0.03465 ( 1181) hydrogen bonds : angle 4.28366 ( 3285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8776 (t-90) cc_final: 0.8352 (t-170) REVERT: A 44 MET cc_start: 0.5834 (mtt) cc_final: 0.5471 (mtt) REVERT: A 82 MET cc_start: 0.8886 (tpt) cc_final: 0.8608 (tpp) REVERT: A 119 MET cc_start: 0.9395 (ttm) cc_final: 0.8968 (mtp) REVERT: A 123 MET cc_start: 0.9349 (mmp) cc_final: 0.9079 (mmm) REVERT: A 227 MET cc_start: 0.9553 (mtp) cc_final: 0.9332 (mtp) REVERT: A 269 MET cc_start: 0.8728 (ptt) cc_final: 0.8475 (ppp) REVERT: A 283 MET cc_start: 0.8962 (tpp) cc_final: 0.8759 (tpp) REVERT: A 299 MET cc_start: 0.8086 (mpp) cc_final: 0.7772 (pmm) REVERT: A 313 MET cc_start: 0.9576 (mmm) cc_final: 0.9243 (tpp) REVERT: B 82 MET cc_start: 0.9137 (tpt) cc_final: 0.8863 (mmm) REVERT: B 313 MET cc_start: 0.9514 (mmm) cc_final: 0.9160 (tpt) REVERT: C 82 MET cc_start: 0.9113 (tpt) cc_final: 0.8318 (tmm) REVERT: D 123 MET cc_start: 0.8999 (tpp) cc_final: 0.8705 (tpp) REVERT: D 236 LEU cc_start: 0.9222 (mp) cc_final: 0.8984 (tt) REVERT: W 75 MET cc_start: 0.9413 (mtt) cc_final: 0.9136 (mmp) REVERT: W 157 MET cc_start: 0.8920 (mmp) cc_final: 0.8431 (mmm) REVERT: W 162 MET cc_start: 0.8741 (tmm) cc_final: 0.8532 (ppp) REVERT: X 162 MET cc_start: 0.9121 (mtp) cc_final: 0.8872 (ptp) REVERT: a 48 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8659 (mm) REVERT: a 115 MET cc_start: 0.9137 (mmm) cc_final: 0.8892 (mmm) REVERT: b 115 MET cc_start: 0.9228 (tpt) cc_final: 0.8813 (tpp) REVERT: c 68 TYR cc_start: 0.8299 (t80) cc_final: 0.8053 (t80) REVERT: c 80 CYS cc_start: 0.8387 (m) cc_final: 0.7982 (m) REVERT: c 115 MET cc_start: 0.8781 (tpt) cc_final: 0.8446 (tpp) REVERT: e 46 GLN cc_start: 0.9083 (mt0) cc_final: 0.8844 (tt0) REVERT: e 115 MET cc_start: 0.8855 (tpt) cc_final: 0.8408 (tpp) outliers start: 22 outliers final: 12 residues processed: 156 average time/residue: 0.1400 time to fit residues: 36.9761 Evaluate side-chains 146 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain W residue 99 ASN Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain d residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 58 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 135 optimal weight: 0.0670 chunk 293 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** W 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 133 HIS e 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.034417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.025624 restraints weight = 266500.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.026602 restraints weight = 116364.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.027243 restraints weight = 69081.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.027678 restraints weight = 48504.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.027982 restraints weight = 37892.707| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24300 Z= 0.234 Angle : 0.630 11.038 32891 Z= 0.317 Chirality : 0.044 0.223 3684 Planarity : 0.004 0.062 4175 Dihedral : 5.141 56.694 3309 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.71 % Rotamer: Outliers : 1.01 % Allowed : 6.35 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2965 helix: 1.29 (0.15), residues: 1277 sheet: -0.28 (0.23), residues: 524 loop : 0.41 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.013 0.001 TYR D 306 PHE 0.019 0.002 PHE W 118 TRP 0.035 0.002 TRP X 207 HIS 0.007 0.001 HIS X 72 Details of bonding type rmsd covalent geometry : bond 0.00519 (24300) covalent geometry : angle 0.62990 (32891) hydrogen bonds : bond 0.03892 ( 1181) hydrogen bonds : angle 4.42910 ( 3285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8849 (t-90) cc_final: 0.8411 (t-170) REVERT: A 119 MET cc_start: 0.9436 (ttm) cc_final: 0.8965 (mtp) REVERT: A 123 MET cc_start: 0.9416 (mmp) cc_final: 0.9143 (mmm) REVERT: A 227 MET cc_start: 0.9545 (mtp) cc_final: 0.9281 (mtp) REVERT: A 299 MET cc_start: 0.8203 (mpp) cc_final: 0.7960 (pmm) REVERT: A 313 MET cc_start: 0.9568 (mmm) cc_final: 0.9278 (tpp) REVERT: B 82 MET cc_start: 0.9211 (tpt) cc_final: 0.8903 (mmm) REVERT: C 82 MET cc_start: 0.9182 (tpt) cc_final: 0.8264 (tmm) REVERT: C 227 MET cc_start: 0.8879 (mmm) cc_final: 0.8675 (mmm) REVERT: D 123 MET cc_start: 0.9126 (tpp) cc_final: 0.8724 (tpp) REVERT: D 236 LEU cc_start: 0.9238 (mp) cc_final: 0.8995 (tt) REVERT: E 283 MET cc_start: 0.9086 (tpp) cc_final: 0.8441 (mpp) REVERT: W 75 MET cc_start: 0.9407 (mtt) cc_final: 0.9166 (mmp) REVERT: W 157 MET cc_start: 0.8930 (mmp) cc_final: 0.8443 (mmm) REVERT: W 162 MET cc_start: 0.8797 (tmm) cc_final: 0.8380 (ppp) REVERT: X 143 TRP cc_start: 0.7426 (p-90) cc_final: 0.7106 (p-90) REVERT: X 162 MET cc_start: 0.9123 (mtp) cc_final: 0.8920 (ptp) REVERT: a 48 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8712 (mm) REVERT: a 115 MET cc_start: 0.9167 (mmm) cc_final: 0.8904 (mmm) REVERT: b 115 MET cc_start: 0.9316 (tpt) cc_final: 0.8893 (tpp) REVERT: c 80 CYS cc_start: 0.8423 (m) cc_final: 0.8010 (m) REVERT: c 115 MET cc_start: 0.8833 (tpt) cc_final: 0.8515 (tpp) REVERT: d 115 MET cc_start: 0.8963 (tpt) cc_final: 0.8331 (tpp) REVERT: e 46 GLN cc_start: 0.9104 (mt0) cc_final: 0.8746 (tt0) REVERT: e 115 MET cc_start: 0.8863 (tpt) cc_final: 0.8390 (tpp) outliers start: 26 outliers final: 15 residues processed: 159 average time/residue: 0.1482 time to fit residues: 39.2791 Evaluate side-chains 150 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain W residue 99 ASN Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 64 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 126 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** W 179 HIS ** 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 = 0.3204 r_free = 0.3204 target = 0.035375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.025781 restraints weight = 308786.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.026815 restraints weight = 125175.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.027483 restraints weight = 72831.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.027908 restraints weight = 51279.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028176 restraints weight = 40658.426| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24300 Z= 0.179 Angle : 0.583 11.586 32891 Z= 0.292 Chirality : 0.043 0.257 3684 Planarity : 0.004 0.063 4175 Dihedral : 5.006 52.075 3309 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 0.77 % Allowed : 6.97 % Favored : 92.26 % 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: 1.01 (0.16), residues: 2965 helix: 1.42 (0.15), residues: 1277 sheet: -0.21 (0.23), residues: 534 loop : 0.45 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 116 TYR 0.014 0.001 TYR A 279 PHE 0.016 0.001 PHE W 118 TRP 0.021 0.001 TRP D 86 HIS 0.005 0.001 HIS X 72 Details of bonding type rmsd covalent geometry : bond 0.00399 (24300) covalent geometry : angle 0.58298 (32891) hydrogen bonds : bond 0.03585 ( 1181) hydrogen bonds : angle 4.29028 ( 3285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.9036 (t-90) cc_final: 0.8640 (t-170) REVERT: A 82 MET cc_start: 0.9053 (tpt) cc_final: 0.8762 (tpp) REVERT: A 119 MET cc_start: 0.9496 (ttm) cc_final: 0.8998 (mtp) REVERT: A 123 MET cc_start: 0.9525 (mmp) cc_final: 0.9219 (mmm) REVERT: A 227 MET cc_start: 0.9569 (mtp) cc_final: 0.9322 (mtp) REVERT: A 283 MET cc_start: 0.8851 (tpp) cc_final: 0.8544 (mpp) REVERT: A 313 MET cc_start: 0.9582 (mmm) cc_final: 0.9284 (tpp) REVERT: B 47 MET cc_start: 0.7413 (tmm) cc_final: 0.7170 (tmm) REVERT: B 82 MET cc_start: 0.9260 (tpt) cc_final: 0.8940 (mmm) REVERT: C 82 MET cc_start: 0.9164 (tpt) cc_final: 0.8729 (tmm) REVERT: C 132 MET cc_start: 0.8127 (ppp) cc_final: 0.7739 (tmm) REVERT: C 227 MET cc_start: 0.8876 (mmm) cc_final: 0.8577 (mmt) REVERT: C 325 MET cc_start: 0.8358 (mmm) cc_final: 0.8151 (mmm) REVERT: D 123 MET cc_start: 0.9110 (tpp) cc_final: 0.8534 (tpp) REVERT: D 236 LEU cc_start: 0.9244 (mp) cc_final: 0.9011 (tt) REVERT: W 157 MET cc_start: 0.9020 (mmp) cc_final: 0.8505 (mmm) REVERT: W 162 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8452 (ppp) REVERT: X 72 HIS cc_start: 0.9256 (OUTLIER) cc_final: 0.8826 (t70) REVERT: a 48 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8748 (mm) REVERT: a 115 MET cc_start: 0.9191 (mmm) cc_final: 0.8917 (mmm) REVERT: b 115 MET cc_start: 0.9272 (tpt) cc_final: 0.8856 (tpp) REVERT: c 68 TYR cc_start: 0.8369 (t80) cc_final: 0.8164 (t80) REVERT: c 80 CYS cc_start: 0.8423 (m) cc_final: 0.7754 (t) REVERT: c 115 MET cc_start: 0.8812 (tpt) cc_final: 0.8479 (tpp) REVERT: d 115 MET cc_start: 0.8965 (tpt) cc_final: 0.8334 (tpp) REVERT: e 46 GLN cc_start: 0.9122 (mt0) cc_final: 0.8753 (tt0) REVERT: e 115 MET cc_start: 0.8852 (tpt) cc_final: 0.8351 (tpp) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.1486 time to fit residues: 37.8786 Evaluate side-chains 147 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain W residue 162 MET Chi-restraints excluded: chain X residue 72 HIS Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 6 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 146 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.034813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.025997 restraints weight = 282824.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.027020 restraints weight = 119214.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.027693 restraints weight = 69148.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.028114 restraints weight = 47729.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.028437 restraints weight = 37132.341| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24300 Z= 0.141 Angle : 0.574 12.165 32891 Z= 0.285 Chirality : 0.043 0.231 3684 Planarity : 0.004 0.062 4175 Dihedral : 4.898 49.230 3309 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 0.81 % Allowed : 7.32 % Favored : 91.87 % 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: 1.11 (0.16), residues: 2965 helix: 1.50 (0.15), residues: 1275 sheet: -0.16 (0.23), residues: 534 loop : 0.52 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.013 0.001 TYR A 279 PHE 0.013 0.001 PHE W 118 TRP 0.029 0.001 TRP X 143 HIS 0.005 0.001 HIS X 72 Details of bonding type rmsd covalent geometry : bond 0.00315 (24300) covalent geometry : angle 0.57384 (32891) hydrogen bonds : bond 0.03420 ( 1181) hydrogen bonds : angle 4.21023 ( 3285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8828 (t-90) cc_final: 0.8440 (t-170) REVERT: A 119 MET cc_start: 0.9429 (ttm) cc_final: 0.8954 (mtp) REVERT: A 123 MET cc_start: 0.9375 (mmp) cc_final: 0.9128 (mmm) REVERT: A 227 MET cc_start: 0.9551 (mtp) cc_final: 0.9281 (mtp) REVERT: A 269 MET cc_start: 0.8881 (ptt) cc_final: 0.8629 (ppp) REVERT: A 283 MET cc_start: 0.8871 (tpp) cc_final: 0.8559 (mpp) REVERT: A 299 MET cc_start: 0.8621 (mpp) cc_final: 0.7965 (pmm) REVERT: A 313 MET cc_start: 0.9510 (mmm) cc_final: 0.9262 (tpp) REVERT: B 82 MET cc_start: 0.9179 (tpt) cc_final: 0.8870 (mmm) REVERT: C 82 MET cc_start: 0.9142 (tpt) cc_final: 0.8709 (tmm) REVERT: C 132 MET cc_start: 0.8118 (ppp) cc_final: 0.7698 (tmm) REVERT: C 227 MET cc_start: 0.8877 (mmm) cc_final: 0.8570 (mmt) REVERT: C 325 MET cc_start: 0.8325 (mmm) cc_final: 0.8120 (mmm) REVERT: E 283 MET cc_start: 0.8987 (tpp) cc_final: 0.8585 (tpp) REVERT: W 58 TYR cc_start: 0.9103 (t80) cc_final: 0.8245 (t80) REVERT: W 75 MET cc_start: 0.9354 (mmp) cc_final: 0.9027 (mpp) REVERT: W 157 MET cc_start: 0.8821 (mmp) cc_final: 0.8371 (mmm) REVERT: W 162 MET cc_start: 0.8796 (tmm) cc_final: 0.8372 (ppp) REVERT: X 72 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.8513 (t70) REVERT: X 176 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8265 (p0) REVERT: a 48 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8692 (mm) REVERT: a 115 MET cc_start: 0.9176 (mmm) cc_final: 0.8918 (mmm) REVERT: b 115 MET cc_start: 0.9249 (tpt) cc_final: 0.8828 (tpp) REVERT: c 80 CYS cc_start: 0.8384 (m) cc_final: 0.7718 (t) REVERT: c 115 MET cc_start: 0.8796 (tpt) cc_final: 0.8458 (tpp) REVERT: d 115 MET cc_start: 0.8939 (tpt) cc_final: 0.8311 (tpp) REVERT: e 46 GLN cc_start: 0.9069 (mt0) cc_final: 0.8800 (tt0) REVERT: e 115 MET cc_start: 0.8853 (tpt) cc_final: 0.8358 (tpp) outliers start: 21 outliers final: 13 residues processed: 153 average time/residue: 0.1424 time to fit residues: 36.5098 Evaluate side-chains 148 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain W residue 99 ASN Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain X residue 72 HIS Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 64 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 128 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 chunk 224 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN ** W 179 HIS ** 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 = 0.3198 r_free = 0.3198 target = 0.034518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.025842 restraints weight = 255188.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.026810 restraints weight = 112437.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.027446 restraints weight = 66623.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.027870 restraints weight = 46679.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.028148 restraints weight = 36426.123| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24300 Z= 0.185 Angle : 0.601 12.480 32891 Z= 0.300 Chirality : 0.043 0.234 3684 Planarity : 0.004 0.062 4175 Dihedral : 4.928 51.162 3309 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 0.74 % Allowed : 7.90 % Favored : 91.37 % 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: 1.11 (0.16), residues: 2965 helix: 1.46 (0.15), residues: 1287 sheet: -0.17 (0.23), residues: 528 loop : 0.55 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.011 0.001 TYR A 279 PHE 0.015 0.001 PHE W 118 TRP 0.023 0.001 TRP X 143 HIS 0.004 0.001 HIS X 72 Details of bonding type rmsd covalent geometry : bond 0.00411 (24300) covalent geometry : angle 0.60096 (32891) hydrogen bonds : bond 0.03590 ( 1181) hydrogen bonds : angle 4.27525 ( 3285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8865 (t-90) cc_final: 0.8482 (t-170) REVERT: A 82 MET cc_start: 0.8951 (tpt) cc_final: 0.8722 (tpp) REVERT: A 119 MET cc_start: 0.9429 (ttm) cc_final: 0.8975 (mtp) REVERT: A 123 MET cc_start: 0.9404 (mmp) cc_final: 0.9128 (mmm) REVERT: A 227 MET cc_start: 0.9556 (mtp) cc_final: 0.9283 (mtp) REVERT: A 269 MET cc_start: 0.8888 (ptt) cc_final: 0.8688 (ppp) REVERT: A 299 MET cc_start: 0.8731 (mpp) cc_final: 0.8147 (pmm) REVERT: A 313 MET cc_start: 0.9501 (mmm) cc_final: 0.9275 (tpp) REVERT: B 82 MET cc_start: 0.9182 (tpt) cc_final: 0.8869 (mmm) REVERT: C 82 MET cc_start: 0.9164 (tpt) cc_final: 0.8742 (tmm) REVERT: C 132 MET cc_start: 0.8161 (ppp) cc_final: 0.7765 (tmm) REVERT: C 227 MET cc_start: 0.8897 (mmm) cc_final: 0.8582 (mmp) REVERT: C 325 MET cc_start: 0.8304 (mmm) cc_final: 0.8096 (mmm) REVERT: D 123 MET cc_start: 0.9133 (tpp) cc_final: 0.8582 (tpp) REVERT: E 283 MET cc_start: 0.9006 (tpp) cc_final: 0.8377 (mpp) REVERT: E 355 MET cc_start: 0.9264 (mmm) cc_final: 0.9062 (tpp) REVERT: W 58 TYR cc_start: 0.9098 (t80) cc_final: 0.8255 (t80) REVERT: W 157 MET cc_start: 0.8844 (mmp) cc_final: 0.8405 (mmm) REVERT: W 162 MET cc_start: 0.8811 (tmm) cc_final: 0.8396 (ppp) REVERT: X 72 HIS cc_start: 0.9021 (OUTLIER) cc_final: 0.8496 (t70) REVERT: X 176 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8250 (p0) REVERT: a 48 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8725 (mm) REVERT: a 115 MET cc_start: 0.9178 (mmm) cc_final: 0.8919 (mmm) REVERT: b 115 MET cc_start: 0.9277 (tpt) cc_final: 0.8846 (tpp) REVERT: c 80 CYS cc_start: 0.8381 (m) cc_final: 0.7737 (t) REVERT: c 115 MET cc_start: 0.8803 (tpt) cc_final: 0.8449 (tpp) REVERT: d 115 MET cc_start: 0.8955 (tpt) cc_final: 0.8337 (tpp) REVERT: e 46 GLN cc_start: 0.9052 (mt0) cc_final: 0.8754 (tt0) REVERT: e 115 MET cc_start: 0.8859 (tpt) cc_final: 0.8366 (tpp) outliers start: 19 outliers final: 14 residues processed: 152 average time/residue: 0.1434 time to fit residues: 36.5429 Evaluate side-chains 147 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain W residue 99 ASN Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain X residue 72 HIS Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 64 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 124 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 172 optimal weight: 0.0030 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 0.0770 chunk 263 optimal weight: 1.9990 overall best weight: 0.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS C 162 ASN D 162 ASN E 162 ASN ** a 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.035208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.026128 restraints weight = 340651.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.027246 restraints weight = 132057.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.027980 restraints weight = 73811.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028473 restraints weight = 49788.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.028800 restraints weight = 37673.505| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24300 Z= 0.097 Angle : 0.565 12.006 32891 Z= 0.278 Chirality : 0.042 0.230 3684 Planarity : 0.004 0.062 4175 Dihedral : 4.710 41.840 3309 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.46 % Rotamer: Outliers : 0.54 % Allowed : 8.21 % Favored : 91.25 % 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: 1.29 (0.16), residues: 2965 helix: 1.64 (0.15), residues: 1270 sheet: -0.10 (0.23), residues: 524 loop : 0.64 (0.20), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.012 0.001 TYR A 279 PHE 0.011 0.001 PHE X 47 TRP 0.026 0.001 TRP X 143 HIS 0.004 0.001 HIS X 72 Details of bonding type rmsd covalent geometry : bond 0.00212 (24300) covalent geometry : angle 0.56533 (32891) hydrogen bonds : bond 0.03043 ( 1181) hydrogen bonds : angle 4.05877 ( 3285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8830 (t-90) cc_final: 0.8479 (t-170) REVERT: A 82 MET cc_start: 0.8937 (tpt) cc_final: 0.8621 (tpp) REVERT: A 119 MET cc_start: 0.9423 (ttm) cc_final: 0.8967 (mtp) REVERT: A 123 MET cc_start: 0.9359 (mmp) cc_final: 0.9107 (mmm) REVERT: A 227 MET cc_start: 0.9568 (mtp) cc_final: 0.9312 (mtp) REVERT: A 299 MET cc_start: 0.8742 (mpp) cc_final: 0.8166 (pmm) REVERT: A 313 MET cc_start: 0.9503 (mmm) cc_final: 0.9262 (tpp) REVERT: B 82 MET cc_start: 0.9171 (tpt) cc_final: 0.8871 (mmm) REVERT: C 82 MET cc_start: 0.9102 (tpt) cc_final: 0.8773 (mmm) REVERT: C 132 MET cc_start: 0.8114 (ppp) cc_final: 0.7691 (tmm) REVERT: C 227 MET cc_start: 0.8844 (mmm) cc_final: 0.8523 (mmp) REVERT: C 325 MET cc_start: 0.8289 (mmm) cc_final: 0.8081 (mmm) REVERT: D 123 MET cc_start: 0.9088 (tpp) cc_final: 0.8340 (tpp) REVERT: E 283 MET cc_start: 0.8940 (tpp) cc_final: 0.8544 (tpp) REVERT: W 75 MET cc_start: 0.9316 (mmp) cc_final: 0.9025 (mpp) REVERT: W 157 MET cc_start: 0.8816 (mmp) cc_final: 0.8358 (mmm) REVERT: W 162 MET cc_start: 0.8773 (tmm) cc_final: 0.8348 (ppp) REVERT: X 72 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8483 (t70) REVERT: X 176 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8266 (p0) REVERT: a 48 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8658 (mm) REVERT: a 115 MET cc_start: 0.9168 (mmm) cc_final: 0.8910 (mmm) REVERT: b 115 MET cc_start: 0.9181 (tpt) cc_final: 0.8771 (tpp) REVERT: c 1 MET cc_start: 0.8818 (ttp) cc_final: 0.8434 (ptm) REVERT: c 80 CYS cc_start: 0.8340 (m) cc_final: 0.7707 (t) REVERT: c 115 MET cc_start: 0.8765 (tpt) cc_final: 0.8417 (tpp) REVERT: d 115 MET cc_start: 0.8891 (tpt) cc_final: 0.8274 (tpp) REVERT: e 46 GLN cc_start: 0.9021 (mt0) cc_final: 0.8787 (tt0) REVERT: e 115 MET cc_start: 0.8825 (tpt) cc_final: 0.8348 (tpp) outliers start: 14 outliers final: 8 residues processed: 153 average time/residue: 0.1454 time to fit residues: 37.0588 Evaluate side-chains 143 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain W residue 99 ASN Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain X residue 72 HIS Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 171 optimal weight: 0.0040 chunk 221 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 187 optimal weight: 0.0870 chunk 273 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 overall best weight: 0.9974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN X 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.035195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.026499 restraints weight = 226631.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.027481 restraints weight = 102527.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.028123 restraints weight = 61520.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.028550 restraints weight = 43336.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.028837 restraints weight = 33964.728| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24300 Z= 0.099 Angle : 0.569 11.875 32891 Z= 0.278 Chirality : 0.042 0.228 3684 Planarity : 0.004 0.062 4175 Dihedral : 4.607 40.033 3309 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 0.46 % Allowed : 8.32 % Favored : 91.21 % 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: 1.22 (0.16), residues: 2965 helix: 1.53 (0.15), residues: 1306 sheet: -0.02 (0.23), residues: 534 loop : 0.56 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 84 TYR 0.022 0.001 TYR W 58 PHE 0.016 0.001 PHE a 128 TRP 0.026 0.001 TRP X 143 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00219 (24300) covalent geometry : angle 0.56913 (32891) hydrogen bonds : bond 0.02983 ( 1181) hydrogen bonds : angle 3.98036 ( 3285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8879 (t-90) cc_final: 0.8537 (t-170) REVERT: A 82 MET cc_start: 0.8985 (tpt) cc_final: 0.8673 (tpp) REVERT: A 119 MET cc_start: 0.9469 (ttm) cc_final: 0.8991 (mtp) REVERT: A 123 MET cc_start: 0.9441 (mmp) cc_final: 0.9159 (mmm) REVERT: A 227 MET cc_start: 0.9574 (mtp) cc_final: 0.9329 (mtp) REVERT: A 299 MET cc_start: 0.8797 (mpp) cc_final: 0.8145 (pmm) REVERT: A 313 MET cc_start: 0.9524 (mmm) cc_final: 0.9257 (tpp) REVERT: B 82 MET cc_start: 0.9289 (tpt) cc_final: 0.8969 (mmm) REVERT: C 82 MET cc_start: 0.9118 (tpt) cc_final: 0.8719 (mmm) REVERT: C 132 MET cc_start: 0.8153 (ppp) cc_final: 0.7641 (tmm) REVERT: C 227 MET cc_start: 0.8838 (mmm) cc_final: 0.8529 (mmp) REVERT: C 325 MET cc_start: 0.8290 (mmm) cc_final: 0.8065 (mmm) REVERT: D 283 MET cc_start: 0.8928 (mmm) cc_final: 0.8717 (mmm) REVERT: E 59 GLN cc_start: 0.9021 (tt0) cc_final: 0.8640 (tm-30) REVERT: E 283 MET cc_start: 0.8963 (tpp) cc_final: 0.8518 (tpp) REVERT: W 58 TYR cc_start: 0.9113 (t80) cc_final: 0.8233 (t80) REVERT: W 75 MET cc_start: 0.9376 (mmp) cc_final: 0.9034 (mpp) REVERT: W 162 MET cc_start: 0.8778 (tmm) cc_final: 0.8383 (ppp) REVERT: X 72 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8563 (t70) REVERT: X 176 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8283 (p0) REVERT: a 48 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8691 (mm) REVERT: a 115 MET cc_start: 0.9194 (mmm) cc_final: 0.8932 (mmm) REVERT: b 115 MET cc_start: 0.9192 (tpt) cc_final: 0.8733 (tpp) REVERT: c 1 MET cc_start: 0.8923 (ttp) cc_final: 0.8659 (ptm) REVERT: c 80 CYS cc_start: 0.8433 (m) cc_final: 0.7608 (t) REVERT: c 115 MET cc_start: 0.8769 (tpt) cc_final: 0.8421 (tpp) REVERT: d 115 MET cc_start: 0.8912 (tpt) cc_final: 0.8256 (tpp) REVERT: e 46 GLN cc_start: 0.9039 (mt0) cc_final: 0.8793 (tt0) REVERT: e 115 MET cc_start: 0.8838 (tpt) cc_final: 0.8333 (tpp) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 0.1405 time to fit residues: 34.3803 Evaluate side-chains 144 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain W residue 99 ASN Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain X residue 72 HIS Chi-restraints excluded: chain X residue 176 ASP Chi-restraints excluded: chain a residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 275 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 217 optimal weight: 10.0000 chunk 195 optimal weight: 0.3980 chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.035311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.026209 restraints weight = 331612.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.027342 restraints weight = 127237.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.028078 restraints weight = 70874.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.028580 restraints weight = 47697.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.028900 restraints weight = 35917.746| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24300 Z= 0.097 Angle : 0.567 11.765 32891 Z= 0.277 Chirality : 0.042 0.222 3684 Planarity : 0.004 0.062 4175 Dihedral : 4.528 38.817 3309 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 0.50 % Allowed : 8.56 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.16), residues: 2965 helix: 1.62 (0.15), residues: 1288 sheet: 0.03 (0.23), residues: 534 loop : 0.59 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 84 TYR 0.020 0.001 TYR W 58 PHE 0.012 0.001 PHE X 47 TRP 0.053 0.001 TRP W 143 HIS 0.006 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00217 (24300) covalent geometry : angle 0.56747 (32891) hydrogen bonds : bond 0.02922 ( 1181) hydrogen bonds : angle 3.92244 ( 3285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5043.23 seconds wall clock time: 87 minutes 43.80 seconds (5263.80 seconds total)