Starting phenix.real_space_refine on Sat Oct 31 06:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38km_78880/10_2026/38km_78880.cif Found real_map, /net/cci-nas-00/data/ceres_data/38km_78880/10_2026/38km_78880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/38km_78880/10_2026/38km_78880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38km_78880/10_2026/38km_78880.map" model { file = "/net/cci-nas-00/data/ceres_data/38km_78880/10_2026/38km_78880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38km_78880/10_2026/38km_78880.cif" } resolution = 2.3 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= 0.001 sd= 0.008 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 16 5.49 5 Mg 8 5.21 5 S 242 5.16 5 C 25590 2.51 5 N 6804 2.21 5 O 7800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40460 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "B" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "C" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "D" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "E" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "F" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "G" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "H" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "X" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4604 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 584} Chain: "Y" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4604 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 584} Chain: "a" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "b" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "c" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "d" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "e" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "f" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 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} Chain: "F" 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: "G" 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: "H" 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: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 13.24, per 1000 atoms: 0.33 Number of scatterers: 40460 At special positions: 0 Unit cell: (135.78, 137.24, 269.37, 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 242 16.00 P 16 15.00 Mg 8 11.99 O 7800 8.00 N 6804 7.00 C 25590 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: 3.16 Conformation dependent library (CDL) restraints added in 2.8 seconds 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9708 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 74 sheets defined 38.1% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.603A pdb=" N GLN A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.893A pdb=" N ILE A 77 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.633A pdb=" N HIS A 103 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.816A pdb=" N THR A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.567A pdb=" N CYS A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 263 through 264 No H-bonds generated for 'chain 'A' and resid 263 through 264' Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 291 through 297 removed outlier: 3.507A pdb=" N ALA A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.262A pdb=" N TYR A 308 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.650A pdb=" N GLN A 356 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 370 through 376 removed outlier: 4.064A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.780A pdb=" N GLN B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.969A pdb=" N ILE B 77 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.725A pdb=" N THR B 196 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 254 through 262 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 263 through 264 No H-bonds generated for 'chain 'B' and resid 263 through 264' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.930A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.786A pdb=" N GLN C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.923A pdb=" N ILE C 77 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.647A pdb=" N THR C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.904A pdb=" N GLN C 356 " --> pdb=" O THR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 370 through 376 removed outlier: 4.018A pdb=" N ARG C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.566A pdb=" N GLN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.966A pdb=" N ILE D 77 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.676A pdb=" N THR D 196 " --> pdb=" O MET D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 204 through 219 Processing helix chain 'D' and resid 224 through 231 Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 254 through 262 Proline residue: D 260 - end of helix Processing helix chain 'D' and resid 263 through 264 No H-bonds generated for 'chain 'D' and resid 263 through 264' Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 291 through 297 removed outlier: 3.513A pdb=" N ALA D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.343A pdb=" N TYR D 308 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 352 through 355 Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.982A pdb=" N ARG D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS D 376 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 63 removed outlier: 4.145A pdb=" N LYS E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.943A pdb=" N ILE E 77 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.558A pdb=" N HIS E 103 " --> pdb=" O PRO E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 174 through 177 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.637A pdb=" N THR E 196 " --> pdb=" O MET E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 204 through 219 Processing helix chain 'E' and resid 224 through 231 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 260 through 264 Processing helix chain 'E' and resid 265 through 270 Processing helix chain 'E' and resid 275 through 286 Processing helix chain 'E' and resid 291 through 298 Processing helix chain 'E' and resid 303 through 308 removed outlier: 3.524A pdb=" N THR E 306 " --> pdb=" O GLY E 303 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR E 308 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 350 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 361 through 368 Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.585A pdb=" N ARG E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.710A pdb=" N GLN F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.857A pdb=" N ILE F 77 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 94 Processing helix chain 'F' and resid 99 through 103 Processing helix chain 'F' and resid 114 through 128 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'F' and resid 174 through 177 removed outlier: 3.649A pdb=" N ILE F 177 " --> pdb=" O PRO F 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 177' Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.646A pdb=" N THR F 196 " --> pdb=" O MET F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 204 through 219 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 254 through 262 Proline residue: F 260 - end of helix Processing helix chain 'F' and resid 263 through 264 No H-bonds generated for 'chain 'F' and resid 263 through 264' Processing helix chain 'F' and resid 265 through 270 Processing helix chain 'F' and resid 275 through 286 Processing helix chain 'F' and resid 291 through 298 Processing helix chain 'F' and resid 303 through 308 removed outlier: 4.206A pdb=" N TYR F 308 " --> pdb=" O THR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 339 through 350 removed outlier: 3.538A pdb=" N SER F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 358 removed outlier: 3.928A pdb=" N GLN F 356 " --> pdb=" O THR F 353 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP F 358 " --> pdb=" O GLN F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 367 Processing helix chain 'F' and resid 370 through 376 removed outlier: 3.699A pdb=" N ARG F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.612A pdb=" N GLN G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.980A pdb=" N ILE G 77 " --> pdb=" O GLU G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 94 Processing helix chain 'G' and resid 99 through 103 removed outlier: 3.553A pdb=" N HIS G 103 " --> pdb=" O PRO G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 128 Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'G' and resid 174 through 177 Processing helix chain 'G' and resid 183 through 196 removed outlier: 3.754A pdb=" N THR G 196 " --> pdb=" O MET G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 199 No H-bonds generated for 'chain 'G' and resid 197 through 199' Processing helix chain 'G' and resid 204 through 219 Processing helix chain 'G' and resid 224 through 231 Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 260 through 264 Processing helix chain 'G' and resid 265 through 270 Processing helix chain 'G' and resid 275 through 286 Processing helix chain 'G' and resid 291 through 297 removed outlier: 3.561A pdb=" N ALA G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 308 removed outlier: 3.501A pdb=" N THR G 306 " --> pdb=" O GLY G 303 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR G 308 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 323 Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'G' and resid 339 through 350 Processing helix chain 'G' and resid 351 through 358 removed outlier: 3.716A pdb=" N GLN G 356 " --> pdb=" O THR G 353 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP G 358 " --> pdb=" O GLN G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 367 Processing helix chain 'G' and resid 370 through 376 removed outlier: 3.984A pdb=" N ARG G 374 " --> pdb=" O SER G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 63 removed outlier: 3.662A pdb=" N GLN H 61 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.597A pdb=" N ILE H 77 " --> pdb=" O GLU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 94 Processing helix chain 'H' and resid 114 through 128 Processing helix chain 'H' and resid 139 through 147 Processing helix chain 'H' and resid 183 through 196 removed outlier: 3.610A pdb=" N THR H 196 " --> pdb=" O MET H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 204 through 219 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 253 through 258 Processing helix chain 'H' and resid 259 through 264 Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 275 through 286 Processing helix chain 'H' and resid 291 through 297 Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'H' and resid 310 through 323 Processing helix chain 'H' and resid 336 through 338 No H-bonds generated for 'chain 'H' and resid 336 through 338' Processing helix chain 'H' and resid 339 through 350 Processing helix chain 'H' and resid 351 through 358 removed outlier: 4.165A pdb=" N GLN H 356 " --> pdb=" O THR H 353 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP H 358 " --> pdb=" O GLN H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 367 Processing helix chain 'H' and resid 370 through 376 removed outlier: 3.613A pdb=" N ARG H 374 " --> pdb=" O SER H 370 " (cutoff:3.500A) Processing helix chain 'X' and resid 282 through 285 Processing helix chain 'X' and resid 401 through 405 Processing helix chain 'Y' and resid 282 through 285 Processing helix chain 'Y' and resid 401 through 405 removed outlier: 3.565A pdb=" N LYS Y 404 " --> pdb=" O ASP Y 401 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 21 removed outlier: 3.839A pdb=" N LYS a 12 " --> pdb=" O ASP a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 61 removed outlier: 3.629A pdb=" N PHE a 53 " --> pdb=" O PRO a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 122 removed outlier: 4.830A pdb=" N ARG a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA a 116 " --> pdb=" O SER a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 137 Processing helix chain 'a' and resid 138 through 148 Processing helix chain 'b' and resid 8 through 20 removed outlier: 3.883A pdb=" N LYS b 12 " --> pdb=" O ASP b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 61 removed outlier: 3.625A pdb=" N PHE b 53 " --> pdb=" O PRO b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 122 removed outlier: 4.805A pdb=" N ARG b 115 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA b 116 " --> pdb=" O SER b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 137 Processing helix chain 'b' and resid 138 through 149 removed outlier: 3.523A pdb=" N ASN b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 22 removed outlier: 3.914A pdb=" N LYS c 12 " --> pdb=" O ASP c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 61 removed outlier: 3.689A pdb=" N PHE c 53 " --> pdb=" O PRO c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 122 removed outlier: 4.729A pdb=" N ARG c 115 " --> pdb=" O ALA c 111 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA c 116 " --> pdb=" O SER c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 133 through 137 Processing helix chain 'c' and resid 138 through 148 Processing helix chain 'd' and resid 8 through 21 removed outlier: 3.803A pdb=" N LYS d 12 " --> pdb=" O ASP d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 61 removed outlier: 3.601A pdb=" N PHE d 53 " --> pdb=" O PRO d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 122 removed outlier: 4.890A pdb=" N ARG d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA d 116 " --> pdb=" O SER d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 137 Processing helix chain 'd' and resid 138 through 149 removed outlier: 3.641A pdb=" N ASN d 149 " --> pdb=" O ASP d 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 20 removed outlier: 3.934A pdb=" N LYS e 12 " --> pdb=" O ASP e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 61 removed outlier: 3.634A pdb=" N PHE e 53 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 removed outlier: 4.901A pdb=" N ARG e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA e 116 " --> pdb=" O SER e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 137 Processing helix chain 'e' and resid 138 through 150 Processing helix chain 'f' and resid 8 through 20 removed outlier: 3.986A pdb=" N LYS f 12 " --> pdb=" O ASP f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 49 through 61 Processing helix chain 'f' and resid 103 through 122 removed outlier: 4.794A pdb=" N ARG f 115 " --> pdb=" O ALA f 111 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA f 116 " --> pdb=" O SER f 112 " (cutoff:3.500A) Processing helix chain 'f' and resid 133 through 137 Processing helix chain 'f' and resid 138 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 4.710A pdb=" N ASN A 14 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.441A pdb=" N ASN A 299 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.585A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.263A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.585A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'C' and resid 171 through 172 removed outlier: 6.420A pdb=" N ASN C 299 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.628A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AB9, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AC1, first strand: chain 'D' and resid 171 through 172 removed outlier: 6.512A pdb=" N ASN D 299 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AC3, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.546A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N CYS E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC5, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AC6, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.514A pdb=" N ASN E 299 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 240 through 243 Processing sheet with id=AC8, first strand: chain 'F' and resid 31 through 34 removed outlier: 6.559A pdb=" N LEU F 10 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR F 108 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N CYS F 12 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AD1, first strand: chain 'F' and resid 171 through 172 Processing sheet with id=AD2, first strand: chain 'F' and resid 171 through 172 removed outlier: 6.359A pdb=" N ASN F 299 " --> pdb=" O ILE F 332 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 240 through 243 Processing sheet with id=AD4, first strand: chain 'G' and resid 31 through 34 removed outlier: 6.516A pdb=" N LEU G 10 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR G 108 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N CYS G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 55 through 56 Processing sheet with id=AD6, first strand: chain 'G' and resid 171 through 172 Processing sheet with id=AD7, first strand: chain 'G' and resid 171 through 172 removed outlier: 6.484A pdb=" N ASN G 299 " --> pdb=" O ILE G 332 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 240 through 243 Processing sheet with id=AD9, first strand: chain 'H' and resid 31 through 34 removed outlier: 3.816A pdb=" N THR H 108 " --> pdb=" O CYS H 12 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN H 14 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 55 through 56 Processing sheet with id=AE2, first strand: chain 'H' and resid 171 through 172 Processing sheet with id=AE3, first strand: chain 'H' and resid 171 through 172 removed outlier: 6.516A pdb=" N ASN H 299 " --> pdb=" O ILE H 332 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 240 through 243 Processing sheet with id=AE5, first strand: chain 'X' and resid 5 through 10 removed outlier: 5.633A pdb=" N GLN X 6 " --> pdb=" O ASN X 608 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN X 608 " --> pdb=" O GLN X 6 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA X 8 " --> pdb=" O PHE X 606 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR X 594 " --> pdb=" O LEU X 590 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 25 through 26 Processing sheet with id=AE7, first strand: chain 'X' and resid 62 through 67 removed outlier: 6.849A pdb=" N GLY X 77 " --> pdb=" O THR X 63 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA X 65 " --> pdb=" O ALA X 75 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA X 75 " --> pdb=" O ALA X 65 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR X 67 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR X 73 " --> pdb=" O THR X 67 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN X 82 " --> pdb=" O ASP X 78 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL X 83 " --> pdb=" O THR X 98 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR X 98 " --> pdb=" O VAL X 83 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE X 85 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 106 through 111 Processing sheet with id=AE9, first strand: chain 'X' and resid 150 through 155 removed outlier: 3.514A pdb=" N SER X 152 " --> pdb=" O GLY X 166 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLU X 176 " --> pdb=" O PHE X 182 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE X 182 " --> pdb=" O GLU X 176 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 193 through 198 removed outlier: 4.560A pdb=" N ILE X 214 " --> pdb=" O PHE X 228 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN X 218 " --> pdb=" O LYS X 224 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS X 224 " --> pdb=" O ASN X 218 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 242 through 247 removed outlier: 3.556A pdb=" N GLY X 244 " --> pdb=" O ALA X 257 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR X 262 " --> pdb=" O SER X 258 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASN X 267 " --> pdb=" O VAL X 273 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL X 273 " --> pdb=" O ASN X 267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 287 through 292 removed outlier: 3.737A pdb=" N GLY X 289 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU X 297 " --> pdb=" O VAL X 309 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN X 318 " --> pdb=" O PHE X 308 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN X 310 " --> pdb=" O ILE X 316 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE X 316 " --> pdb=" O ASN X 310 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 327 through 332 Processing sheet with id=AF5, first strand: chain 'X' and resid 370 through 375 removed outlier: 3.669A pdb=" N GLY X 372 " --> pdb=" O VAL X 384 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS X 389 " --> pdb=" O SER X 385 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 414 through 419 removed outlier: 3.798A pdb=" N HIS X 433 " --> pdb=" O CYS X 430 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 451 through 456 removed outlier: 6.776A pdb=" N GLY X 466 " --> pdb=" O SER X 452 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL X 454 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA X 464 " --> pdb=" O VAL X 454 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU X 456 " --> pdb=" O PHE X 462 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE X 462 " --> pdb=" O LEU X 456 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS X 471 " --> pdb=" O GLY X 467 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS X 476 " --> pdb=" O GLU X 484 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU X 484 " --> pdb=" O LYS X 476 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER X 478 " --> pdb=" O VAL X 482 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL X 482 " --> pdb=" O SER X 478 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 494 through 499 removed outlier: 3.720A pdb=" N SER X 496 " --> pdb=" O THR X 509 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU X 525 " --> pdb=" O SER X 519 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 539 through 544 Processing sheet with id=AG1, first strand: chain 'Y' and resid 5 through 10 removed outlier: 6.888A pdb=" N PHE Y 606 " --> pdb=" O THR Y 7 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU Y 9 " --> pdb=" O ILE Y 604 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE Y 604 " --> pdb=" O LEU Y 9 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR Y 594 " --> pdb=" O LEU Y 590 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 25 through 26 Processing sheet with id=AG3, first strand: chain 'Y' and resid 62 through 67 removed outlier: 6.846A pdb=" N GLY Y 77 " --> pdb=" O THR Y 63 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA Y 65 " --> pdb=" O ALA Y 75 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA Y 75 " --> pdb=" O ALA Y 65 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR Y 67 " --> pdb=" O TYR Y 73 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR Y 73 " --> pdb=" O THR Y 67 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN Y 82 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL Y 83 " --> pdb=" O THR Y 98 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR Y 98 " --> pdb=" O VAL Y 83 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE Y 85 " --> pdb=" O LYS Y 96 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 106 through 111 Processing sheet with id=AG5, first strand: chain 'Y' and resid 150 through 155 removed outlier: 5.770A pdb=" N GLU Y 176 " --> pdb=" O PHE Y 182 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N PHE Y 182 " --> pdb=" O GLU Y 176 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 193 through 198 removed outlier: 4.551A pdb=" N ILE Y 214 " --> pdb=" O PHE Y 228 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN Y 218 " --> pdb=" O LYS Y 224 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS Y 224 " --> pdb=" O ASN Y 218 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 242 through 247 removed outlier: 3.566A pdb=" N GLY Y 244 " --> pdb=" O ALA Y 257 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR Y 262 " --> pdb=" O SER Y 258 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN Y 267 " --> pdb=" O VAL Y 273 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL Y 273 " --> pdb=" O ASN Y 267 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 287 through 292 removed outlier: 3.739A pdb=" N GLY Y 289 " --> pdb=" O ILE Y 300 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU Y 297 " --> pdb=" O VAL Y 309 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN Y 318 " --> pdb=" O PHE Y 308 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN Y 310 " --> pdb=" O ILE Y 316 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE Y 316 " --> pdb=" O ASN Y 310 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 327 through 332 Processing sheet with id=AH1, first strand: chain 'Y' and resid 370 through 375 removed outlier: 3.691A pdb=" N GLY Y 372 " --> pdb=" O VAL Y 384 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS Y 389 " --> pdb=" O SER Y 385 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 414 through 419 removed outlier: 3.924A pdb=" N HIS Y 433 " --> pdb=" O CYS Y 430 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 451 through 456 removed outlier: 6.773A pdb=" N GLY Y 466 " --> pdb=" O SER Y 452 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL Y 454 " --> pdb=" O ALA Y 464 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA Y 464 " --> pdb=" O VAL Y 454 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU Y 456 " --> pdb=" O PHE Y 462 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE Y 462 " --> pdb=" O LEU Y 456 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS Y 471 " --> pdb=" O GLY Y 467 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL Y 472 " --> pdb=" O THR Y 487 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR Y 487 " --> pdb=" O VAL Y 472 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL Y 474 " --> pdb=" O VAL Y 485 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 494 through 499 removed outlier: 3.833A pdb=" N SER Y 496 " --> pdb=" O THR Y 509 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU Y 525 " --> pdb=" O SER Y 519 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 539 through 544 Processing sheet with id=AH6, first strand: chain 'a' and resid 6 through 7 removed outlier: 6.913A pdb=" N LYS a 6 " --> pdb=" O ILE a 38 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N VAL a 40 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL a 40 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS a 30 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE a 127 " --> pdb=" O VAL a 92 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 6 through 7 removed outlier: 6.956A pdb=" N LYS b 6 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N VAL b 40 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL b 40 " --> pdb=" O LYS b 30 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS b 30 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE b 127 " --> pdb=" O VAL b 92 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'c' and resid 6 through 7 removed outlier: 6.957A pdb=" N LYS c 6 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N VAL c 40 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL c 40 " --> pdb=" O LYS c 30 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS c 30 " --> pdb=" O VAL c 40 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE c 127 " --> pdb=" O VAL c 92 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'd' and resid 6 through 7 removed outlier: 6.868A pdb=" N LYS d 6 " --> pdb=" O ILE d 38 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL d 40 " --> pdb=" O LYS d 6 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL d 40 " --> pdb=" O LYS d 30 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS d 30 " --> pdb=" O VAL d 40 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE d 127 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.409A pdb=" N LYS e 6 " --> pdb=" O ILE e 38 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N VAL e 40 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL e 40 " --> pdb=" O LYS e 30 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS e 30 " --> pdb=" O VAL e 40 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE e 127 " --> pdb=" O VAL e 92 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'f' and resid 6 through 7 removed outlier: 7.284A pdb=" N LYS f 6 " --> pdb=" O ILE f 38 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N VAL f 40 " --> pdb=" O LYS f 6 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL f 40 " --> pdb=" O LYS f 30 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS f 30 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE f 127 " --> pdb=" O VAL f 92 " (cutoff:3.500A) 1832 hydrogen bonds defined for protein. 4751 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: 10.11 Time building geometry restraints manager: 4.40 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: 13101 1.34 - 1.46: 8653 1.46 - 1.58: 19200 1.58 - 1.70: 24 1.70 - 1.81: 416 Bond restraints: 41394 Sorted by residual: bond pdb=" C4 ADP B 400 " pdb=" C5 ADP B 400 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C4 ADP D 400 " pdb=" C5 ADP D 400 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" C4 ADP G 400 " pdb=" C5 ADP G 400 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 ADP C 400 " pdb=" C5 ADP C 400 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C4 ADP E 400 " pdb=" C5 ADP E 400 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 41389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 54848 1.41 - 2.83: 1192 2.83 - 4.24: 244 4.24 - 5.65: 53 5.65 - 7.07: 19 Bond angle restraints: 56356 Sorted by residual: angle pdb=" N GLU f 56 " pdb=" CA GLU f 56 " pdb=" CB GLU f 56 " ideal model delta sigma weight residual 110.16 115.53 -5.37 1.48e+00 4.57e-01 1.32e+01 angle pdb=" N VAL X 279 " pdb=" CA VAL X 279 " pdb=" C VAL X 279 " ideal model delta sigma weight residual 111.90 109.13 2.77 8.10e-01 1.52e+00 1.17e+01 angle pdb=" CA MET E 46 " pdb=" CB MET E 46 " pdb=" CG MET E 46 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.45e+00 angle pdb=" CA GLU f 124 " pdb=" CB GLU f 124 " pdb=" CG GLU f 124 " ideal model delta sigma weight residual 114.10 119.56 -5.46 2.00e+00 2.50e-01 7.46e+00 angle pdb=" CA ASP Y 387 " pdb=" C ASP Y 387 " pdb=" N ASP Y 388 " ideal model delta sigma weight residual 118.27 114.11 4.16 1.59e+00 3.96e-01 6.85e+00 ... (remaining 56351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 23586 17.52 - 35.05: 1264 35.05 - 52.57: 222 52.57 - 70.09: 56 70.09 - 87.62: 48 Dihedral angle restraints: 25176 sinusoidal: 9946 harmonic: 15230 Sorted by residual: dihedral pdb=" C5' ADP B 400 " pdb=" O5' ADP B 400 " pdb=" PA ADP B 400 " pdb=" O2A ADP B 400 " ideal model delta sinusoidal sigma weight residual -60.00 26.58 -86.58 1 2.00e+01 2.50e-03 2.26e+01 dihedral pdb=" C5' ADP D 400 " pdb=" O5' ADP D 400 " pdb=" PA ADP D 400 " pdb=" O2A ADP D 400 " ideal model delta sinusoidal sigma weight residual -60.00 23.30 -83.29 1 2.00e+01 2.50e-03 2.12e+01 dihedral pdb=" C5' ADP C 400 " pdb=" O5' ADP C 400 " pdb=" PA ADP C 400 " pdb=" O2A ADP C 400 " ideal model delta sinusoidal sigma weight residual -60.00 22.20 -82.20 1 2.00e+01 2.50e-03 2.07e+01 ... (remaining 25173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3964 0.035 - 0.070: 1505 0.070 - 0.104: 616 0.104 - 0.139: 251 0.139 - 0.174: 18 Chirality restraints: 6354 Sorted by residual: chirality pdb=" CB BILE H 73 " pdb=" CA BILE H 73 " pdb=" CG1BILE H 73 " pdb=" CG2BILE H 73 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" C3' ADP C 400 " pdb=" C2' ADP C 400 " pdb=" C4' ADP C 400 " pdb=" O3' ADP C 400 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB ILE D 153 " pdb=" CA ILE D 153 " pdb=" CG1 ILE D 153 " pdb=" CG2 ILE D 153 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 6351 not shown) Planarity restraints: 7236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 165 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO G 166 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 166 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 166 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Y 516 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO Y 517 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO Y 517 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO Y 517 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE X 516 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO X 517 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO X 517 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO X 517 " -0.023 5.00e-02 4.00e+02 ... (remaining 7233 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 56 2.56 - 3.14: 31588 3.14 - 3.73: 63055 3.73 - 4.31: 94758 4.31 - 4.90: 155340 Nonbonded interactions: 344797 Sorted by model distance: nonbonded pdb=" O1B ADP F 400 " pdb="MG MG F 401 " model vdw 1.971 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 1.975 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 1.998 2.170 nonbonded pdb="MG MG E 401 " pdb=" O HOH E 505 " model vdw 2.005 2.170 nonbonded pdb="MG MG F 401 " pdb=" O HOH F 505 " model vdw 2.007 2.170 ... (remaining 344792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'B' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'C' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'D' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'E' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'F' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'G' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'H' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) } ncs_group { reference = chain 'X' selection = chain 'Y' } ncs_group { reference = (chain 'a' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'b' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'c' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'd' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'e' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'f' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) } 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=0.10 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.150 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: 0.060 Extract box with map and model: 0.790 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 44.560 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 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 : 0.002 0.036 41394 Z= 0.117 Angle : 0.554 7.068 56356 Z= 0.291 Chirality : 0.046 0.174 6354 Planarity : 0.004 0.057 7236 Dihedral : 11.992 87.616 15468 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.24 % Rotamer: Outliers : 0.25 % Allowed : 0.70 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.06 (0.12), residues: 5184 helix: 0.97 (0.14), residues: 1524 sheet: 0.53 (0.14), residues: 1276 loop : 0.85 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 117 TYR 0.014 0.001 TYR Y 217 PHE 0.018 0.001 PHE f 29 TRP 0.018 0.002 TRP H 88 HIS 0.009 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (41394) covalent geometry : angle 0.55427 / 0.29 (56356) hydrogen bonds : bond 0.13369 / 9.10 ( 1816) hydrogen bonds : angle 6.13942 / 4.33 ( 4751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9506 (tp) cc_final: 0.9037 (tp) REVERT: B 49 MET cc_start: 0.1051 (mmt) cc_final: 0.0611 (mmt) REVERT: B 125 MET cc_start: 0.9416 (mmp) cc_final: 0.9158 (mmt) REVERT: E 84 MET cc_start: 0.9253 (tpt) cc_final: 0.8961 (tpt) REVERT: E 290 ASP cc_start: 0.8557 (p0) cc_final: 0.7904 (p0) REVERT: H 84 MET cc_start: 0.9150 (tpt) cc_final: 0.8927 (mmm) REVERT: H 178 MET cc_start: 0.7169 (mtt) cc_final: 0.6904 (mtt) REVERT: H 301 MET cc_start: 0.8218 (mtm) cc_final: 0.7664 (ptp) REVERT: H 357 MET cc_start: 0.7508 (tpp) cc_final: 0.7148 (tpp) REVERT: a 63 ASP cc_start: 0.8502 (p0) cc_final: 0.8244 (p0) REVERT: a 138 ASP cc_start: 0.8921 (t70) cc_final: 0.8710 (t70) REVERT: b 57 MET cc_start: 0.9205 (mmm) cc_final: 0.8736 (tpt) REVERT: c 1 MET cc_start: 0.5072 (mmp) cc_final: 0.3702 (ptm) REVERT: f 47 ASN cc_start: 0.8577 (m110) cc_final: 0.8366 (m110) REVERT: f 79 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7948 (tp-100) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.8277 time to fit residues: 302.3327 Evaluate side-chains 253 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [432, 197, 388, 455, 215, 20, 132, 494, 261, 248, 207] chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN B 164 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 GLN E 164 ASN ** H 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 461 GLN Y 468 GLN b 149 ASN c 23 GLN d 13 ASN d 128 GLN e 81 GLN f 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.081950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.048412 restraints weight = 473150.874| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 5.26 r_work: 0.2511 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 41394 Z= 0.312 Angle : 0.641 7.384 56356 Z= 0.332 Chirality : 0.052 0.262 6354 Planarity : 0.005 0.050 7236 Dihedral : 6.280 95.759 5842 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 0.76 % Allowed : 4.05 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 (0.12), residues: 5184 helix: 0.85 (0.13), residues: 1612 sheet: 0.46 (0.14), residues: 1326 loop : 0.69 (0.14), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 374 TYR 0.022 0.002 TYR D 145 PHE 0.024 0.002 PHE f 29 TRP 0.015 0.002 TRP D 342 HIS 0.014 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.31 (41394) covalent geometry : angle 0.64139 / 0.33 (56356) hydrogen bonds : bond 0.05343 / 3.62 ( 1816) hydrogen bonds : angle 5.19152 / 3.68 ( 4751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: B 49 MET cc_start: 0.0915 (mmt) cc_final: 0.0617 (mmt) REVERT: E 84 MET cc_start: 0.9393 (tpt) cc_final: 0.9117 (tpt) REVERT: G 49 MET cc_start: 0.5009 (mpp) cc_final: 0.4742 (mmp) REVERT: H 84 MET cc_start: 0.9052 (tpt) cc_final: 0.8843 (mmm) REVERT: H 178 MET cc_start: 0.7276 (mtt) cc_final: 0.6803 (mtt) REVERT: H 301 MET cc_start: 0.8688 (mtm) cc_final: 0.7417 (ptp) REVERT: H 357 MET cc_start: 0.7317 (tpp) cc_final: 0.6865 (tpp) REVERT: a 8 ASP cc_start: 0.8770 (t70) cc_final: 0.8495 (t70) REVERT: a 63 ASP cc_start: 0.8682 (p0) cc_final: 0.8447 (p0) REVERT: a 138 ASP cc_start: 0.8689 (t70) cc_final: 0.8185 (t70) REVERT: c 145 ASP cc_start: 0.8868 (m-30) cc_final: 0.8612 (m-30) REVERT: f 47 ASN cc_start: 0.8720 (m110) cc_final: 0.8446 (m110) REVERT: f 79 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7432 (tp-100) REVERT: f 96 GLN cc_start: 0.8792 (tt0) cc_final: 0.8409 (mt0) outliers start: 17 outliers final: 5 residues processed: 261 average time/residue: 0.7957 time to fit residues: 250.3311 Evaluate side-chains 255 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 250 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [393, 14, 244, 265, 274, 320, 353, 408, 299, 315, 476] chunk 393 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 265 optimal weight: 0.9980 chunk 274 optimal weight: 40.0000 chunk 320 optimal weight: 7.9990 chunk 353 optimal weight: 20.0000 chunk 408 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 476 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.082715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.049431 restraints weight = 489341.872| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 5.37 r_work: 0.2534 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41394 Z= 0.188 Angle : 0.562 7.131 56356 Z= 0.289 Chirality : 0.048 0.190 6354 Planarity : 0.004 0.048 7236 Dihedral : 6.096 90.337 5842 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.89 % Rotamer: Outliers : 0.94 % Allowed : 4.63 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.06 (0.12), residues: 5184 helix: 1.01 (0.13), residues: 1612 sheet: 0.44 (0.14), residues: 1318 loop : 0.88 (0.14), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG f 68 TYR 0.025 0.001 TYR f 26 PHE 0.018 0.001 PHE f 29 TRP 0.013 0.002 TRP D 342 HIS 0.012 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (41394) covalent geometry : angle 0.56217 / 0.29 (56356) hydrogen bonds : bond 0.04424 / 2.99 ( 1816) hydrogen bonds : angle 4.94624 / 3.50 ( 4751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 1.563 Fit side-chains REVERT: B 49 MET cc_start: 0.0984 (mmt) cc_final: 0.0652 (mmt) REVERT: E 84 MET cc_start: 0.9400 (tpt) cc_final: 0.9143 (tpt) REVERT: G 49 MET cc_start: 0.4990 (mpp) cc_final: 0.4761 (mmp) REVERT: H 84 MET cc_start: 0.9069 (tpt) cc_final: 0.8857 (mmm) REVERT: H 178 MET cc_start: 0.7364 (mtt) cc_final: 0.6926 (mtt) REVERT: H 301 MET cc_start: 0.8680 (mtm) cc_final: 0.7574 (ptp) REVERT: H 357 MET cc_start: 0.7377 (tpp) cc_final: 0.6888 (tpp) REVERT: X 126 GLU cc_start: 0.8014 (pt0) cc_final: 0.7680 (pm20) REVERT: Y 234 LYS cc_start: 0.8513 (tppt) cc_final: 0.8309 (tppt) REVERT: a 8 ASP cc_start: 0.8775 (t70) cc_final: 0.8506 (t70) REVERT: a 63 ASP cc_start: 0.8672 (p0) cc_final: 0.8415 (p0) REVERT: c 115 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8632 (ttp-170) REVERT: d 8 ASP cc_start: 0.8700 (t0) cc_final: 0.8245 (t0) REVERT: e 115 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8756 (ttp-170) REVERT: e 150 GLN cc_start: 0.8495 (mm110) cc_final: 0.8250 (mm-40) REVERT: f 47 ASN cc_start: 0.8728 (m110) cc_final: 0.8444 (m110) REVERT: f 79 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7573 (tp-100) outliers start: 24 outliers final: 3 residues processed: 262 average time/residue: 0.8213 time to fit residues: 258.3273 Evaluate side-chains 258 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 253 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain X residue 565 MET Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain e residue 115 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [212, 222, 458, 166, 416, 230, 399, 260, 232, 164, 236] chunk 212 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 458 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 416 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 399 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 HIS ** 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 = 0.3522 r_free = 0.3522 target = 0.081823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.048350 restraints weight = 507985.678| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 5.66 r_work: 0.2495 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 41394 Z= 0.240 Angle : 0.589 8.547 56356 Z= 0.303 Chirality : 0.049 0.227 6354 Planarity : 0.004 0.048 7236 Dihedral : 6.160 92.144 5842 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.45 % Favored : 97.53 % Rotamer: Outliers : 1.08 % Allowed : 5.04 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.09 (0.12), residues: 5184 helix: 1.02 (0.13), residues: 1612 sheet: 0.55 (0.14), residues: 1280 loop : 0.83 (0.14), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 374 TYR 0.026 0.002 TYR f 26 PHE 0.020 0.002 PHE b 29 TRP 0.014 0.002 TRP D 342 HIS 0.010 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (41394) covalent geometry : angle 0.58911 / 0.30 (56356) hydrogen bonds : bond 0.04702 / 3.18 ( 1816) hydrogen bonds : angle 4.91628 / 3.49 ( 4751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 1.598 Fit side-chains REVERT: A 178 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8895 (mtm) REVERT: B 41 ARG cc_start: 0.7952 (ptm-80) cc_final: 0.7744 (ptm-80) REVERT: E 84 MET cc_start: 0.9375 (tpt) cc_final: 0.9120 (tpt) REVERT: F 84 MET cc_start: 0.9034 (tpt) cc_final: 0.8735 (tpt) REVERT: G 49 MET cc_start: 0.5029 (mpp) cc_final: 0.4826 (mmp) REVERT: G 178 MET cc_start: 0.8693 (mmt) cc_final: 0.8464 (mtp) REVERT: H 49 MET cc_start: 0.6150 (pmm) cc_final: 0.4451 (ptm) REVERT: H 178 MET cc_start: 0.7338 (mtt) cc_final: 0.6981 (mtt) REVERT: H 301 MET cc_start: 0.8689 (mtm) cc_final: 0.7525 (ptp) REVERT: H 357 MET cc_start: 0.7361 (tpp) cc_final: 0.6859 (tpp) REVERT: X 126 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: X 369 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8208 (tpp) REVERT: Y 234 LYS cc_start: 0.8650 (tppt) cc_final: 0.8430 (tppt) REVERT: Y 235 ASN cc_start: 0.8821 (t0) cc_final: 0.8461 (t0) REVERT: a 8 ASP cc_start: 0.8763 (t70) cc_final: 0.8472 (t70) REVERT: a 63 ASP cc_start: 0.8626 (p0) cc_final: 0.8349 (p0) REVERT: c 115 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8630 (ttp-170) REVERT: c 145 ASP cc_start: 0.8848 (m-30) cc_final: 0.8583 (m-30) REVERT: d 8 ASP cc_start: 0.8652 (t0) cc_final: 0.8126 (t0) REVERT: f 47 ASN cc_start: 0.8705 (m110) cc_final: 0.8435 (m110) REVERT: f 79 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7549 (tp-100) REVERT: f 96 GLN cc_start: 0.8792 (tt0) cc_final: 0.8506 (mt0) outliers start: 28 outliers final: 9 residues processed: 263 average time/residue: 0.7900 time to fit residues: 251.4194 Evaluate side-chains 262 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain X residue 126 GLU Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain X residue 400 VAL Chi-restraints excluded: chain X residue 565 MET Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 134 MET Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [241, 42, 199, 418, 216, 367, 52, 65, 274, 276, 471] chunk 241 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 418 optimal weight: 0.4980 chunk 216 optimal weight: 0.8980 chunk 367 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 274 optimal weight: 50.0000 chunk 276 optimal weight: 8.9990 chunk 471 optimal weight: 9.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN d 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.082575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049438 restraints weight = 525793.147| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 5.57 r_work: 0.2525 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41394 Z= 0.156 Angle : 0.540 7.671 56356 Z= 0.276 Chirality : 0.047 0.185 6354 Planarity : 0.004 0.046 7236 Dihedral : 5.958 86.587 5842 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 1.03 % Allowed : 5.47 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.20 (0.12), residues: 5184 helix: 1.16 (0.13), residues: 1612 sheet: 0.54 (0.14), residues: 1294 loop : 0.91 (0.14), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 374 TYR 0.027 0.001 TYR f 26 PHE 0.017 0.001 PHE b 29 TRP 0.013 0.002 TRP D 342 HIS 0.010 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (41394) covalent geometry : angle 0.54015 / 0.28 (56356) hydrogen bonds : bond 0.04021 / 2.72 ( 1816) hydrogen bonds : angle 4.76157 / 3.37 ( 4751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 1.559 Fit side-chains REVERT: E 46 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.3719 (tmt) REVERT: E 84 MET cc_start: 0.9417 (tpt) cc_final: 0.9177 (tpt) REVERT: G 49 MET cc_start: 0.5086 (mpp) cc_final: 0.4869 (mmp) REVERT: G 178 MET cc_start: 0.8770 (mmt) cc_final: 0.8564 (mtp) REVERT: H 49 MET cc_start: 0.6108 (pmm) cc_final: 0.4454 (ptm) REVERT: H 178 MET cc_start: 0.7368 (mtt) cc_final: 0.6952 (mtt) REVERT: H 301 MET cc_start: 0.8689 (mtm) cc_final: 0.7516 (ptp) REVERT: H 357 MET cc_start: 0.7393 (tpp) cc_final: 0.6855 (tpp) REVERT: X 126 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: X 369 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8221 (tpp) REVERT: Y 234 LYS cc_start: 0.8615 (tppt) cc_final: 0.8399 (tppt) REVERT: Y 235 ASN cc_start: 0.8839 (t0) cc_final: 0.8471 (t0) REVERT: a 63 ASP cc_start: 0.8648 (p0) cc_final: 0.8373 (p0) REVERT: c 145 ASP cc_start: 0.8866 (m-30) cc_final: 0.8548 (m-30) REVERT: d 8 ASP cc_start: 0.8724 (t0) cc_final: 0.8184 (t0) REVERT: e 115 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8774 (ttp-170) REVERT: f 47 ASN cc_start: 0.8732 (m110) cc_final: 0.8469 (m110) REVERT: f 96 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8433 (mt0) outliers start: 21 outliers final: 6 residues processed: 255 average time/residue: 0.8201 time to fit residues: 252.2296 Evaluate side-chains 258 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 247 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain X residue 126 GLU Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain X residue 565 MET Chi-restraints excluded: chain e residue 115 ARG Chi-restraints excluded: chain f residue 96 GLN Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [458, 280, 455, 462, 268, 233, 257, 361, 203, 24, 319] chunk 458 optimal weight: 0.8980 chunk 280 optimal weight: 20.0000 chunk 455 optimal weight: 7.9990 chunk 462 optimal weight: 0.9980 chunk 268 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 overall best weight: 3.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 HIS ** 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 = 0.3523 r_free = 0.3523 target = 0.081862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.048382 restraints weight = 505726.030| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 5.39 r_work: 0.2507 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41394 Z= 0.226 Angle : 0.574 8.491 56356 Z= 0.294 Chirality : 0.049 0.223 6354 Planarity : 0.004 0.047 7236 Dihedral : 6.034 90.253 5842 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.33 % Allowed : 5.51 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.16 (0.12), residues: 5184 helix: 1.11 (0.13), residues: 1612 sheet: 0.54 (0.14), residues: 1294 loop : 0.88 (0.14), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 374 TYR 0.027 0.001 TYR f 26 PHE 0.020 0.001 PHE b 29 TRP 0.014 0.002 TRP D 342 HIS 0.009 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (41394) covalent geometry : angle 0.57404 / 0.29 (56356) hydrogen bonds : bond 0.04475 / 3.03 ( 1816) hydrogen bonds : angle 4.81763 / 3.42 ( 4751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 1.450 Fit side-chains REVERT: E 84 MET cc_start: 0.9423 (tpt) cc_final: 0.9175 (tpt) REVERT: G 178 MET cc_start: 0.8798 (mmt) cc_final: 0.8574 (mtp) REVERT: H 49 MET cc_start: 0.6238 (pmm) cc_final: 0.4602 (ptm) REVERT: H 178 MET cc_start: 0.7382 (mtt) cc_final: 0.7015 (mtt) REVERT: H 301 MET cc_start: 0.8670 (mtm) cc_final: 0.7504 (ptp) REVERT: H 357 MET cc_start: 0.7381 (tpp) cc_final: 0.6886 (tpp) REVERT: X 126 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: X 369 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8185 (tpp) REVERT: X 415 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8716 (mm) REVERT: Y 235 ASN cc_start: 0.8840 (t0) cc_final: 0.8509 (t0) REVERT: a 8 ASP cc_start: 0.8775 (t70) cc_final: 0.8473 (t70) REVERT: a 63 ASP cc_start: 0.8639 (p0) cc_final: 0.8311 (p0) REVERT: d 8 ASP cc_start: 0.8712 (t0) cc_final: 0.8125 (t0) REVERT: e 115 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8764 (ttp-170) REVERT: f 47 ASN cc_start: 0.8738 (m110) cc_final: 0.8476 (m110) REVERT: f 56 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: f 96 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8429 (mt0) outliers start: 31 outliers final: 10 residues processed: 263 average time/residue: 0.7760 time to fit residues: 248.3639 Evaluate side-chains 264 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain X residue 126 GLU Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain X residue 400 VAL Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain X residue 565 MET Chi-restraints excluded: chain e residue 115 ARG Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 96 GLN Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [319, 450, 150, 117, 406, 500, 455, 232, 372, 347, 11] chunk 319 optimal weight: 9.9990 chunk 450 optimal weight: 5.9990 chunk 150 optimal weight: 0.1980 chunk 117 optimal weight: 0.5980 chunk 406 optimal weight: 10.0000 chunk 500 optimal weight: 20.0000 chunk 455 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 372 optimal weight: 2.9990 chunk 347 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.083451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049750 restraints weight = 511863.361| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 5.50 r_work: 0.2558 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 41394 Z= 0.110 Angle : 0.518 10.766 56356 Z= 0.263 Chirality : 0.046 0.179 6354 Planarity : 0.004 0.045 7236 Dihedral : 5.703 80.691 5842 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.97 % Allowed : 6.23 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.28 (0.12), residues: 5184 helix: 1.27 (0.14), residues: 1612 sheet: 0.58 (0.14), residues: 1292 loop : 0.92 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 374 TYR 0.030 0.001 TYR f 26 PHE 0.015 0.001 PHE b 29 TRP 0.012 0.001 TRP A 342 HIS 0.009 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (41394) covalent geometry : angle 0.51838 / 0.26 (56356) hydrogen bonds : bond 0.03498 / 2.36 ( 1816) hydrogen bonds : angle 4.61536 / 3.27 ( 4751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 1.796 Fit side-chains REVERT: E 46 MET cc_start: 0.5026 (mpp) cc_final: 0.3973 (tmt) REVERT: E 84 MET cc_start: 0.9396 (tpt) cc_final: 0.9173 (tpt) REVERT: F 64 ARG cc_start: 0.6805 (mpt180) cc_final: 0.6018 (mpp-170) REVERT: G 178 MET cc_start: 0.8786 (mmt) cc_final: 0.8559 (mtp) REVERT: H 49 MET cc_start: 0.6277 (pmm) cc_final: 0.4523 (ptm) REVERT: H 178 MET cc_start: 0.7376 (mtt) cc_final: 0.6972 (mtt) REVERT: H 301 MET cc_start: 0.8662 (mtm) cc_final: 0.7560 (ptp) REVERT: H 357 MET cc_start: 0.7375 (tpp) cc_final: 0.6856 (tpp) REVERT: X 126 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: X 369 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8165 (tpp) REVERT: Y 235 ASN cc_start: 0.8818 (t0) cc_final: 0.8449 (t0) REVERT: a 63 ASP cc_start: 0.8621 (p0) cc_final: 0.8326 (p0) REVERT: d 8 ASP cc_start: 0.8720 (t0) cc_final: 0.8132 (t0) REVERT: e 52 GLU cc_start: 0.9029 (tt0) cc_final: 0.8787 (tm-30) REVERT: f 47 ASN cc_start: 0.8720 (m110) cc_final: 0.8451 (m110) REVERT: f 56 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: f 79 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7538 (tp-100) REVERT: f 96 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8377 (mt0) outliers start: 15 outliers final: 6 residues processed: 258 average time/residue: 0.8177 time to fit residues: 253.4880 Evaluate side-chains 261 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 251 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain X residue 126 GLU Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain X residue 400 VAL Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 96 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [159, 466, 202, 386, 214, 357, 58, 107, 66, 11, 394] chunk 159 optimal weight: 0.9980 chunk 466 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 386 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 357 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 394 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.082965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.049447 restraints weight = 521831.672| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 5.40 r_work: 0.2542 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41394 Z= 0.134 Angle : 0.530 11.075 56356 Z= 0.268 Chirality : 0.046 0.185 6354 Planarity : 0.004 0.046 7236 Dihedral : 5.649 79.427 5842 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.10 % Allowed : 6.28 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.31 (0.12), residues: 5184 helix: 1.29 (0.14), residues: 1612 sheet: 0.61 (0.14), residues: 1292 loop : 0.94 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 374 TYR 0.029 0.001 TYR f 26 PHE 0.016 0.001 PHE b 29 TRP 0.012 0.001 TRP D 342 HIS 0.008 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (41394) covalent geometry : angle 0.52969 / 0.27 (56356) hydrogen bonds : bond 0.03687 / 2.49 ( 1816) hydrogen bonds : angle 4.61844 / 3.27 ( 4751) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.9205 (mtp) cc_final: 0.8938 (mmm) REVERT: B 46 MET cc_start: 0.4142 (mmm) cc_final: 0.3503 (mmm) REVERT: E 49 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.5511 (pmt) REVERT: E 84 MET cc_start: 0.9410 (tpt) cc_final: 0.9172 (tpt) REVERT: F 64 ARG cc_start: 0.6825 (mpt180) cc_final: 0.5965 (mpp-170) REVERT: G 178 MET cc_start: 0.8800 (mmt) cc_final: 0.8569 (mtp) REVERT: H 49 MET cc_start: 0.6319 (pmm) cc_final: 0.4514 (ptm) REVERT: H 178 MET cc_start: 0.7367 (mtt) cc_final: 0.7012 (mtt) REVERT: H 301 MET cc_start: 0.8664 (mtm) cc_final: 0.7564 (ptp) REVERT: H 357 MET cc_start: 0.7357 (tpp) cc_final: 0.6826 (tpp) REVERT: X 126 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: X 369 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8190 (tpp) REVERT: X 415 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8704 (mm) REVERT: Y 235 ASN cc_start: 0.8814 (t0) cc_final: 0.8437 (t0) REVERT: a 63 ASP cc_start: 0.8634 (p0) cc_final: 0.8291 (p0) REVERT: d 8 ASP cc_start: 0.8711 (t0) cc_final: 0.8085 (t0) REVERT: e 52 GLU cc_start: 0.9029 (tt0) cc_final: 0.8792 (tm-30) REVERT: f 47 ASN cc_start: 0.8729 (m110) cc_final: 0.8457 (m110) REVERT: f 79 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7517 (tp-100) REVERT: f 96 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8388 (mt0) outliers start: 19 outliers final: 10 residues processed: 262 average time/residue: 0.7890 time to fit residues: 248.7345 Evaluate side-chains 265 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain X residue 126 GLU Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain X residue 400 VAL Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 96 GLN Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [22, 194, 366, 203, 314, 276, 0, 283, 169, 23, 36] chunk 22 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 366 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 314 optimal weight: 0.0470 chunk 276 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** 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 = 0.3545 r_free = 0.3545 target = 0.083083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.049769 restraints weight = 528254.193| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 5.53 r_work: 0.2542 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41394 Z= 0.131 Angle : 0.528 11.594 56356 Z= 0.267 Chirality : 0.046 0.181 6354 Planarity : 0.004 0.046 7236 Dihedral : 5.614 78.857 5842 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.06 % Allowed : 6.39 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.32 (0.12), residues: 5184 helix: 1.29 (0.14), residues: 1612 sheet: 0.62 (0.14), residues: 1292 loop : 0.94 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 374 TYR 0.031 0.001 TYR f 26 PHE 0.016 0.001 PHE b 29 TRP 0.012 0.001 TRP D 342 HIS 0.005 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (41394) covalent geometry : angle 0.52778 / 0.27 (56356) hydrogen bonds : bond 0.03644 / 2.46 ( 1816) hydrogen bonds : angle 4.60784 / 3.27 ( 4751) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 1.533 Fit side-chains REVERT: B 46 MET cc_start: 0.4135 (mmm) cc_final: 0.3506 (mmm) REVERT: E 49 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.5519 (pmt) REVERT: E 84 MET cc_start: 0.9407 (tpt) cc_final: 0.9157 (tpt) REVERT: F 64 ARG cc_start: 0.6813 (mpt180) cc_final: 0.5968 (mpp-170) REVERT: G 178 MET cc_start: 0.8801 (mmt) cc_final: 0.8570 (mtp) REVERT: H 49 MET cc_start: 0.6320 (pmm) cc_final: 0.4524 (ptm) REVERT: H 178 MET cc_start: 0.7383 (mtt) cc_final: 0.7026 (mtt) REVERT: H 301 MET cc_start: 0.8608 (mtm) cc_final: 0.7508 (ptp) REVERT: H 357 MET cc_start: 0.7366 (tpp) cc_final: 0.6834 (tpp) REVERT: X 126 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: X 369 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8203 (tpp) REVERT: X 415 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8707 (mm) REVERT: Y 235 ASN cc_start: 0.8808 (t0) cc_final: 0.8424 (t0) REVERT: a 63 ASP cc_start: 0.8631 (p0) cc_final: 0.8286 (p0) REVERT: d 8 ASP cc_start: 0.8701 (t0) cc_final: 0.8066 (t0) REVERT: e 52 GLU cc_start: 0.9034 (tt0) cc_final: 0.8793 (tm-30) REVERT: f 47 ASN cc_start: 0.8734 (m110) cc_final: 0.8468 (m110) REVERT: f 56 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: f 79 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7540 (tp-100) REVERT: f 96 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8406 (mt0) outliers start: 16 outliers final: 7 residues processed: 255 average time/residue: 0.7908 time to fit residues: 244.0512 Evaluate side-chains 263 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 250 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain X residue 126 GLU Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain X residue 400 VAL Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 96 GLN Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [48, 161, 209, 415, 461, 494, 149, 342, 489, 123, 47] chunk 48 optimal weight: 2.9990 chunk 161 optimal weight: 0.0870 chunk 209 optimal weight: 6.9990 chunk 415 optimal weight: 9.9990 chunk 461 optimal weight: 1.9990 chunk 494 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 342 optimal weight: 9.9990 chunk 489 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** 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 = 0.3555 r_free = 0.3555 target = 0.083602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050286 restraints weight = 490539.646| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 5.41 r_work: 0.2564 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 41394 Z= 0.109 Angle : 0.520 11.646 56356 Z= 0.262 Chirality : 0.045 0.174 6354 Planarity : 0.004 0.045 7236 Dihedral : 5.492 75.731 5842 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.99 % Allowed : 6.48 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 1.33 (0.12), residues: 5184 helix: 1.32 (0.14), residues: 1612 sheet: 0.61 (0.14), residues: 1298 loop : 0.95 (0.14), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 374 TYR 0.030 0.001 TYR f 26 PHE 0.015 0.001 PHE b 29 TRP 0.011 0.001 TRP H 88 HIS 0.010 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (41394) covalent geometry : angle 0.51954 / 0.26 (56356) hydrogen bonds : bond 0.03412 / 2.30 ( 1816) hydrogen bonds : angle 4.54172 / 3.22 ( 4751) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 1.617 Fit side-chains REVERT: B 46 MET cc_start: 0.4148 (mmm) cc_final: 0.3548 (mmm) REVERT: E 84 MET cc_start: 0.9388 (tpt) cc_final: 0.9162 (tpt) REVERT: F 64 ARG cc_start: 0.6818 (mpt180) cc_final: 0.6022 (mpp-170) REVERT: G 178 MET cc_start: 0.8785 (mmt) cc_final: 0.8560 (mtp) REVERT: H 49 MET cc_start: 0.6316 (pmm) cc_final: 0.4511 (ptm) REVERT: H 178 MET cc_start: 0.7378 (mtt) cc_final: 0.7023 (mtt) REVERT: H 301 MET cc_start: 0.8608 (mtm) cc_final: 0.7503 (ptp) REVERT: H 357 MET cc_start: 0.7399 (tpp) cc_final: 0.6884 (tpp) REVERT: X 126 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: X 369 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8166 (tpp) REVERT: X 415 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8678 (mm) REVERT: Y 235 ASN cc_start: 0.8813 (t0) cc_final: 0.8436 (t0) REVERT: a 63 ASP cc_start: 0.8627 (p0) cc_final: 0.8305 (p0) REVERT: a 138 ASP cc_start: 0.8627 (t70) cc_final: 0.7995 (t70) REVERT: b 57 MET cc_start: 0.9202 (mmm) cc_final: 0.8665 (tpt) REVERT: d 8 ASP cc_start: 0.8701 (t0) cc_final: 0.8078 (t0) REVERT: e 52 GLU cc_start: 0.9026 (tt0) cc_final: 0.8807 (tm-30) REVERT: f 47 ASN cc_start: 0.8732 (m110) cc_final: 0.8461 (m110) REVERT: f 56 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: f 79 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7580 (tp-100) REVERT: f 96 GLN cc_start: 0.8757 (tt0) cc_final: 0.8409 (mt0) outliers start: 13 outliers final: 6 residues processed: 260 average time/residue: 0.8103 time to fit residues: 255.4789 Evaluate side-chains 263 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 253 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain X residue 126 GLU Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain X residue 400 VAL Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [341, 481, 186, 237, 502, 274, 423, 369, 175, 433, 32] chunk 341 optimal weight: 6.9990 chunk 481 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 502 optimal weight: 9.9990 chunk 274 optimal weight: 40.0000 chunk 423 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 433 optimal weight: 0.0070 chunk 32 optimal weight: 0.0030 overall best weight: 3.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 117 ASN ** 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 = 0.3533 r_free = 0.3533 target = 0.082406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.048816 restraints weight = 502717.165| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 5.43 r_work: 0.2522 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41394 Z= 0.188 Angle : 0.558 10.968 56356 Z= 0.284 Chirality : 0.047 0.211 6354 Planarity : 0.004 0.047 7236 Dihedral : 5.737 86.197 5842 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.94 % Allowed : 6.66 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 (0.12), residues: 5184 helix: 1.24 (0.14), residues: 1612 sheet: 0.62 (0.14), residues: 1294 loop : 0.94 (0.14), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 374 TYR 0.029 0.001 TYR f 26 PHE 0.019 0.001 PHE b 29 TRP 0.013 0.002 TRP H 88 HIS 0.006 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (41394) covalent geometry : angle 0.55849 / 0.28 (56356) hydrogen bonds : bond 0.04151 / 2.81 ( 1816) hydrogen bonds : angle 4.69350 / 3.33 ( 4751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19416.46 seconds wall clock time: 329 minutes 49.79 seconds (19789.79 seconds total)