Starting phenix.real_space_refine on Fri Oct 30 12:38:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38jl_78858/10_2026/38jl_78858.cif Found real_map, /net/cci-nas-00/data/ceres_data/38jl_78858/10_2026/38jl_78858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/38jl_78858/10_2026/38jl_78858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38jl_78858/10_2026/38jl_78858.map" model { file = "/net/cci-nas-00/data/ceres_data/38jl_78858/10_2026/38jl_78858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38jl_78858/10_2026/38jl_78858.cif" } resolution = 2.29 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 233 5.16 5 C 22686 2.51 5 N 6015 2.21 5 O 6898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 35856 Number of models: 1 Model: "" Number of chains: 31 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: "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: 12.53, per 1000 atoms: 0.35 Number of scatterers: 35856 At special positions: 0 Unit cell: (123.37, 122.64, 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 233 16.00 P 16 15.00 Mg 8 11.99 O 6898 8.00 N 6015 7.00 C 22686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 2.6 seconds 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8590 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 60 sheets defined 43.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.927A 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 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: 3.874A 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 259 Processing helix chain 'A' and resid 260 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 287 through 290 removed outlier: 5.841A pdb=" N ASP A 290 " --> pdb=" O CYS A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.292A 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 351 through 357 removed outlier: 3.808A pdb=" N GLN A 356 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.954A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.611A pdb=" N GLN B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.982A 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 195 Processing helix chain 'B' and resid 196 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 259 Processing helix chain 'B' and resid 260 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 291 through 297 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 349 Processing helix chain 'B' and resid 350 through 351 No H-bonds generated for 'chain 'B' and resid 350 through 351' Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.775A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.953A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.554A pdb=" N GLN C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.878A 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: 3.756A 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 349 Processing helix chain 'C' and resid 350 through 351 No H-bonds generated for 'chain 'C' and resid 350 through 351' Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.743A 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: 4.013A pdb=" N ARG C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.616A pdb=" N GLN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.971A 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: 3.770A 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 254 through 259 Processing helix chain 'D' and resid 260 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 Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.344A 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 350 Processing helix chain 'D' and resid 351 through 357 removed outlier: 4.154A pdb=" N GLN D 356 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.769A pdb=" N ARG D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.700A pdb=" N GLN E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.891A 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 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: 3.731A 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 287 through 290 removed outlier: 5.907A pdb=" N ASP E 290 " --> pdb=" O CYS E 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 287 through 290' Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 303 through 307 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 357 removed outlier: 3.910A pdb=" N GLN E 356 " --> pdb=" O THR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 367 Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.830A pdb=" N ARG E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.628A pdb=" N GLN F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.941A 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 Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.671A 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 231 Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 260 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 288 through 290 No H-bonds generated for 'chain 'F' and resid 288 through 290' Processing helix chain 'F' and resid 291 through 297 removed outlier: 3.602A pdb=" N ALA F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 308 removed outlier: 4.236A 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 349 Processing helix chain 'F' and resid 350 through 351 No H-bonds generated for 'chain 'F' and resid 350 through 351' Processing helix chain 'F' and resid 352 through 358 removed outlier: 3.692A pdb=" N GLN F 356 " --> pdb=" O THR F 353 " (cutoff:3.500A) removed outlier: 3.807A 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: 3.833A pdb=" N ARG F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.758A pdb=" N GLN G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.666A 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: 3.611A 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: 3.734A 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 232 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: 3.697A pdb=" N ALA G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 308 removed outlier: 4.269A 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 349 Processing helix chain 'G' and resid 350 through 351 No H-bonds generated for 'chain 'G' and resid 350 through 351' Processing helix chain 'G' and resid 352 through 358 removed outlier: 3.756A pdb=" N GLN G 356 " --> pdb=" O THR G 353 " (cutoff:3.500A) removed outlier: 3.696A 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: 3.835A pdb=" N ARG G 374 " --> pdb=" O SER G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 63 removed outlier: 3.543A pdb=" N GLN H 61 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.752A 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 148 removed outlier: 3.511A pdb=" N GLY H 148 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 removed outlier: 3.532A pdb=" N ILE H 177 " --> pdb=" O PRO H 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 183 through 196 removed outlier: 3.725A 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 231 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 removed outlier: 3.552A pdb=" N ALA H 297 " --> pdb=" O LYS H 293 " (cutoff:3.500A) 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 349 Processing helix chain 'H' and resid 350 through 351 No H-bonds generated for 'chain 'H' and resid 350 through 351' Processing helix chain 'H' and resid 352 through 358 removed outlier: 3.517A pdb=" N GLN H 356 " --> pdb=" O THR H 353 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.769A 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 removed outlier: 3.532A pdb=" N ALA X 405 " --> pdb=" O SER X 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.996A pdb=" N LYS a 12 " --> pdb=" O ASP a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 61 removed outlier: 3.717A pdb=" N PHE a 53 " --> pdb=" O PRO a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 122 removed outlier: 4.750A pdb=" N ARG a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 5.019A 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: 3.892A pdb=" N LYS b 12 " --> pdb=" O ASP b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 61 removed outlier: 3.748A pdb=" N PHE b 53 " --> pdb=" O PRO b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 122 removed outlier: 4.811A pdb=" N ARG b 115 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 5.104A 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 Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.881A pdb=" N LYS c 12 " --> pdb=" O ASP c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 61 removed outlier: 3.623A pdb=" N PHE c 53 " --> pdb=" O PRO c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 122 removed outlier: 4.896A pdb=" N ARG c 115 " --> pdb=" O ALA c 111 " (cutoff:3.500A) removed outlier: 5.081A 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 149 Processing helix chain 'd' and resid 8 through 21 removed outlier: 3.924A pdb=" N LYS d 12 " --> pdb=" O ASP d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 61 removed outlier: 3.714A pdb=" N PHE d 53 " --> pdb=" O PRO d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 122 removed outlier: 4.836A pdb=" N ARG d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) removed outlier: 5.092A 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: 3.537A pdb=" N ASN d 149 " --> pdb=" O ASP d 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 21 removed outlier: 4.014A pdb=" N LYS e 12 " --> pdb=" O ASP e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 61 removed outlier: 3.649A pdb=" N PHE e 53 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 removed outlier: 4.695A pdb=" N ARG e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 5.044A 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 removed outlier: 3.697A pdb=" N GLN e 150 " --> pdb=" O LEU e 146 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 20 removed outlier: 3.988A pdb=" N LYS f 12 " --> pdb=" O ASP f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 49 through 61 removed outlier: 3.559A pdb=" N PHE f 53 " --> pdb=" O PRO f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 122 removed outlier: 4.807A pdb=" N ARG f 115 " --> pdb=" O ALA f 111 " (cutoff:3.500A) removed outlier: 4.921A 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: 6.626A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N CYS A 12 " --> 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: 6.475A 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: 6.516A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.025A 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: 6.442A 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: 6.530A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 7.957A 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: 6.357A 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: 6.567A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.032A 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: 6.515A 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: 6.513A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 8.395A 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: 6.476A 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: 6.639A pdb=" N LEU F 10 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR F 108 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 7.982A 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: 6.392A 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: 6.635A pdb=" N LEU G 10 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR G 108 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 7.882A 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: 6.459A 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: 3.534A pdb=" N THR H 108 " --> pdb=" O CYS H 12 " (cutoff:3.500A) removed outlier: 4.778A 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: 6.421A 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: 5.669A pdb=" N GLN X 6 " --> pdb=" O ASN X 608 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN X 608 " --> pdb=" O GLN X 6 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA X 8 " --> pdb=" O PHE X 606 " (cutoff:3.500A) removed outlier: 6.602A 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: 6.830A pdb=" N GLY X 77 " --> pdb=" O THR X 63 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA X 65 " --> pdb=" O ALA X 75 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA X 75 " --> pdb=" O ALA X 65 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR X 67 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR X 73 " --> pdb=" O THR X 67 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN X 82 " --> pdb=" O ASP X 78 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR X 97 " --> pdb=" O ILE X 85 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP X 87 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU X 95 " --> pdb=" O ASP X 87 " (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: 5.646A pdb=" N GLU X 176 " --> pdb=" O PHE X 182 " (cutoff:3.500A) removed outlier: 5.639A 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: 4.450A pdb=" N ILE X 214 " --> pdb=" O PHE X 228 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN X 218 " --> pdb=" O LYS X 224 " (cutoff:3.500A) removed outlier: 6.431A 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: 3.629A pdb=" N GLY X 244 " --> pdb=" O ALA X 257 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR X 262 " --> pdb=" O SER X 258 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE X 263 " --> pdb=" O THR X 276 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR X 276 " --> pdb=" O ILE X 263 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE X 265 " --> pdb=" O GLU X 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS X 272 " --> pdb=" O ASN X 267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 287 through 292 removed outlier: 3.786A pdb=" N GLY X 289 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU X 297 " --> pdb=" O VAL X 309 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE X 306 " --> pdb=" O VAL X 319 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL X 319 " --> pdb=" O ILE X 306 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE X 308 " --> pdb=" O ASP X 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER X 315 " --> 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: 3.712A pdb=" N GLY X 372 " --> pdb=" O VAL X 384 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.597A pdb=" N GLY X 416 " --> pdb=" O ALA X 429 " (cutoff:3.500A) removed outlier: 3.827A 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: 6.799A pdb=" N GLY X 466 " --> pdb=" O SER X 452 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL X 454 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA X 464 " --> pdb=" O VAL X 454 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU X 456 " --> pdb=" O PHE X 462 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE X 462 " --> pdb=" O LEU X 456 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS X 471 " --> pdb=" O GLY X 467 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS X 476 " --> pdb=" O GLU X 484 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU X 484 " --> pdb=" O LYS X 476 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER X 478 " --> pdb=" O VAL X 482 " (cutoff:3.500A) removed outlier: 5.151A 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: 3.681A pdb=" N SER X 496 " --> pdb=" O THR X 509 " (cutoff:3.500A) removed outlier: 3.701A 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 'a' and resid 6 through 7 removed outlier: 7.011A pdb=" N LYS a 6 " --> pdb=" O ILE a 38 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N VAL a 40 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL a 40 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS a 30 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE a 127 " --> pdb=" O VAL a 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'b' and resid 6 through 7 removed outlier: 6.858A pdb=" N LYS b 6 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N VAL b 40 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL b 40 " --> pdb=" O LYS b 30 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS b 30 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE b 127 " --> pdb=" O VAL b 92 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.049A pdb=" N LYS c 6 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N VAL c 40 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL c 40 " --> pdb=" O LYS c 30 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS c 30 " --> pdb=" O VAL c 40 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE c 127 " --> pdb=" O VAL c 92 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'd' and resid 6 through 7 removed outlier: 6.850A pdb=" N LYS d 6 " --> pdb=" O ILE d 38 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N VAL d 40 " --> pdb=" O LYS d 6 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL d 40 " --> pdb=" O LYS d 30 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS d 30 " --> pdb=" O VAL d 40 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE d 127 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 6 through 7 removed outlier: 6.959A pdb=" N LYS e 6 " --> pdb=" O ILE e 38 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N VAL e 40 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL e 40 " --> pdb=" O LYS e 30 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS e 30 " --> pdb=" O VAL e 40 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE e 127 " --> pdb=" O VAL e 92 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'f' and resid 6 through 7 removed outlier: 6.996A pdb=" N LYS f 6 " --> pdb=" O ILE f 38 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N VAL f 40 " --> pdb=" O LYS f 6 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL f 40 " --> pdb=" O LYS f 30 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS f 30 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE f 127 " --> pdb=" O VAL f 92 " (cutoff:3.500A) 1681 hydrogen bonds defined for protein. 4295 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: 9.27 Time building geometry restraints manager: 3.83 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: 11356 1.34 - 1.46: 5873 1.46 - 1.58: 19025 1.58 - 1.70: 24 1.70 - 1.82: 403 Bond restraints: 36681 Sorted by residual: bond pdb=" C4 ADP D 400 " pdb=" C5 ADP D 400 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C4 ADP B 400 " pdb=" C5 ADP B 400 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C4 ADP F 400 " pdb=" C5 ADP F 400 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C4 ADP C 400 " pdb=" C5 ADP C 400 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C4 ADP E 400 " pdb=" C5 ADP E 400 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.61e+00 ... (remaining 36676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 48441 1.45 - 2.90: 1183 2.90 - 4.36: 224 4.36 - 5.81: 58 5.81 - 7.26: 26 Bond angle restraints: 49932 Sorted by residual: angle pdb=" N VAL X 365 " pdb=" CA VAL X 365 " pdb=" C VAL X 365 " ideal model delta sigma weight residual 112.96 106.58 6.38 1.00e+00 1.00e+00 4.07e+01 angle pdb=" N GLU b 55 " pdb=" CA GLU b 55 " pdb=" CB GLU b 55 " ideal model delta sigma weight residual 110.28 115.59 -5.31 1.55e+00 4.16e-01 1.17e+01 angle pdb=" N ASP X 260 " pdb=" CA ASP X 260 " pdb=" C ASP X 260 " ideal model delta sigma weight residual 113.15 109.27 3.88 1.19e+00 7.06e-01 1.06e+01 angle pdb=" C PRO X 363 " pdb=" N ASP X 364 " pdb=" CA ASP X 364 " ideal model delta sigma weight residual 122.19 129.38 -7.19 2.30e+00 1.89e-01 9.76e+00 angle pdb=" CB ARG C 374 " pdb=" CG ARG C 374 " pdb=" CD ARG C 374 " ideal model delta sigma weight residual 111.30 117.52 -6.22 2.30e+00 1.89e-01 7.31e+00 ... (remaining 49927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 21176 17.69 - 35.37: 998 35.37 - 53.05: 172 53.05 - 70.74: 44 70.74 - 88.42: 35 Dihedral angle restraints: 22425 sinusoidal: 8935 harmonic: 13490 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 27.67 -87.67 1 2.00e+01 2.50e-03 2.30e+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 23.82 -83.81 1 2.00e+01 2.50e-03 2.14e+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 23.47 -83.47 1 2.00e+01 2.50e-03 2.13e+01 ... (remaining 22422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3790 0.043 - 0.085: 1276 0.085 - 0.128: 498 0.128 - 0.171: 42 0.171 - 0.214: 7 Chirality restraints: 5613 Sorted by residual: chirality pdb=" CB BILE D 73 " pdb=" CA BILE D 73 " pdb=" CG1BILE D 73 " pdb=" CG2BILE D 73 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB BILE E 73 " pdb=" CA BILE E 73 " pdb=" CG1BILE E 73 " pdb=" CG2BILE E 73 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 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 2.45 0.20 2.00e-01 2.50e+01 9.86e-01 ... (remaining 5610 not shown) Planarity restraints: 6412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 165 " 0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO G 166 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO G 166 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 166 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE X 516 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO X 517 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO X 517 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO X 517 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 244 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO G 245 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 245 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 245 " -0.024 5.00e-02 4.00e+02 ... (remaining 6409 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 52 2.52 - 3.11: 26601 3.11 - 3.71: 54996 3.71 - 4.30: 84557 4.30 - 4.90: 138806 Nonbonded interactions: 305012 Sorted by model distance: nonbonded pdb="MG MG D 401 " pdb=" O HOH D 503 " model vdw 1.925 2.170 nonbonded pdb="MG MG F 401 " pdb=" O HOH F 502 " model vdw 1.925 2.170 nonbonded pdb="MG MG H 401 " pdb=" O HOH H 501 " model vdw 1.932 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 502 " model vdw 1.939 2.170 nonbonded pdb="MG MG E 401 " pdb=" O HOH E 503 " model vdw 1.948 2.170 ... (remaining 305007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 '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=0.20 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: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 41.910 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9238 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36681 Z= 0.169 Angle : 0.601 7.260 49932 Z= 0.317 Chirality : 0.048 0.214 5613 Planarity : 0.004 0.064 6412 Dihedral : 11.500 88.425 13835 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.25 % Allowed : 0.69 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.26 (0.13), residues: 4576 helix: 0.88 (0.13), residues: 1580 sheet: 0.71 (0.16), residues: 1036 loop : 1.13 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 107 TYR 0.019 0.002 TYR d 69 PHE 0.018 0.002 PHE c 29 TRP 0.020 0.002 TRP X 111 HIS 0.005 0.001 HIS X 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (36681) covalent geometry : angle 0.60133 / 0.32 (49932) hydrogen bonds : bond 0.13780 / 9.07 ( 1665) hydrogen bonds : angle 6.17280 / 4.37 ( 4295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: B 357 MET cc_start: 0.9259 (mmm) cc_final: 0.9011 (mmm) REVERT: D 49 MET cc_start: 0.5705 (pmm) cc_final: 0.5146 (tmm) REVERT: E 357 MET cc_start: 0.8903 (mmm) cc_final: 0.8481 (mmm) REVERT: F 357 MET cc_start: 0.8757 (mmm) cc_final: 0.8477 (mtp) REVERT: G 42 HIS cc_start: 0.7313 (m-70) cc_final: 0.7023 (m-70) REVERT: H 285 MET cc_start: 0.8720 (mmm) cc_final: 0.8516 (mmm) REVERT: a 1 MET cc_start: 0.4786 (ttp) cc_final: 0.3763 (mmt) REVERT: a 145 ASP cc_start: 0.8788 (m-30) cc_final: 0.8471 (m-30) REVERT: b 8 ASP cc_start: 0.8550 (t70) cc_final: 0.8231 (t0) REVERT: b 65 LYS cc_start: 0.7627 (mppt) cc_final: 0.6629 (tptt) REVERT: d 1 MET cc_start: 0.5178 (ttp) cc_final: 0.3860 (mpt) REVERT: e 1 MET cc_start: 0.4630 (ttp) cc_final: 0.2905 (mpt) REVERT: e 13 ASN cc_start: 0.8822 (m-40) cc_final: 0.8611 (m-40) REVERT: f 73 ASP cc_start: 0.7806 (t0) cc_final: 0.7454 (t0) REVERT: f 90 ASN cc_start: 0.8623 (m-40) cc_final: 0.8170 (m-40) REVERT: f 136 ASP cc_start: 0.8711 (m-30) cc_final: 0.8451 (m-30) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.8293 time to fit residues: 304.5221 Evaluate side-chains 259 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 164 ASN B 227 ASN D 164 ASN D 248 GLN D 355 GLN E 43 GLN E 164 ASN E 227 ASN H 163 HIS ** H 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 ASN a 96 GLN b 34 ASN b 128 GLN c 13 ASN c 128 GLN c 150 GLN d 13 ASN d 23 GLN d 149 ASN e 23 GLN e 81 GLN f 13 ASN f 20 ASN f 79 GLN f 96 GLN f 128 GLN f 149 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.080436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049185 restraints weight = 465670.081| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 5.52 r_work: 0.2558 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 36681 Z= 0.246 Angle : 0.606 7.925 49932 Z= 0.309 Chirality : 0.049 0.229 5613 Planarity : 0.005 0.054 6412 Dihedral : 6.115 86.501 5204 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.74 % Allowed : 4.17 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.37 (0.13), residues: 4576 helix: 1.03 (0.13), residues: 1612 sheet: 0.65 (0.16), residues: 1044 loop : 1.22 (0.16), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 374 TYR 0.020 0.002 TYR c 69 PHE 0.020 0.002 PHE F 377 TRP 0.017 0.002 TRP H 81 HIS 0.008 0.001 HIS E 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (36681) covalent geometry : angle 0.60567 / 0.31 (49932) hydrogen bonds : bond 0.04688 / 3.13 ( 1665) hydrogen bonds : angle 4.86816 / 3.45 ( 4295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 357 MET cc_start: 0.9239 (mmm) cc_final: 0.8781 (mmm) REVERT: D 49 MET cc_start: 0.5808 (pmm) cc_final: 0.5071 (tmm) REVERT: E 46 MET cc_start: 0.5422 (mpp) cc_final: 0.4178 (mmm) REVERT: E 357 MET cc_start: 0.8913 (mmm) cc_final: 0.8317 (mmm) REVERT: E 374 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7858 (mtt-85) REVERT: F 357 MET cc_start: 0.8763 (mmm) cc_final: 0.8321 (mtp) REVERT: G 42 HIS cc_start: 0.7706 (m-70) cc_final: 0.7257 (m-70) REVERT: H 285 MET cc_start: 0.8555 (mmm) cc_final: 0.8340 (mmm) REVERT: H 327 MET cc_start: 0.6852 (mmm) cc_final: 0.6369 (mmt) REVERT: a 1 MET cc_start: 0.5006 (ttp) cc_final: 0.3315 (mmt) REVERT: a 145 ASP cc_start: 0.8847 (m-30) cc_final: 0.8522 (m-30) REVERT: b 8 ASP cc_start: 0.8538 (t70) cc_final: 0.7993 (t0) REVERT: b 65 LYS cc_start: 0.7846 (mppt) cc_final: 0.6562 (tptt) REVERT: c 57 MET cc_start: 0.9141 (tpt) cc_final: 0.8840 (tpt) REVERT: d 1 MET cc_start: 0.5090 (ttp) cc_final: 0.3706 (mpt) REVERT: e 1 MET cc_start: 0.4571 (ttp) cc_final: 0.2709 (mpt) REVERT: e 13 ASN cc_start: 0.8644 (m-40) cc_final: 0.8432 (m-40) REVERT: f 73 ASP cc_start: 0.7543 (t0) cc_final: 0.7019 (t0) REVERT: f 90 ASN cc_start: 0.8482 (m-40) cc_final: 0.7971 (m-40) REVERT: f 136 ASP cc_start: 0.8548 (m-30) cc_final: 0.8223 (m-30) REVERT: f 145 ASP cc_start: 0.8897 (m-30) cc_final: 0.8657 (m-30) outliers start: 14 outliers final: 4 residues processed: 270 average time/residue: 0.7931 time to fit residues: 254.8680 Evaluate side-chains 260 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 255 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 374 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [75, 281, 273, 194, 430, 343, 149, 112, 374, 300, 269] chunk 75 optimal weight: 1.9990 chunk 281 optimal weight: 20.0000 chunk 273 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 430 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 374 optimal weight: 2.9990 chunk 300 optimal weight: 0.3980 chunk 269 optimal weight: 0.0980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 13 ASN ** e 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.082045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050910 restraints weight = 458490.040| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 5.58 r_work: 0.2606 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36681 Z= 0.109 Angle : 0.520 8.490 49932 Z= 0.261 Chirality : 0.045 0.163 5613 Planarity : 0.004 0.048 6412 Dihedral : 5.756 78.307 5204 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.76 % Allowed : 4.85 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.60 (0.13), residues: 4576 helix: 1.23 (0.13), residues: 1612 sheet: 0.78 (0.16), residues: 1020 loop : 1.33 (0.16), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 374 TYR 0.017 0.001 TYR e 50 PHE 0.015 0.001 PHE c 29 TRP 0.015 0.001 TRP H 81 HIS 0.003 0.001 HIS H 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (36681) covalent geometry : angle 0.52040 / 0.26 (49932) hydrogen bonds : bond 0.03617 / 2.41 ( 1665) hydrogen bonds : angle 4.55443 / 3.22 ( 4295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 264 time to evaluate : 1.369 Fit side-chains REVERT: A 374 ARG cc_start: 0.8746 (ptp-110) cc_final: 0.8427 (mtp-110) REVERT: B 357 MET cc_start: 0.9237 (mmm) cc_final: 0.8716 (mmm) REVERT: D 49 MET cc_start: 0.5948 (pmm) cc_final: 0.5151 (tmm) REVERT: E 46 MET cc_start: 0.5560 (mpp) cc_final: 0.4641 (mmm) REVERT: E 357 MET cc_start: 0.8892 (mmm) cc_final: 0.8281 (mmm) REVERT: E 374 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7820 (mtt-85) REVERT: F 357 MET cc_start: 0.8774 (mmm) cc_final: 0.8352 (mtp) REVERT: G 42 HIS cc_start: 0.7650 (m-70) cc_final: 0.7122 (m-70) REVERT: H 285 MET cc_start: 0.8535 (mmm) cc_final: 0.8333 (mmm) REVERT: a 1 MET cc_start: 0.5025 (ttp) cc_final: 0.3674 (mpp) REVERT: a 145 ASP cc_start: 0.8807 (m-30) cc_final: 0.8471 (m-30) REVERT: b 8 ASP cc_start: 0.8510 (t70) cc_final: 0.8096 (t0) REVERT: b 65 LYS cc_start: 0.7708 (mppt) cc_final: 0.6471 (tptt) REVERT: d 1 MET cc_start: 0.5212 (ttp) cc_final: 0.3544 (mpt) REVERT: e 1 MET cc_start: 0.4593 (ttp) cc_final: 0.2569 (mpt) REVERT: e 13 ASN cc_start: 0.8662 (m-40) cc_final: 0.8460 (m-40) REVERT: e 138 ASP cc_start: 0.8571 (t70) cc_final: 0.8204 (t0) REVERT: f 49 PRO cc_start: 0.8047 (Cg_exo) cc_final: 0.7844 (Cg_endo) REVERT: f 73 ASP cc_start: 0.7541 (t0) cc_final: 0.7024 (t0) REVERT: f 90 ASN cc_start: 0.8469 (m-40) cc_final: 0.7968 (m-40) REVERT: f 136 ASP cc_start: 0.8567 (m-30) cc_final: 0.8201 (m-30) REVERT: f 145 ASP cc_start: 0.8909 (m-30) cc_final: 0.8670 (m-30) outliers start: 14 outliers final: 3 residues processed: 268 average time/residue: 0.7633 time to fit residues: 243.2847 Evaluate side-chains 259 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 255 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 374 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [164, 187, 221, 96, 46, 354, 37, 285, 256, 441, 242] chunk 164 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 354 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 441 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 13 ASN f 13 ASN f 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.080521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050118 restraints weight = 479500.239| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 5.28 r_work: 0.2581 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36681 Z= 0.177 Angle : 0.549 8.868 49932 Z= 0.277 Chirality : 0.047 0.214 5613 Planarity : 0.004 0.047 6412 Dihedral : 5.857 80.956 5204 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.71 % Allowed : 5.67 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.53 (0.13), residues: 4576 helix: 1.25 (0.13), residues: 1612 sheet: 0.64 (0.16), residues: 1058 loop : 1.30 (0.16), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 374 TYR 0.016 0.001 TYR c 69 PHE 0.017 0.001 PHE a 29 TRP 0.015 0.002 TRP H 81 HIS 0.004 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (36681) covalent geometry : angle 0.54895 / 0.28 (49932) hydrogen bonds : bond 0.04080 / 2.73 ( 1665) hydrogen bonds : angle 4.55442 / 3.22 ( 4295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 260 time to evaluate : 1.522 Fit side-chains REVERT: A 374 ARG cc_start: 0.8741 (ptp-110) cc_final: 0.8401 (mtp-110) REVERT: B 357 MET cc_start: 0.9225 (mmm) cc_final: 0.8749 (mmm) REVERT: C 41 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7779 (ttm-80) REVERT: C 49 MET cc_start: 0.4218 (ptm) cc_final: 0.3869 (ptt) REVERT: D 49 MET cc_start: 0.5942 (pmm) cc_final: 0.5156 (tmm) REVERT: E 46 MET cc_start: 0.5713 (mpp) cc_final: 0.4947 (mmm) REVERT: E 357 MET cc_start: 0.8898 (mmm) cc_final: 0.8287 (mmm) REVERT: E 374 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7817 (mtt-85) REVERT: F 46 MET cc_start: 0.2037 (tpt) cc_final: 0.1755 (tpp) REVERT: F 357 MET cc_start: 0.8769 (mmm) cc_final: 0.8346 (mtp) REVERT: G 42 HIS cc_start: 0.7622 (m-70) cc_final: 0.7122 (m-70) REVERT: H 327 MET cc_start: 0.7087 (mmm) cc_final: 0.6497 (mmt) REVERT: a 1 MET cc_start: 0.5378 (ttp) cc_final: 0.3969 (mpp) REVERT: a 145 ASP cc_start: 0.8825 (m-30) cc_final: 0.8491 (m-30) REVERT: b 8 ASP cc_start: 0.8491 (t70) cc_final: 0.8023 (t0) REVERT: b 65 LYS cc_start: 0.7854 (mppt) cc_final: 0.6537 (tptt) REVERT: d 1 MET cc_start: 0.5151 (ttp) cc_final: 0.3629 (mpt) REVERT: e 1 MET cc_start: 0.4648 (ttp) cc_final: 0.2766 (mpt) REVERT: e 13 ASN cc_start: 0.8678 (m-40) cc_final: 0.8462 (m-40) REVERT: e 138 ASP cc_start: 0.8559 (t70) cc_final: 0.8194 (t0) REVERT: f 73 ASP cc_start: 0.7529 (t0) cc_final: 0.6981 (t0) REVERT: f 90 ASN cc_start: 0.8459 (m-40) cc_final: 0.7957 (m-40) REVERT: f 136 ASP cc_start: 0.8556 (m-30) cc_final: 0.8232 (m-30) REVERT: f 145 ASP cc_start: 0.8906 (m-30) cc_final: 0.8668 (m-30) outliers start: 11 outliers final: 7 residues processed: 262 average time/residue: 0.7721 time to fit residues: 241.2200 Evaluate side-chains 264 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 256 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 374 ARG Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain e residue 149 ASN Chi-restraints excluded: chain f residue 57 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [271, 253, 127, 94, 304, 224, 37, 169, 190, 287, 108] chunk 271 optimal weight: 9.9990 chunk 253 optimal weight: 0.3980 chunk 127 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 13 ASN ** e 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.049088 restraints weight = 480248.064| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 5.51 r_work: 0.2559 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 36681 Z= 0.201 Angle : 0.564 8.300 49932 Z= 0.285 Chirality : 0.048 0.218 5613 Planarity : 0.004 0.047 6412 Dihedral : 6.019 84.340 5204 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.86 % Allowed : 5.89 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.47 (0.13), residues: 4576 helix: 1.20 (0.13), residues: 1612 sheet: 0.62 (0.16), residues: 1058 loop : 1.26 (0.16), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 374 TYR 0.016 0.001 TYR c 69 PHE 0.018 0.001 PHE c 29 TRP 0.018 0.002 TRP H 81 HIS 0.004 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (36681) covalent geometry : angle 0.56374 / 0.28 (49932) hydrogen bonds : bond 0.04274 / 2.85 ( 1665) hydrogen bonds : angle 4.55472 / 3.22 ( 4295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 259 time to evaluate : 1.572 Fit side-chains REVERT: A 374 ARG cc_start: 0.8741 (ptp-110) cc_final: 0.8402 (mtp-110) REVERT: B 357 MET cc_start: 0.9249 (mmm) cc_final: 0.8754 (mmm) REVERT: C 49 MET cc_start: 0.4505 (ptm) cc_final: 0.4198 (ptt) REVERT: D 49 MET cc_start: 0.5948 (pmm) cc_final: 0.5194 (tmm) REVERT: E 46 MET cc_start: 0.5780 (mpp) cc_final: 0.5111 (mmm) REVERT: E 357 MET cc_start: 0.8910 (mmm) cc_final: 0.8287 (mmm) REVERT: E 374 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7833 (mtt-85) REVERT: F 46 MET cc_start: 0.2001 (tpt) cc_final: 0.1727 (tpp) REVERT: F 357 MET cc_start: 0.8792 (mmm) cc_final: 0.8320 (mtp) REVERT: G 42 HIS cc_start: 0.7692 (m-70) cc_final: 0.7181 (m-70) REVERT: a 1 MET cc_start: 0.5584 (ttp) cc_final: 0.4045 (mpp) REVERT: a 145 ASP cc_start: 0.8855 (m-30) cc_final: 0.8528 (m-30) REVERT: b 8 ASP cc_start: 0.8495 (t70) cc_final: 0.7981 (t0) REVERT: b 65 LYS cc_start: 0.8021 (mppt) cc_final: 0.6635 (tptt) REVERT: d 1 MET cc_start: 0.5175 (ttp) cc_final: 0.3641 (mpt) REVERT: e 1 MET cc_start: 0.4748 (ttp) cc_final: 0.2909 (mpt) REVERT: e 13 ASN cc_start: 0.8691 (m-40) cc_final: 0.8473 (m-40) REVERT: e 138 ASP cc_start: 0.8556 (t70) cc_final: 0.8204 (t0) REVERT: f 73 ASP cc_start: 0.7520 (t0) cc_final: 0.6989 (t0) REVERT: f 90 ASN cc_start: 0.8442 (m-40) cc_final: 0.7940 (m-40) REVERT: f 136 ASP cc_start: 0.8543 (m-30) cc_final: 0.8234 (m-30) REVERT: f 145 ASP cc_start: 0.8903 (m-30) cc_final: 0.8663 (m-30) outliers start: 14 outliers final: 9 residues processed: 263 average time/residue: 0.7545 time to fit residues: 236.1824 Evaluate side-chains 267 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 257 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 374 ARG Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain e residue 149 ASN Chi-restraints excluded: chain f residue 57 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [184, 346, 385, 163, 87, 265, 423, 399, 279, 11, 309] chunk 184 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 385 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 423 optimal weight: 9.9990 chunk 399 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 309 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 13 ASN ** e 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN f 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.079630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.048536 restraints weight = 464042.416| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 5.45 r_work: 0.2545 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 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: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 36681 Z= 0.240 Angle : 0.588 10.865 49932 Z= 0.298 Chirality : 0.049 0.229 5613 Planarity : 0.004 0.048 6412 Dihedral : 6.220 87.302 5204 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.78 % Rotamer: Outliers : 0.97 % Allowed : 6.15 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.39 (0.13), residues: 4576 helix: 1.14 (0.13), residues: 1612 sheet: 0.58 (0.16), residues: 1064 loop : 1.20 (0.16), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 374 TYR 0.017 0.001 TYR c 69 PHE 0.019 0.002 PHE c 29 TRP 0.018 0.002 TRP H 81 HIS 0.005 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (36681) covalent geometry : angle 0.58835 / 0.30 (49932) hydrogen bonds : bond 0.04571 / 3.06 ( 1665) hydrogen bonds : angle 4.59578 / 3.24 ( 4295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 1.377 Fit side-chains REVERT: A 374 ARG cc_start: 0.8799 (ptp-110) cc_final: 0.8439 (mtp-110) REVERT: B 357 MET cc_start: 0.9246 (mmm) cc_final: 0.8738 (mmm) REVERT: D 49 MET cc_start: 0.5882 (pmm) cc_final: 0.5175 (tmm) REVERT: E 46 MET cc_start: 0.5889 (mpp) cc_final: 0.5335 (mmm) REVERT: E 357 MET cc_start: 0.8918 (mmm) cc_final: 0.8288 (mmm) REVERT: E 374 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7857 (mtt-85) REVERT: F 357 MET cc_start: 0.8788 (mmm) cc_final: 0.8323 (mtp) REVERT: G 42 HIS cc_start: 0.7773 (m-70) cc_final: 0.7251 (m-70) REVERT: H 327 MET cc_start: 0.7119 (mmm) cc_final: 0.6616 (mmt) REVERT: H 357 MET cc_start: 0.8158 (ptp) cc_final: 0.7931 (ptp) REVERT: X 369 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8740 (ttp) REVERT: a 1 MET cc_start: 0.5684 (ttp) cc_final: 0.4251 (mpp) REVERT: a 145 ASP cc_start: 0.8876 (m-30) cc_final: 0.8574 (m-30) REVERT: b 8 ASP cc_start: 0.8536 (t70) cc_final: 0.7930 (t0) REVERT: b 65 LYS cc_start: 0.8148 (mppt) cc_final: 0.6746 (tptt) REVERT: d 1 MET cc_start: 0.5343 (ttp) cc_final: 0.3700 (mpt) REVERT: e 1 MET cc_start: 0.4800 (ttp) cc_final: 0.3088 (mpt) REVERT: e 13 ASN cc_start: 0.8680 (m-40) cc_final: 0.8459 (m-40) REVERT: e 138 ASP cc_start: 0.8579 (t70) cc_final: 0.8207 (t0) REVERT: f 1 MET cc_start: 0.4238 (mpp) cc_final: 0.4026 (mpt) REVERT: f 73 ASP cc_start: 0.7515 (t0) cc_final: 0.6993 (t0) REVERT: f 90 ASN cc_start: 0.8425 (m-40) cc_final: 0.7923 (m-40) REVERT: f 136 ASP cc_start: 0.8548 (m-30) cc_final: 0.8253 (m-30) REVERT: f 145 ASP cc_start: 0.8891 (m-30) cc_final: 0.8651 (m-30) outliers start: 15 outliers final: 9 residues processed: 264 average time/residue: 0.7761 time to fit residues: 243.3101 Evaluate side-chains 266 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 255 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 374 ARG Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain e residue 149 ASN Chi-restraints excluded: chain f residue 57 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [233, 23, 11, 156, 78, 359, 128, 373, 341, 318, 261] chunk 233 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 359 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 373 optimal weight: 4.9990 chunk 341 optimal weight: 9.9990 chunk 318 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 373 HIS c 13 ASN ** e 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN f 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050405 restraints weight = 469612.795| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 5.37 r_work: 0.2593 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36681 Z= 0.120 Angle : 0.524 9.304 49932 Z= 0.262 Chirality : 0.045 0.173 5613 Planarity : 0.004 0.047 6412 Dihedral : 5.860 78.689 5204 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.89 % Favored : 98.09 % Rotamer: Outliers : 0.94 % Allowed : 6.22 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.52 (0.13), residues: 4576 helix: 1.30 (0.13), residues: 1612 sheet: 0.61 (0.16), residues: 1058 loop : 1.25 (0.16), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 374 TYR 0.013 0.001 TYR e 50 PHE 0.015 0.001 PHE c 29 TRP 0.016 0.002 TRP H 81 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (36681) covalent geometry : angle 0.52365 / 0.26 (49932) hydrogen bonds : bond 0.03541 / 2.37 ( 1665) hydrogen bonds : angle 4.38881 / 3.10 ( 4295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 1.484 Fit side-chains REVERT: A 374 ARG cc_start: 0.8781 (ptp-110) cc_final: 0.8408 (mtp-110) REVERT: B 357 MET cc_start: 0.9239 (mmm) cc_final: 0.8722 (mmm) REVERT: D 49 MET cc_start: 0.5965 (pmm) cc_final: 0.5183 (tmm) REVERT: E 46 MET cc_start: 0.5838 (mpp) cc_final: 0.5349 (mmm) REVERT: E 357 MET cc_start: 0.8894 (mmm) cc_final: 0.8242 (mmm) REVERT: E 374 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7943 (mtm180) REVERT: F 46 MET cc_start: 0.1989 (tpt) cc_final: 0.1711 (tpp) REVERT: F 357 MET cc_start: 0.8788 (mmm) cc_final: 0.8268 (mtp) REVERT: G 42 HIS cc_start: 0.7715 (m-70) cc_final: 0.7115 (m-70) REVERT: H 327 MET cc_start: 0.7218 (mmm) cc_final: 0.6641 (mmt) REVERT: H 357 MET cc_start: 0.8144 (ptp) cc_final: 0.7917 (ptp) REVERT: X 369 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8833 (ttp) REVERT: a 1 MET cc_start: 0.5699 (ttp) cc_final: 0.4536 (mpp) REVERT: a 145 ASP cc_start: 0.8829 (m-30) cc_final: 0.8515 (m-30) REVERT: b 65 LYS cc_start: 0.8000 (mppt) cc_final: 0.6602 (tptt) REVERT: d 1 MET cc_start: 0.5173 (ttp) cc_final: 0.3590 (mpt) REVERT: e 1 MET cc_start: 0.4805 (ttp) cc_final: 0.2927 (mpt) REVERT: e 13 ASN cc_start: 0.8704 (m-40) cc_final: 0.8499 (m-40) REVERT: e 138 ASP cc_start: 0.8536 (t70) cc_final: 0.8189 (t0) REVERT: f 1 MET cc_start: 0.4135 (mpp) cc_final: 0.3933 (mpt) REVERT: f 73 ASP cc_start: 0.7525 (t0) cc_final: 0.6999 (t0) REVERT: f 90 ASN cc_start: 0.8448 (m-40) cc_final: 0.7932 (m-40) REVERT: f 136 ASP cc_start: 0.8522 (m-30) cc_final: 0.8251 (m-30) REVERT: f 145 ASP cc_start: 0.8898 (m-30) cc_final: 0.8664 (m-30) outliers start: 13 outliers final: 3 residues processed: 264 average time/residue: 0.7534 time to fit residues: 236.5423 Evaluate side-chains 262 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 257 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 374 ARG Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [312, 421, 234, 301, 158, 274, 49, 259, 431, 369, 432] chunk 312 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 301 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 274 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 259 optimal weight: 30.0000 chunk 431 optimal weight: 10.0000 chunk 369 optimal weight: 2.9990 chunk 432 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 373 HIS c 13 ASN e 81 GLN f 13 ASN f 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.078870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.047839 restraints weight = 477137.542| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 5.56 r_work: 0.2525 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 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: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 36681 Z= 0.319 Angle : 0.640 12.351 49932 Z= 0.324 Chirality : 0.052 0.268 5613 Planarity : 0.005 0.048 6412 Dihedral : 6.414 90.713 5204 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.97 % Allowed : 6.43 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 4576 helix: 1.07 (0.13), residues: 1612 sheet: 0.56 (0.16), residues: 1066 loop : 1.12 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 374 TYR 0.020 0.002 TYR c 69 PHE 0.022 0.002 PHE a 29 TRP 0.022 0.002 TRP H 81 HIS 0.006 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.32 (36681) covalent geometry : angle 0.63991 / 0.32 (49932) hydrogen bonds : bond 0.05045 / 3.38 ( 1665) hydrogen bonds : angle 4.67515 / 3.30 ( 4295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 256 time to evaluate : 1.420 Fit side-chains REVERT: A 374 ARG cc_start: 0.8800 (ptp-110) cc_final: 0.8434 (mtp-110) REVERT: B 357 MET cc_start: 0.9246 (mmm) cc_final: 0.8817 (mmm) REVERT: C 49 MET cc_start: 0.6441 (pmm) cc_final: 0.5933 (ptt) REVERT: D 49 MET cc_start: 0.5882 (pmm) cc_final: 0.5167 (tmm) REVERT: E 46 MET cc_start: 0.6156 (mpp) cc_final: 0.5821 (mmm) REVERT: E 66 ILE cc_start: 0.8489 (pt) cc_final: 0.8287 (pt) REVERT: E 357 MET cc_start: 0.8945 (mmm) cc_final: 0.8299 (mmm) REVERT: E 374 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7859 (mtt-85) REVERT: F 357 MET cc_start: 0.8794 (mmm) cc_final: 0.8289 (mtp) REVERT: G 42 HIS cc_start: 0.7817 (m-70) cc_final: 0.7295 (m-70) REVERT: H 327 MET cc_start: 0.7260 (mmm) cc_final: 0.6710 (mmt) REVERT: H 357 MET cc_start: 0.8139 (ptp) cc_final: 0.7901 (ptp) REVERT: X 369 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8726 (ttp) REVERT: a 1 MET cc_start: 0.5663 (ttp) cc_final: 0.4562 (mpp) REVERT: a 145 ASP cc_start: 0.8896 (m-30) cc_final: 0.8571 (m-30) REVERT: b 65 LYS cc_start: 0.8266 (mppt) cc_final: 0.6829 (tptt) REVERT: d 1 MET cc_start: 0.5388 (ttp) cc_final: 0.3685 (mpt) REVERT: e 1 MET cc_start: 0.4858 (ttp) cc_final: 0.3159 (mpt) REVERT: e 13 ASN cc_start: 0.8674 (m-40) cc_final: 0.8452 (m-40) REVERT: e 138 ASP cc_start: 0.8593 (t70) cc_final: 0.8230 (t0) REVERT: f 73 ASP cc_start: 0.7470 (t0) cc_final: 0.6955 (t0) REVERT: f 90 ASN cc_start: 0.8455 (m-40) cc_final: 0.7944 (m-40) REVERT: f 136 ASP cc_start: 0.8507 (m-30) cc_final: 0.8217 (m-30) outliers start: 13 outliers final: 5 residues processed: 260 average time/residue: 0.7633 time to fit residues: 236.1126 Evaluate side-chains 262 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 255 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 374 ARG Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain e residue 149 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [245, 103, 10, 69, 278, 317, 12, 411, 331, 408, 349] chunk 245 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 317 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 408 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 13 ASN e 81 GLN f 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.080696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050232 restraints weight = 466487.338| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 5.34 r_work: 0.2581 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36681 Z= 0.124 Angle : 0.544 12.953 49932 Z= 0.272 Chirality : 0.046 0.174 5613 Planarity : 0.004 0.050 6412 Dihedral : 6.073 83.128 5204 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 0.81 % Allowed : 6.68 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.42 (0.13), residues: 4576 helix: 1.25 (0.13), residues: 1612 sheet: 0.56 (0.16), residues: 1060 loop : 1.16 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 374 TYR 0.015 0.001 TYR f 15 PHE 0.015 0.001 PHE c 29 TRP 0.020 0.002 TRP H 81 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (36681) covalent geometry : angle 0.54449 / 0.27 (49932) hydrogen bonds : bond 0.03740 / 2.50 ( 1665) hydrogen bonds : angle 4.45312 / 3.14 ( 4295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 257 time to evaluate : 1.411 Fit side-chains REVERT: A 374 ARG cc_start: 0.8778 (ptp-110) cc_final: 0.8395 (mtp-110) REVERT: B 357 MET cc_start: 0.9232 (mmm) cc_final: 0.8734 (mmm) REVERT: B 374 ARG cc_start: 0.8824 (mtp-110) cc_final: 0.8616 (ptp90) REVERT: C 49 MET cc_start: 0.6390 (pmm) cc_final: 0.6015 (ptt) REVERT: C 357 MET cc_start: 0.8984 (mmm) cc_final: 0.8549 (mmm) REVERT: D 49 MET cc_start: 0.5895 (pmm) cc_final: 0.5152 (tmm) REVERT: E 46 MET cc_start: 0.6005 (mpp) cc_final: 0.5676 (mmm) REVERT: E 66 ILE cc_start: 0.8510 (pt) cc_final: 0.8298 (pt) REVERT: E 357 MET cc_start: 0.8910 (mmm) cc_final: 0.8243 (mmm) REVERT: E 374 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7951 (mtm180) REVERT: F 357 MET cc_start: 0.8767 (mmm) cc_final: 0.8279 (mtp) REVERT: G 42 HIS cc_start: 0.7748 (m-70) cc_final: 0.7216 (m-70) REVERT: H 134 MET cc_start: 0.7477 (ppp) cc_final: 0.6595 (ppp) REVERT: H 327 MET cc_start: 0.7235 (mmm) cc_final: 0.6701 (mmt) REVERT: H 357 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7899 (ptp) REVERT: X 369 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8835 (ttp) REVERT: a 1 MET cc_start: 0.5794 (ttp) cc_final: 0.4559 (mpp) REVERT: a 145 ASP cc_start: 0.8856 (m-30) cc_final: 0.8569 (m-30) REVERT: b 1 MET cc_start: 0.5125 (OUTLIER) cc_final: 0.3940 (mmt) REVERT: b 65 LYS cc_start: 0.8101 (mppt) cc_final: 0.6664 (tptt) REVERT: d 1 MET cc_start: 0.5239 (ttp) cc_final: 0.3679 (mpt) REVERT: e 1 MET cc_start: 0.4786 (ttp) cc_final: 0.2950 (mpt) REVERT: e 13 ASN cc_start: 0.8704 (m-40) cc_final: 0.8499 (m-40) REVERT: e 138 ASP cc_start: 0.8558 (t70) cc_final: 0.8189 (t0) REVERT: f 73 ASP cc_start: 0.7493 (t0) cc_final: 0.6979 (t0) REVERT: f 90 ASN cc_start: 0.8431 (m-40) cc_final: 0.7908 (m-40) REVERT: f 136 ASP cc_start: 0.8516 (m-30) cc_final: 0.8251 (m-30) outliers start: 7 outliers final: 2 residues processed: 258 average time/residue: 0.7742 time to fit residues: 237.8255 Evaluate side-chains 262 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 256 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 374 ARG Chi-restraints excluded: chain H residue 357 MET Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [26, 314, 374, 198, 116, 270, 176, 23, 389, 356, 126] chunk 26 optimal weight: 0.9980 chunk 314 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 389 optimal weight: 2.9990 chunk 356 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 13 ASN ** e 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN f 13 ASN f 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051137 restraints weight = 477634.275| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 5.24 r_work: 0.2608 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36681 Z= 0.111 Angle : 0.521 11.032 49932 Z= 0.258 Chirality : 0.045 0.170 5613 Planarity : 0.004 0.052 6412 Dihedral : 5.685 88.809 5204 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.78 % Rotamer: Outliers : 0.81 % Allowed : 6.81 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.60 (0.13), residues: 4576 helix: 1.37 (0.14), residues: 1612 sheet: 0.69 (0.16), residues: 1024 loop : 1.24 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 374 TYR 0.012 0.001 TYR e 50 PHE 0.014 0.001 PHE c 29 TRP 0.021 0.002 TRP H 81 HIS 0.002 0.000 HIS X 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (36681) covalent geometry : angle 0.52138 / 0.26 (49932) hydrogen bonds : bond 0.03296 / 2.21 ( 1665) hydrogen bonds : angle 4.29280 / 3.02 ( 4295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9152 Ramachandran restraints generated. 4576 Oldfield, 0 Emsley, 4576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 260 time to evaluate : 1.609 Fit side-chains REVERT: A 374 ARG cc_start: 0.8777 (ptp-110) cc_final: 0.8551 (ptm-80) REVERT: B 357 MET cc_start: 0.9198 (mmm) cc_final: 0.8653 (mmm) REVERT: C 49 MET cc_start: 0.6403 (pmm) cc_final: 0.6177 (ptt) REVERT: C 357 MET cc_start: 0.8949 (mmm) cc_final: 0.8488 (mmm) REVERT: D 49 MET cc_start: 0.5975 (pmm) cc_final: 0.5190 (tmm) REVERT: E 46 MET cc_start: 0.5823 (mpp) cc_final: 0.5546 (mmm) REVERT: E 357 MET cc_start: 0.8903 (mmm) cc_final: 0.8232 (mmm) REVERT: E 374 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7960 (mtm180) REVERT: F 357 MET cc_start: 0.8750 (mmm) cc_final: 0.8257 (mtp) REVERT: G 42 HIS cc_start: 0.7699 (m-70) cc_final: 0.7092 (m-70) REVERT: H 134 MET cc_start: 0.7453 (ppp) cc_final: 0.6610 (ppp) REVERT: H 327 MET cc_start: 0.7213 (mmm) cc_final: 0.6693 (mmt) REVERT: H 357 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7905 (ptp) REVERT: X 369 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8874 (ttp) REVERT: a 1 MET cc_start: 0.5786 (ttp) cc_final: 0.4458 (mpt) REVERT: a 145 ASP cc_start: 0.8831 (m-30) cc_final: 0.8542 (m-30) REVERT: b 65 LYS cc_start: 0.7937 (mppt) cc_final: 0.6549 (tptt) REVERT: d 1 MET cc_start: 0.5190 (ttp) cc_final: 0.3558 (mpt) REVERT: e 1 MET cc_start: 0.4847 (ttp) cc_final: 0.2960 (mpt) REVERT: e 13 ASN cc_start: 0.8691 (m-40) cc_final: 0.8488 (m-40) REVERT: e 138 ASP cc_start: 0.8518 (t70) cc_final: 0.8169 (t0) REVERT: f 73 ASP cc_start: 0.7523 (t0) cc_final: 0.7032 (t0) REVERT: f 90 ASN cc_start: 0.8456 (m-40) cc_final: 0.7966 (m-40) REVERT: f 136 ASP cc_start: 0.8499 (m-30) cc_final: 0.8193 (m-30) outliers start: 7 outliers final: 3 residues processed: 262 average time/residue: 0.7671 time to fit residues: 239.4786 Evaluate side-chains 263 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 257 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain E residue 374 ARG Chi-restraints excluded: chain H residue 357 MET Chi-restraints excluded: chain X residue 369 MET Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: [407, 23, 31, 94, 184, 437, 45, 403, 137, 300, 110] chunk 407 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 437 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 403 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 300 optimal weight: 6.9990 chunk 110 optimal weight: 0.0060 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 13 ASN e 81 GLN f 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.081340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050491 restraints weight = 492985.586| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 5.81 r_work: 0.2591 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36681 Z= 0.120 Angle : 0.528 11.940 49932 Z= 0.262 Chirality : 0.045 0.175 5613 Planarity : 0.004 0.052 6412 Dihedral : 5.676 89.569 5204 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.87 % Rotamer: Outliers : 0.81 % Allowed : 6.78 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 1.61 (0.13), residues: 4576 helix: 1.38 (0.14), residues: 1612 sheet: 0.70 (0.16), residues: 1024 loop : 1.25 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 374 TYR 0.012 0.001 TYR e 50 PHE 0.015 0.001 PHE b 29 TRP 0.019 0.002 TRP H 81 HIS 0.002 0.000 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (36681) covalent geometry : angle 0.52847 / 0.26 (49932) hydrogen bonds : bond 0.03429 / 2.30 ( 1665) hydrogen bonds : angle 4.29974 / 3.03 ( 4295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16985.67 seconds wall clock time: 288 minutes 41.65 seconds (17321.65 seconds total)