Starting phenix.real_space_refine on Sat Oct 31 07:08:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38kq_78884/10_2026/38kq_78884.cif Found real_map, /net/cci-nas-00/data/ceres_data/38kq_78884/10_2026/38kq_78884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/38kq_78884/10_2026/38kq_78884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38kq_78884/10_2026/38kq_78884.map" model { file = "/net/cci-nas-00/data/ceres_data/38kq_78884/10_2026/38kq_78884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38kq_78884/10_2026/38kq_78884.cif" } resolution = 2.86 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= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 242 5.16 5 C 25590 2.51 5 N 6804 2.21 5 O 7800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40460 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "B" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "C" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "D" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "E" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "F" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "G" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "H" Number of atoms: 2972 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2858 Chain: "X" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4604 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 584} Chain: "Y" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4604 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 584} Chain: "a" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "b" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "c" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "d" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "e" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "f" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Conformer: "B" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} bond proxies already assigned to first conformer: 1198 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 12.43, per 1000 atoms: 0.31 Number of scatterers: 40460 At special positions: 0 Unit cell: (123.37, 125.56, 267.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 242 16.00 P 16 15.00 Mg 8 11.99 O 7800 8.00 N 6804 7.00 C 25590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 2.9 seconds 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9708 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 75 sheets defined 37.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.642A pdb=" N GLN A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.752A pdb=" N ILE A 77 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.695A pdb=" N HIS A 103 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.831A 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 232 Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.522A pdb=" N CYS A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 263 through 264 No H-bonds generated for 'chain 'A' and resid 263 through 264' Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.830A pdb=" N GLN A 356 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 370 through 376 removed outlier: 4.101A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.668A pdb=" N GLN B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.886A 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 removed outlier: 3.616A pdb=" N HIS B 103 " --> pdb=" O PRO B 100 " (cutoff:3.500A) 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 262 removed outlier: 3.527A pdb=" N CYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 263 through 264 No H-bonds generated for 'chain 'B' and resid 263 through 264' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 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 350 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.764A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.700A pdb=" N GLN C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.862A 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 removed outlier: 3.533A pdb=" N HIS C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) 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 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 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 4.271A pdb=" N TYR C 308 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.866A 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: 3.980A 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: 3.701A pdb=" N LYS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.825A 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: 3.753A 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: 3.560A pdb=" N THR D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR D 308 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 352 through 358 removed outlier: 4.446A pdb=" N GLN D 356 " --> pdb=" O THR D 353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP D 358 " --> pdb=" O GLN D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.950A pdb=" N ARG D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 63 removed outlier: 4.170A pdb=" N LYS E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.829A pdb=" N ILE E 77 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.557A pdb=" N HIS E 103 " --> pdb=" O PRO E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.605A pdb=" N THR E 196 " --> pdb=" O MET E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 204 through 219 Processing helix chain 'E' and resid 224 through 231 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 260 through 264 Processing helix chain 'E' and resid 265 through 270 Processing helix chain 'E' and resid 275 through 286 Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 303 through 308 removed outlier: 3.538A pdb=" N THR E 306 " --> pdb=" O GLY E 303 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR E 308 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 350 Processing helix chain 'E' and resid 361 through 368 Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.619A pdb=" N ARG E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.646A pdb=" N GLN F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.821A pdb=" N ILE F 77 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 94 Processing helix chain 'F' and resid 99 through 103 Processing helix chain 'F' and resid 114 through 128 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'F' and resid 174 through 177 removed outlier: 3.521A pdb=" N ILE F 177 " --> pdb=" O PRO F 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 177' Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.781A pdb=" N THR F 196 " --> pdb=" O MET F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 204 through 219 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 254 through 262 Proline residue: F 260 - end of helix Processing helix chain 'F' and resid 263 through 264 No H-bonds generated for 'chain 'F' and resid 263 through 264' Processing helix chain 'F' and resid 265 through 269 Processing helix chain 'F' and resid 275 through 286 Processing helix chain 'F' and resid 291 through 298 Processing helix chain 'F' and resid 303 through 308 removed outlier: 4.221A pdb=" N TYR F 308 " --> pdb=" O THR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 339 through 350 removed outlier: 3.665A pdb=" N SER F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 357 removed outlier: 3.894A pdb=" N GLN F 356 " --> pdb=" O THR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 368 Processing helix chain 'F' and resid 370 through 376 removed outlier: 3.678A pdb=" N ARG F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.629A pdb=" N GLN G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.825A 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: 3.523A 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 removed outlier: 3.628A pdb=" N ILE G 177 " --> pdb=" O PRO G 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 174 through 177' Processing helix chain 'G' and resid 183 through 196 removed outlier: 3.541A 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 269 Processing helix chain 'G' and resid 275 through 286 Processing helix chain 'G' and resid 291 through 297 removed outlier: 3.597A pdb=" N LEU G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 308 removed outlier: 4.256A pdb=" N TYR G 308 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 323 Processing helix chain 'G' and resid 339 through 350 Processing helix chain 'G' and resid 351 through 358 removed outlier: 3.734A pdb=" N GLN G 356 " --> pdb=" O THR G 353 " (cutoff:3.500A) removed outlier: 3.697A 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: 3.881A pdb=" N ARG G 374 " --> pdb=" O SER G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 63 removed outlier: 3.713A pdb=" N GLN H 61 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 80 through 93 Processing helix chain 'H' and resid 114 through 129 removed outlier: 3.519A pdb=" N ARG H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 147 Processing helix chain 'H' and resid 183 through 196 removed outlier: 3.567A pdb=" N THR H 196 " --> pdb=" O MET H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 204 through 219 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 253 through 258 Processing helix chain 'H' and resid 259 through 264 Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 275 through 287 Processing helix chain 'H' and resid 291 through 297 Processing helix chain 'H' and resid 303 through 308 removed outlier: 3.577A pdb=" N THR H 306 " --> pdb=" O GLY H 303 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR H 308 " --> pdb=" O THR H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 323 Processing helix chain 'H' and resid 339 through 350 Processing helix chain 'H' and resid 351 through 355 Processing helix chain 'H' and resid 361 through 368 Processing helix chain 'H' and resid 370 through 376 removed outlier: 3.724A pdb=" N ARG H 374 " --> pdb=" O SER H 370 " (cutoff:3.500A) Processing helix chain 'X' and resid 282 through 285 Processing helix chain 'X' and resid 401 through 405 Processing helix chain 'Y' and resid 282 through 285 Processing helix chain 'Y' and resid 401 through 405 removed outlier: 3.511A pdb=" N LYS Y 404 " --> pdb=" O ASP Y 401 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 21 removed outlier: 3.983A pdb=" N LYS a 12 " --> pdb=" O ASP a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 61 removed outlier: 3.580A pdb=" N PHE a 53 " --> pdb=" O PRO a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 122 removed outlier: 4.749A pdb=" N ARG a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 4.864A 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 21 removed outlier: 3.948A pdb=" N LYS b 12 " --> pdb=" O ASP b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 61 removed outlier: 3.552A pdb=" N PHE b 53 " --> pdb=" O PRO b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 122 removed outlier: 4.830A pdb=" N ARG b 115 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA b 116 " --> pdb=" O SER b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 137 Processing helix chain 'b' and resid 138 through 149 removed outlier: 3.555A pdb=" N ASN b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 21 removed outlier: 3.859A pdb=" N LYS c 12 " --> pdb=" O ASP c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 61 removed outlier: 3.624A pdb=" N PHE c 53 " --> pdb=" O PRO c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 122 removed outlier: 4.704A pdb=" N ARG c 115 " --> pdb=" O ALA c 111 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA c 116 " --> pdb=" O SER c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 133 through 137 Processing helix chain 'c' and resid 138 through 148 Processing helix chain 'd' and resid 8 through 21 removed outlier: 3.873A pdb=" N LYS d 12 " --> pdb=" O ASP d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 61 removed outlier: 3.560A pdb=" N PHE d 53 " --> pdb=" O PRO d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 122 removed outlier: 4.758A pdb=" N ARG d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) removed outlier: 4.852A 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: 3.603A pdb=" N ASN d 149 " --> pdb=" O ASP d 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 20 removed outlier: 3.948A pdb=" N LYS e 12 " --> pdb=" O ASP e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 61 removed outlier: 3.604A pdb=" N PHE e 53 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 removed outlier: 4.809A pdb=" N ARG e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 4.667A 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: 3.508A pdb=" N GLN e 150 " --> pdb=" O LEU e 146 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 21 removed outlier: 3.959A pdb=" N LYS f 12 " --> pdb=" O ASP f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 49 through 61 Processing helix chain 'f' and resid 103 through 122 removed outlier: 4.823A pdb=" N ARG f 115 " --> pdb=" O ALA f 111 " (cutoff:3.500A) removed outlier: 4.643A 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: 6.726A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 7.964A 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: 6.535A 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: 6.608A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.012A 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: 6.235A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 6.595A 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: 6.608A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 7.940A 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: 6.495A 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: 3.594A pdb=" N THR D 108 " --> pdb=" O CYS D 12 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASN D 14 " --> 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: 6.520A 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: 6.577A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 7.879A 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: 6.554A 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: 6.576A pdb=" N LEU F 10 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR F 108 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 7.946A 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: 6.375A 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: 3.932A pdb=" N THR G 108 " --> pdb=" O CYS G 12 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASN G 14 " --> 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: 6.466A pdb=" N ILE G 153 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER G 302 " --> pdb=" O ILE G 153 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU G 155 " --> pdb=" O SER G 302 " (cutoff:3.500A) removed outlier: 6.576A 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: 3.845A pdb=" N THR H 108 " --> pdb=" O CYS H 12 " (cutoff:3.500A) removed outlier: 4.742A 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 133 through 134 Processing sheet with id=AE3, first strand: chain 'H' and resid 171 through 172 Processing sheet with id=AE4, first strand: chain 'H' and resid 171 through 172 removed outlier: 6.299A pdb=" N ASN H 299 " --> pdb=" O ILE H 332 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 240 through 243 Processing sheet with id=AE6, first strand: chain 'X' and resid 5 through 10 removed outlier: 5.599A pdb=" N GLN X 6 " --> pdb=" O ASN X 608 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN X 608 " --> pdb=" O GLN X 6 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA X 8 " --> pdb=" O PHE X 606 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR X 594 " --> pdb=" O LEU X 590 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 25 through 26 Processing sheet with id=AE8, first strand: chain 'X' and resid 62 through 67 removed outlier: 6.879A pdb=" N GLY X 77 " --> pdb=" O THR X 63 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA X 65 " --> pdb=" O ALA X 75 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA X 75 " --> pdb=" O ALA X 65 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR X 67 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR X 73 " --> pdb=" O THR X 67 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN X 82 " --> pdb=" O ASP X 78 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR X 97 " --> pdb=" O ILE X 85 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP X 87 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU X 95 " --> pdb=" O ASP X 87 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 106 through 111 Processing sheet with id=AF1, first strand: chain 'X' and resid 150 through 155 removed outlier: 3.529A pdb=" N SER X 152 " --> pdb=" O GLY X 166 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLU X 176 " --> pdb=" O PHE X 182 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE X 182 " --> pdb=" O GLU X 176 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 193 through 198 removed outlier: 4.601A pdb=" N ILE X 214 " --> pdb=" O PHE X 228 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASN X 218 " --> pdb=" O LYS X 224 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS X 224 " --> pdb=" O ASN X 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 242 through 247 removed outlier: 3.576A pdb=" N GLY X 244 " --> pdb=" O ALA X 257 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR X 262 " --> pdb=" O SER X 258 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE X 263 " --> pdb=" O THR X 276 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR X 276 " --> pdb=" O ILE X 263 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE X 265 " --> pdb=" O GLU X 274 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS X 272 " --> pdb=" O ASN X 267 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 287 through 292 removed outlier: 3.717A pdb=" N GLY X 289 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU X 297 " --> pdb=" O VAL X 309 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN X 318 " --> pdb=" O PHE X 308 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN X 310 " --> pdb=" O ILE X 316 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE X 316 " --> pdb=" O ASN X 310 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 327 through 332 Processing sheet with id=AF6, first strand: chain 'X' and resid 370 through 375 removed outlier: 3.719A pdb=" N GLY X 372 " --> pdb=" O VAL X 384 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS X 389 " --> pdb=" O SER X 385 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 414 through 419 removed outlier: 3.977A pdb=" N HIS X 433 " --> pdb=" O CYS X 430 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 451 through 456 removed outlier: 6.789A pdb=" N GLY X 466 " --> pdb=" O SER X 452 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL X 454 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA X 464 " --> pdb=" O VAL X 454 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU X 456 " --> pdb=" O PHE X 462 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE X 462 " --> pdb=" O LEU X 456 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS X 471 " --> pdb=" O GLY X 467 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS X 476 " --> pdb=" O GLU X 484 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU X 484 " --> pdb=" O LYS X 476 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER X 478 " --> pdb=" O VAL X 482 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL X 482 " --> pdb=" O SER X 478 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 494 through 499 removed outlier: 3.699A pdb=" N SER X 496 " --> pdb=" O THR X 509 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU X 525 " --> pdb=" O SER X 519 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 539 through 544 Processing sheet with id=AG2, first strand: chain 'Y' and resid 5 through 10 removed outlier: 5.608A pdb=" N GLN Y 6 " --> pdb=" O ASN Y 608 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN Y 608 " --> pdb=" O GLN Y 6 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA Y 8 " --> pdb=" O PHE Y 606 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR Y 594 " --> pdb=" O LEU Y 590 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 25 through 26 Processing sheet with id=AG4, first strand: chain 'Y' and resid 62 through 67 removed outlier: 6.753A pdb=" N GLY Y 77 " --> pdb=" O THR Y 63 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA Y 65 " --> pdb=" O ALA Y 75 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA Y 75 " --> pdb=" O ALA Y 65 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR Y 67 " --> pdb=" O TYR Y 73 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR Y 73 " --> pdb=" O THR Y 67 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN Y 82 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR Y 97 " --> pdb=" O ILE Y 85 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP Y 87 " --> pdb=" O LEU Y 95 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU Y 95 " --> pdb=" O ASP Y 87 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 106 through 111 Processing sheet with id=AG6, first strand: chain 'Y' and resid 150 through 155 removed outlier: 5.713A pdb=" N GLU Y 176 " --> pdb=" O PHE Y 182 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE Y 182 " --> pdb=" O GLU Y 176 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 193 through 198 removed outlier: 4.469A pdb=" N ILE Y 214 " --> pdb=" O PHE Y 228 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN Y 218 " --> pdb=" O LYS Y 224 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS Y 224 " --> pdb=" O ASN Y 218 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 242 through 247 removed outlier: 3.650A pdb=" N GLY Y 244 " --> pdb=" O ALA Y 257 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR Y 262 " --> pdb=" O SER Y 258 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE Y 263 " --> pdb=" O THR Y 276 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR Y 276 " --> pdb=" O ILE Y 263 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE Y 265 " --> pdb=" O GLU Y 274 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS Y 272 " --> pdb=" O ASN Y 267 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 287 through 292 removed outlier: 3.747A pdb=" N GLY Y 289 " --> pdb=" O ILE Y 300 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU Y 297 " --> pdb=" O VAL Y 309 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN Y 318 " --> pdb=" O PHE Y 308 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN Y 310 " --> pdb=" O ILE Y 316 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE Y 316 " --> pdb=" O ASN Y 310 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 327 through 332 Processing sheet with id=AH2, first strand: chain 'Y' and resid 370 through 375 removed outlier: 3.699A pdb=" N GLY Y 372 " --> pdb=" O VAL Y 384 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS Y 389 " --> pdb=" O SER Y 385 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 414 through 419 removed outlier: 3.649A pdb=" N GLY Y 416 " --> pdb=" O ALA Y 429 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS Y 433 " --> pdb=" O CYS Y 430 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 451 through 456 removed outlier: 6.781A pdb=" N GLY Y 466 " --> pdb=" O SER Y 452 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL Y 454 " --> pdb=" O ALA Y 464 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA Y 464 " --> pdb=" O VAL Y 454 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU Y 456 " --> pdb=" O PHE Y 462 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE Y 462 " --> pdb=" O LEU Y 456 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS Y 471 " --> pdb=" O GLY Y 467 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS Y 476 " --> pdb=" O GLU Y 484 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU Y 484 " --> pdb=" O LYS Y 476 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N SER Y 478 " --> pdb=" O VAL Y 482 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL Y 482 " --> pdb=" O SER Y 478 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 494 through 499 removed outlier: 6.692A pdb=" N THR Y 509 " --> pdb=" O THR Y 495 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL Y 497 " --> pdb=" O VAL Y 507 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL Y 507 " --> pdb=" O VAL Y 497 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE Y 499 " --> pdb=" O PHE Y 505 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE Y 505 " --> pdb=" O PHE Y 499 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU Y 525 " --> pdb=" O SER Y 519 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 539 through 544 Processing sheet with id=AH7, first strand: chain 'a' and resid 6 through 7 removed outlier: 6.985A pdb=" N LYS a 6 " --> pdb=" O ILE a 38 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N VAL a 40 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL a 40 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS a 30 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE a 127 " --> pdb=" O VAL a 92 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 6 through 7 removed outlier: 6.959A pdb=" N LYS b 6 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N VAL b 40 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL b 40 " --> pdb=" O LYS b 30 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS b 30 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE b 127 " --> pdb=" O VAL b 92 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.060A pdb=" N LYS c 6 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL c 40 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL c 40 " --> pdb=" O LYS c 30 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS c 30 " --> pdb=" O VAL c 40 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE c 127 " --> pdb=" O VAL c 92 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'd' and resid 6 through 7 removed outlier: 6.882A pdb=" N LYS d 6 " --> pdb=" O ILE d 38 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N VAL d 40 " --> pdb=" O LYS d 6 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL d 40 " --> pdb=" O LYS d 30 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS d 30 " --> pdb=" O VAL d 40 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE d 127 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.402A pdb=" N LYS e 6 " --> pdb=" O ILE e 38 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL e 40 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL e 40 " --> pdb=" O LYS e 30 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS e 30 " --> pdb=" O VAL e 40 " (cutoff:3.500A) removed outlier: 9.843A pdb=" N PHE e 127 " --> pdb=" O ASN e 90 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL e 92 " --> pdb=" O PHE e 127 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N VAL e 129 " --> pdb=" O VAL e 92 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE e 94 " --> pdb=" O VAL e 129 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA e 131 " --> pdb=" O PHE e 94 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLN e 96 " --> pdb=" O ALA e 131 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'f' and resid 6 through 7 removed outlier: 7.112A pdb=" N LYS f 6 " --> pdb=" O ILE f 38 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N VAL f 40 " --> pdb=" O LYS f 6 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL f 40 " --> pdb=" O LYS f 30 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS f 30 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE f 127 " --> pdb=" O VAL f 92 " (cutoff:3.500A) 1814 hydrogen bonds defined for protein. 4727 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: 11.57 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13080 1.34 - 1.46: 6795 1.46 - 1.57: 21079 1.57 - 1.69: 24 1.69 - 1.81: 416 Bond restraints: 41394 Sorted by residual: bond pdb=" CB MET C 192 " pdb=" CG MET C 192 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.68e+00 bond pdb=" SD MET C 192 " pdb=" CE MET C 192 " ideal model delta sigma weight residual 1.791 1.751 0.040 2.50e-02 1.60e+03 2.59e+00 bond pdb=" C ILE Y 99 " pdb=" N PRO Y 100 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.01e-02 9.80e+03 2.59e+00 bond pdb=" CD2 PHE G 202 " pdb=" CE2 PHE G 202 " ideal model delta sigma weight residual 1.382 1.429 -0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" CG1 ILE G 284 " pdb=" CD1 ILE G 284 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.05e+00 ... (remaining 41389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 55452 1.92 - 3.85: 760 3.85 - 5.77: 124 5.77 - 7.70: 18 7.70 - 9.62: 2 Bond angle restraints: 56356 Sorted by residual: angle pdb=" N VAL Y 365 " pdb=" CA VAL Y 365 " pdb=" C VAL Y 365 " ideal model delta sigma weight residual 112.96 107.21 5.75 1.00e+00 1.00e+00 3.31e+01 angle pdb=" N ILE F 66 " pdb=" CA ILE F 66 " pdb=" C ILE F 66 " ideal model delta sigma weight residual 112.29 108.78 3.51 9.40e-01 1.13e+00 1.39e+01 angle pdb=" N VAL X 279 " pdb=" CA VAL X 279 " pdb=" C VAL X 279 " ideal model delta sigma weight residual 112.96 109.47 3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" C LYS f 46 " pdb=" N ASN f 47 " pdb=" CA ASN f 47 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N VAL Y 79 " pdb=" CA VAL Y 79 " pdb=" C VAL Y 79 " ideal model delta sigma weight residual 112.98 108.85 4.13 1.25e+00 6.40e-01 1.09e+01 ... (remaining 56351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 23612 17.52 - 35.03: 1258 35.03 - 52.55: 209 52.55 - 70.06: 54 70.06 - 87.58: 43 Dihedral angle restraints: 25176 sinusoidal: 9946 harmonic: 15230 Sorted by residual: dihedral pdb=" CA GLY G 48 " pdb=" C GLY G 48 " pdb=" N MET G 49 " pdb=" CA MET G 49 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ARG Y 125 " pdb=" C ARG Y 125 " pdb=" N GLU Y 126 " pdb=" CA GLU Y 126 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU E 67 " pdb=" C LEU E 67 " pdb=" N THR E 68 " pdb=" CA THR E 68 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 25173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3960 0.036 - 0.071: 1502 0.071 - 0.107: 648 0.107 - 0.143: 227 0.143 - 0.178: 17 Chirality restraints: 6354 Sorted by residual: chirality pdb=" CB ILE e 28 " pdb=" CA ILE e 28 " pdb=" CG1 ILE e 28 " pdb=" CG2 ILE e 28 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA GLU G 102 " pdb=" N GLU G 102 " pdb=" C GLU G 102 " pdb=" CB GLU G 102 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB ILE H 359 " pdb=" CA ILE H 359 " pdb=" CG1 ILE H 359 " pdb=" CG2 ILE H 359 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 6351 not shown) Planarity restraints: 7236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 165 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO G 166 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 166 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 166 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 336 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C GLU H 336 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU H 336 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG H 337 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 103 " 0.019 2.00e-02 2.50e+03 1.69e-02 4.28e+00 pdb=" CG HIS G 103 " -0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS G 103 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS G 103 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS G 103 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS G 103 " 0.016 2.00e-02 2.50e+03 ... (remaining 7233 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 59 2.51 - 3.11: 29916 3.11 - 3.71: 61932 3.71 - 4.30: 95277 4.30 - 4.90: 157205 Nonbonded interactions: 344389 Sorted by model distance: nonbonded pdb="MG MG D 401 " pdb=" O HOH D 505 " model vdw 1.913 2.170 nonbonded pdb="MG MG F 401 " pdb=" O HOH F 501 " model vdw 1.936 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 505 " model vdw 1.962 2.170 nonbonded pdb="MG MG E 401 " pdb=" O HOH E 501 " model vdw 1.965 2.170 nonbonded pdb="MG MG H 401 " pdb=" O HOH H 501 " model vdw 1.970 2.170 ... (remaining 344384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'B' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'C' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'D' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'E' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'F' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'G' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) selection = (chain 'H' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 72 or resid 74 through 92 or resid 94 through 119 or resid 122 or resi \ d 124 through 170 or resid 172 or resid 174 or resid 176 through 181 or resid 18 \ 3 through 202 or resid 204 through 278 or resid 280 through 401)) } ncs_group { reference = chain 'X' selection = chain 'Y' } ncs_group { reference = (chain 'a' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'b' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'c' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'd' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'e' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) selection = (chain 'f' and (resid 1 through 4 or resid 6 through 16 or resid 18 through 152) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 45.730 Find NCS groups from input model: 0.810 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: 0.010 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 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 : 0.003 0.056 41394 Z= 0.138 Angle : 0.582 9.621 56356 Z= 0.304 Chirality : 0.047 0.178 6354 Planarity : 0.004 0.067 7236 Dihedral : 11.736 87.577 15468 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.67 % Favored : 97.31 % Rotamer: Outliers : 0.25 % Allowed : 0.72 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 5184 helix: 1.15 (0.14), residues: 1524 sheet: 0.47 (0.14), residues: 1322 loop : 0.94 (0.14), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 179 TYR 0.025 0.001 TYR G 168 PHE 0.019 0.001 PHE Y 102 TRP 0.034 0.002 TRP H 358 HIS 0.015 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (41394) covalent geometry : angle 0.58185 / 0.30 (56356) hydrogen bonds : bond 0.12917 / 8.72 ( 1798) hydrogen bonds : angle 6.30894 / 4.45 ( 4727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: -0.0602 (mmt) cc_final: -0.1718 (ttt) REVERT: A 366 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8279 (mm-30) REVERT: B 36 ILE cc_start: 0.9223 (pt) cc_final: 0.9021 (pp) REVERT: B 49 MET cc_start: 0.0014 (mmt) cc_final: -0.0332 (mpm) REVERT: C 49 MET cc_start: 0.4001 (ppp) cc_final: 0.3654 (ppp) REVERT: C 357 MET cc_start: 0.8904 (mmm) cc_final: 0.8612 (mtp) REVERT: E 46 MET cc_start: 0.1891 (mtm) cc_final: 0.1620 (mmm) REVERT: E 62 SER cc_start: 0.7732 (m) cc_final: 0.7245 (p) REVERT: F 46 MET cc_start: 0.4857 (mmp) cc_final: 0.4518 (mmt) REVERT: F 49 MET cc_start: 0.4779 (pmm) cc_final: 0.3905 (tpt) REVERT: G 46 MET cc_start: 0.4919 (mpp) cc_final: 0.3776 (mmt) REVERT: G 125 MET cc_start: 0.8024 (mmp) cc_final: 0.7736 (mmt) REVERT: G 223 LEU cc_start: 0.6391 (pp) cc_final: 0.6176 (tm) REVERT: G 285 MET cc_start: 0.7291 (mmm) cc_final: 0.6944 (mmm) REVERT: G 357 MET cc_start: 0.6734 (mtt) cc_final: 0.6472 (mtp) REVERT: H 201 SER cc_start: 0.8735 (t) cc_final: 0.8213 (p) REVERT: H 285 MET cc_start: 0.3753 (mmp) cc_final: 0.3454 (tpt) REVERT: Y 79 VAL cc_start: 0.7749 (p) cc_final: 0.7418 (p) REVERT: Y 127 ARG cc_start: 0.6431 (ttp80) cc_final: 0.6087 (ttp80) REVERT: a 1 MET cc_start: 0.4481 (mmm) cc_final: 0.4051 (mmm) REVERT: a 8 ASP cc_start: 0.8625 (t70) cc_final: 0.8079 (p0) REVERT: a 138 ASP cc_start: 0.8689 (t0) cc_final: 0.8360 (t0) REVERT: a 147 MET cc_start: 0.8792 (mtp) cc_final: 0.8586 (mtt) REVERT: b 8 ASP cc_start: 0.8513 (t0) cc_final: 0.8301 (t0) REVERT: c 6 LYS cc_start: 0.8981 (mttt) cc_final: 0.8314 (tttt) REVERT: c 8 ASP cc_start: 0.8310 (t0) cc_final: 0.7841 (t0) REVERT: c 55 GLU cc_start: 0.8626 (tp30) cc_final: 0.8425 (tp30) REVERT: c 108 MET cc_start: 0.8992 (tpt) cc_final: 0.8693 (tpt) REVERT: d 8 ASP cc_start: 0.8662 (t70) cc_final: 0.8429 (t0) REVERT: d 36 THR cc_start: 0.9215 (p) cc_final: 0.8763 (t) REVERT: d 65 LYS cc_start: 0.8233 (mppt) cc_final: 0.7109 (tptt) REVERT: d 138 ASP cc_start: 0.8289 (t70) cc_final: 0.7772 (t70) REVERT: e 65 LYS cc_start: 0.7974 (mppt) cc_final: 0.7090 (tmtm) REVERT: e 138 ASP cc_start: 0.7771 (t70) cc_final: 0.7517 (t0) REVERT: e 147 MET cc_start: 0.7702 (mtt) cc_final: 0.7483 (mpp) REVERT: f 73 ASP cc_start: 0.7910 (t0) cc_final: 0.7399 (m-30) outliers start: 0 outliers final: 2 residues processed: 428 average time/residue: 0.7472 time to fit residues: 387.7563 Evaluate side-chains 309 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [432, 197, 388, 455, 215, 20, 132, 494, 261, 248, 207] chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN B 94 ASN C 14 ASN C 164 ASN E 90 HIS F 163 HIS G 94 ASN G 299 ASN G 356 GLN H 14 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 HIS X 130 HIS X 318 GLN X 528 HIS Y 82 ASN Y 130 HIS Y 140 ASN a 47 ASN a 96 GLN b 23 GLN b 150 GLN c 13 ASN c 34 ASN c 149 ASN ** d 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 ASN e 23 GLN e 34 ASN ** e 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 128 GLN f 23 GLN f 81 GLN f 90 ASN f 96 GLN f 130 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060490 restraints weight = 453841.097| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 5.72 r_work: 0.2699 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 41394 Z= 0.331 Angle : 0.706 9.203 56356 Z= 0.364 Chirality : 0.053 0.241 6354 Planarity : 0.005 0.060 7236 Dihedral : 6.089 87.006 5846 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 1.60 % Allowed : 6.03 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 5184 helix: 0.61 (0.13), residues: 1612 sheet: 0.32 (0.14), residues: 1312 loop : 0.74 (0.14), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 41 TYR 0.032 0.002 TYR E 145 PHE 0.027 0.002 PHE c 29 TRP 0.023 0.002 TRP H 88 HIS 0.008 0.002 HIS e 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.33 (41394) covalent geometry : angle 0.70574 / 0.36 (56356) hydrogen bonds : bond 0.04965 / 3.27 ( 1798) hydrogen bonds : angle 5.37991 / 3.80 ( 4727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8409 (mm-30) REVERT: B 36 ILE cc_start: 0.9267 (pt) cc_final: 0.9062 (pp) REVERT: B 41 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7015 (ptm-80) REVERT: B 49 MET cc_start: -0.0071 (mmt) cc_final: -0.0326 (mpm) REVERT: B 357 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7620 (mtt) REVERT: C 49 MET cc_start: 0.4126 (ppp) cc_final: 0.3818 (ppp) REVERT: C 357 MET cc_start: 0.8987 (mmm) cc_final: 0.8655 (mtp) REVERT: D 49 MET cc_start: 0.2862 (ptp) cc_final: 0.2430 (ttt) REVERT: D 118 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.7934 (ttp80) REVERT: E 46 MET cc_start: 0.1841 (mtm) cc_final: 0.1510 (mmm) REVERT: E 49 MET cc_start: 0.6301 (pmm) cc_final: 0.5021 (ptm) REVERT: F 49 MET cc_start: 0.4930 (pmm) cc_final: 0.4327 (tpt) REVERT: G 83 ASP cc_start: 0.7489 (m-30) cc_final: 0.7119 (m-30) REVERT: G 122 THR cc_start: 0.8661 (m) cc_final: 0.8315 (p) REVERT: G 125 MET cc_start: 0.8353 (mmp) cc_final: 0.8042 (mmt) REVERT: G 163 HIS cc_start: 0.7354 (OUTLIER) cc_final: 0.6284 (t-90) REVERT: G 192 MET cc_start: 0.7696 (ttp) cc_final: 0.7450 (ttp) REVERT: G 201 SER cc_start: 0.8002 (t) cc_final: 0.7630 (m) REVERT: G 242 TYR cc_start: 0.8221 (t80) cc_final: 0.7929 (t80) REVERT: G 285 MET cc_start: 0.7231 (mmm) cc_final: 0.6876 (mmm) REVERT: G 357 MET cc_start: 0.6751 (mtt) cc_final: 0.6481 (mtp) REVERT: G 362 GLN cc_start: 0.8557 (mp10) cc_final: 0.8321 (pm20) REVERT: H 225 PHE cc_start: 0.6771 (t80) cc_final: 0.6245 (t80) REVERT: Y 20 THR cc_start: 0.8141 (m) cc_final: 0.7629 (p) REVERT: Y 581 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8264 (mtt) REVERT: a 8 ASP cc_start: 0.8665 (t70) cc_final: 0.7875 (p0) REVERT: a 138 ASP cc_start: 0.8600 (t0) cc_final: 0.8185 (t70) REVERT: b 1 MET cc_start: 0.4851 (OUTLIER) cc_final: 0.3965 (mtt) REVERT: b 8 ASP cc_start: 0.8568 (t0) cc_final: 0.8221 (t0) REVERT: b 101 ASN cc_start: 0.8629 (p0) cc_final: 0.8392 (p0) REVERT: c 6 LYS cc_start: 0.9058 (mttt) cc_final: 0.8346 (tttt) REVERT: c 8 ASP cc_start: 0.8154 (t0) cc_final: 0.7673 (t0) REVERT: c 55 GLU cc_start: 0.8666 (tp30) cc_final: 0.8463 (tp30) REVERT: c 115 ARG cc_start: 0.8879 (tmm-80) cc_final: 0.8652 (tmm160) REVERT: d 8 ASP cc_start: 0.8610 (t70) cc_final: 0.8381 (t70) REVERT: d 36 THR cc_start: 0.9342 (p) cc_final: 0.8879 (t) REVERT: d 65 LYS cc_start: 0.8454 (mppt) cc_final: 0.7341 (tptt) REVERT: e 16 ASP cc_start: 0.8309 (m-30) cc_final: 0.8062 (m-30) REVERT: e 52 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: e 65 LYS cc_start: 0.8110 (mppt) cc_final: 0.7207 (tptt) REVERT: e 138 ASP cc_start: 0.7290 (t70) cc_final: 0.7018 (t0) REVERT: f 151 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.4709 (mtt90) outliers start: 53 outliers final: 14 residues processed: 332 average time/residue: 0.7521 time to fit residues: 302.5878 Evaluate side-chains 301 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain G residue 163 HIS Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain Y residue 134 PHE Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 536 THR Chi-restraints excluded: chain Y residue 581 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 106 ARG Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain f residue 151 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [393, 14, 244, 265, 274, 320, 353, 408, 299, 315, 476] chunk 393 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 274 optimal weight: 4.9990 chunk 320 optimal weight: 0.9990 chunk 353 optimal weight: 9.9990 chunk 408 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 476 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN B 42 HIS F 43 GLN G 89 HIS ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 HIS ** Y 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 HIS e 34 ASN e 90 ASN e 101 ASN e 128 GLN f 19 HIS f 23 GLN f 81 GLN f 90 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062154 restraints weight = 472709.681| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 6.07 r_work: 0.2723 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41394 Z= 0.172 Angle : 0.580 10.056 56356 Z= 0.295 Chirality : 0.048 0.182 6354 Planarity : 0.004 0.056 7236 Dihedral : 5.812 87.018 5842 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.33 % Favored : 97.65 % Rotamer: Outliers : 1.53 % Allowed : 7.40 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.12), residues: 5184 helix: 0.88 (0.13), residues: 1612 sheet: 0.31 (0.14), residues: 1256 loop : 0.74 (0.14), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 115 TYR 0.019 0.001 TYR e 50 PHE 0.018 0.001 PHE b 29 TRP 0.016 0.002 TRP F 342 HIS 0.009 0.001 HIS G 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (41394) covalent geometry : angle 0.58014 / 0.29 (56356) hydrogen bonds : bond 0.03932 / 2.59 ( 1798) hydrogen bonds : angle 5.05428 / 3.58 ( 4727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 294 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8301 (mm-30) REVERT: B 49 MET cc_start: -0.0281 (mmt) cc_final: -0.0629 (mpm) REVERT: C 46 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.2399 (tmm) REVERT: C 49 MET cc_start: 0.4239 (ppp) cc_final: 0.3897 (ppp) REVERT: C 357 MET cc_start: 0.8938 (mmm) cc_final: 0.8593 (mtp) REVERT: D 49 MET cc_start: 0.2829 (ptp) cc_final: 0.2392 (ttt) REVERT: D 118 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7887 (ttp80) REVERT: E 46 MET cc_start: 0.1948 (mtm) cc_final: 0.1546 (mmm) REVERT: E 49 MET cc_start: 0.6216 (pmm) cc_final: 0.5109 (ptm) REVERT: E 62 SER cc_start: 0.7644 (m) cc_final: 0.7327 (p) REVERT: E 178 MET cc_start: 0.8981 (mmm) cc_final: 0.8770 (mmm) REVERT: F 49 MET cc_start: 0.5008 (pmm) cc_final: 0.4346 (tpt) REVERT: F 62 SER cc_start: 0.6995 (m) cc_final: 0.6668 (p) REVERT: G 46 MET cc_start: 0.4545 (mpt) cc_final: 0.2919 (mmp) REVERT: G 52 LYS cc_start: 0.6445 (mtpt) cc_final: 0.6147 (mttp) REVERT: G 122 THR cc_start: 0.8736 (m) cc_final: 0.8413 (p) REVERT: G 125 MET cc_start: 0.8422 (mmp) cc_final: 0.7925 (mmt) REVERT: G 242 TYR cc_start: 0.8144 (t80) cc_final: 0.7905 (t80) REVERT: G 285 MET cc_start: 0.7220 (mmm) cc_final: 0.6887 (mmm) REVERT: G 357 MET cc_start: 0.6777 (mtt) cc_final: 0.6557 (mtp) REVERT: G 362 GLN cc_start: 0.8555 (mp10) cc_final: 0.8245 (pm20) REVERT: H 225 PHE cc_start: 0.6671 (t80) cc_final: 0.6215 (t80) REVERT: X 164 ILE cc_start: 0.8881 (pt) cc_final: 0.8440 (pp) REVERT: Y 20 THR cc_start: 0.8040 (m) cc_final: 0.7527 (p) REVERT: Y 581 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8309 (mtt) REVERT: a 8 ASP cc_start: 0.8705 (t70) cc_final: 0.7991 (p0) REVERT: a 138 ASP cc_start: 0.8627 (t0) cc_final: 0.8186 (t70) REVERT: b 1 MET cc_start: 0.4812 (OUTLIER) cc_final: 0.3734 (mtt) REVERT: b 8 ASP cc_start: 0.8564 (t0) cc_final: 0.8125 (t0) REVERT: c 6 LYS cc_start: 0.9050 (mttt) cc_final: 0.8335 (tttt) REVERT: c 55 GLU cc_start: 0.8609 (tp30) cc_final: 0.8390 (tp30) REVERT: c 65 LYS cc_start: 0.7910 (mmtp) cc_final: 0.6710 (tmtt) REVERT: c 115 ARG cc_start: 0.8851 (tmm-80) cc_final: 0.8644 (tmm160) REVERT: d 8 ASP cc_start: 0.8583 (t70) cc_final: 0.8298 (t70) REVERT: d 36 THR cc_start: 0.9330 (p) cc_final: 0.8875 (t) REVERT: d 65 LYS cc_start: 0.8412 (mppt) cc_final: 0.7247 (tptt) REVERT: e 16 ASP cc_start: 0.8341 (m-30) cc_final: 0.8106 (m-30) REVERT: e 101 ASN cc_start: 0.9084 (t0) cc_final: 0.8755 (t0) REVERT: e 138 ASP cc_start: 0.7362 (t70) cc_final: 0.7114 (t0) REVERT: e 150 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: f 73 ASP cc_start: 0.8039 (t0) cc_final: 0.7389 (m-30) outliers start: 45 outliers final: 12 residues processed: 309 average time/residue: 0.7254 time to fit residues: 272.8103 Evaluate side-chains 295 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 159 ARG Chi-restraints excluded: chain Y residue 369 MET Chi-restraints excluded: chain Y residue 536 THR Chi-restraints excluded: chain Y residue 565 MET Chi-restraints excluded: chain Y residue 581 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain e residue 150 GLN Chi-restraints excluded: chain f residue 106 ARG Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [212, 222, 458, 166, 416, 230, 399, 260, 232, 164, 236] chunk 212 optimal weight: 1.9990 chunk 222 optimal weight: 20.0000 chunk 458 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 416 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 399 optimal weight: 8.9990 chunk 260 optimal weight: 30.0000 chunk 232 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 236 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 43 GLN G 89 HIS ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 HIS Y 26 ASN ** Y 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 318 GLN c 34 ASN e 101 ASN e 128 GLN f 23 GLN f 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061434 restraints weight = 489841.023| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 6.04 r_work: 0.2709 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 41394 Z= 0.202 Angle : 0.589 9.684 56356 Z= 0.299 Chirality : 0.048 0.199 6354 Planarity : 0.004 0.054 7236 Dihedral : 5.787 88.883 5842 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 1.78 % Allowed : 7.69 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.12), residues: 5184 helix: 0.93 (0.13), residues: 1606 sheet: 0.26 (0.14), residues: 1260 loop : 0.71 (0.14), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG f 115 TYR 0.018 0.001 TYR e 50 PHE 0.019 0.001 PHE b 29 TRP 0.017 0.002 TRP H 88 HIS 0.038 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (41394) covalent geometry : angle 0.58946 / 0.30 (56356) hydrogen bonds : bond 0.03938 / 2.59 ( 1798) hydrogen bonds : angle 4.97901 / 3.52 ( 4727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 1.159 Fit side-chains REVERT: A 366 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8299 (mm-30) REVERT: B 41 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6892 (ptm-80) REVERT: B 49 MET cc_start: -0.0278 (mmt) cc_final: -0.0603 (mpm) REVERT: B 70 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8230 (mtpp) REVERT: C 46 MET cc_start: 0.3540 (OUTLIER) cc_final: 0.2418 (tmm) REVERT: C 49 MET cc_start: 0.4370 (ppp) cc_final: 0.4004 (ppp) REVERT: C 357 MET cc_start: 0.8997 (mmm) cc_final: 0.8657 (mtp) REVERT: D 49 MET cc_start: 0.2815 (ptp) cc_final: 0.2383 (ttt) REVERT: E 46 MET cc_start: 0.2150 (mtm) cc_final: 0.1600 (mmm) REVERT: E 49 MET cc_start: 0.6180 (pmm) cc_final: 0.5181 (ptm) REVERT: E 62 SER cc_start: 0.7698 (m) cc_final: 0.7395 (p) REVERT: E 178 MET cc_start: 0.8986 (mmm) cc_final: 0.8786 (mmm) REVERT: F 49 MET cc_start: 0.5002 (pmm) cc_final: 0.4316 (tpt) REVERT: G 46 MET cc_start: 0.4638 (mpt) cc_final: 0.2970 (mmp) REVERT: G 122 THR cc_start: 0.8845 (m) cc_final: 0.8519 (p) REVERT: G 285 MET cc_start: 0.7177 (mmm) cc_final: 0.6856 (mmm) REVERT: G 357 MET cc_start: 0.6758 (mtt) cc_final: 0.6524 (mtp) REVERT: G 362 GLN cc_start: 0.8577 (mp10) cc_final: 0.8291 (pm20) REVERT: H 225 PHE cc_start: 0.6455 (t80) cc_final: 0.6156 (t80) REVERT: H 361 LYS cc_start: 0.4006 (OUTLIER) cc_final: 0.3705 (mmtp) REVERT: X 164 ILE cc_start: 0.8843 (pt) cc_final: 0.8392 (pp) REVERT: Y 20 THR cc_start: 0.8081 (m) cc_final: 0.7553 (p) REVERT: Y 581 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8434 (mtt) REVERT: a 1 MET cc_start: 0.5151 (mmm) cc_final: 0.4308 (mmm) REVERT: a 8 ASP cc_start: 0.8710 (t70) cc_final: 0.7934 (p0) REVERT: a 138 ASP cc_start: 0.8659 (t0) cc_final: 0.8186 (t70) REVERT: b 1 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.3739 (mtt) REVERT: b 8 ASP cc_start: 0.8573 (t0) cc_final: 0.8041 (t0) REVERT: c 6 LYS cc_start: 0.9046 (mttt) cc_final: 0.8322 (tttt) REVERT: c 55 GLU cc_start: 0.8567 (tp30) cc_final: 0.8357 (tp30) REVERT: d 8 ASP cc_start: 0.8585 (t70) cc_final: 0.8331 (t70) REVERT: d 36 THR cc_start: 0.9342 (p) cc_final: 0.8894 (t) REVERT: d 65 LYS cc_start: 0.8448 (mppt) cc_final: 0.7279 (tptt) REVERT: e 16 ASP cc_start: 0.8339 (m-30) cc_final: 0.8095 (m-30) REVERT: e 138 ASP cc_start: 0.7389 (t70) cc_final: 0.7133 (t0) REVERT: e 150 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: f 47 ASN cc_start: 0.8426 (m110) cc_final: 0.8010 (p0) REVERT: f 73 ASP cc_start: 0.8044 (t0) cc_final: 0.7354 (m-30) REVERT: f 115 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8278 (tmm-80) outliers start: 52 outliers final: 17 residues processed: 315 average time/residue: 0.7228 time to fit residues: 277.7625 Evaluate side-chains 301 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 277 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 369 MET Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 445 VAL Chi-restraints excluded: chain Y residue 536 THR Chi-restraints excluded: chain Y residue 581 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain e residue 150 GLN Chi-restraints excluded: chain f residue 106 ARG Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [241, 42, 199, 418, 216, 367, 52, 65, 274, 276, 471] chunk 241 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 367 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 471 optimal weight: 5.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 HIS C 14 ASN F 43 GLN F 164 ASN G 89 HIS G 373 HIS H 163 HIS ** Y 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 128 GLN d 34 ASN e 128 GLN f 23 GLN f 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060038 restraints weight = 494620.572| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 6.17 r_work: 0.2675 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 41394 Z= 0.271 Angle : 0.644 11.065 56356 Z= 0.328 Chirality : 0.050 0.221 6354 Planarity : 0.005 0.095 7236 Dihedral : 5.973 84.562 5842 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 2.16 % Allowed : 8.39 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 5184 helix: 0.75 (0.13), residues: 1606 sheet: 0.14 (0.14), residues: 1258 loop : 0.61 (0.14), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Y 159 TYR 0.019 0.002 TYR E 145 PHE 0.022 0.002 PHE c 29 TRP 0.024 0.002 TRP G 81 HIS 0.009 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 (41394) covalent geometry : angle 0.64413 / 0.33 (56356) hydrogen bonds : bond 0.04417 / 2.90 ( 1798) hydrogen bonds : angle 5.08348 / 3.60 ( 4727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 1.670 Fit side-chains revert: symmetry clash REVERT: A 366 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8356 (mm-30) REVERT: B 41 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7142 (ptm-80) REVERT: B 49 MET cc_start: -0.0458 (mmt) cc_final: -0.0724 (mpm) REVERT: B 70 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8468 (mtpp) REVERT: C 49 MET cc_start: 0.4383 (ppp) cc_final: 0.4134 (ppp) REVERT: C 357 MET cc_start: 0.9039 (mmm) cc_final: 0.8703 (mtp) REVERT: E 46 MET cc_start: 0.2113 (mtm) cc_final: 0.1621 (mmm) REVERT: E 49 MET cc_start: 0.6343 (pmm) cc_final: 0.5284 (ptm) REVERT: E 62 SER cc_start: 0.7794 (m) cc_final: 0.7487 (p) REVERT: E 178 MET cc_start: 0.9039 (mmm) cc_final: 0.8837 (mmm) REVERT: F 49 MET cc_start: 0.5139 (pmm) cc_final: 0.4468 (tpt) REVERT: G 12 CYS cc_start: 0.8436 (t) cc_final: 0.8170 (t) REVERT: G 46 MET cc_start: 0.4654 (mpt) cc_final: 0.4348 (pmm) REVERT: G 285 MET cc_start: 0.7177 (mmm) cc_final: 0.6821 (mmm) REVERT: G 357 MET cc_start: 0.6874 (mtt) cc_final: 0.6663 (mtp) REVERT: G 362 GLN cc_start: 0.8606 (mp10) cc_final: 0.8248 (pm20) REVERT: H 84 MET cc_start: 0.6276 (tpt) cc_final: 0.6058 (tpp) REVERT: H 101 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: H 113 ASN cc_start: 0.3259 (OUTLIER) cc_final: 0.2652 (t0) REVERT: H 129 PHE cc_start: 0.5382 (m-10) cc_final: 0.5049 (m-10) REVERT: H 361 LYS cc_start: 0.4110 (OUTLIER) cc_final: 0.3432 (mttm) REVERT: Y 20 THR cc_start: 0.8129 (m) cc_final: 0.7580 (p) REVERT: Y 581 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8524 (mtt) REVERT: a 1 MET cc_start: 0.5371 (mmm) cc_final: 0.4448 (mmm) REVERT: a 8 ASP cc_start: 0.8758 (t70) cc_final: 0.7856 (p0) REVERT: a 138 ASP cc_start: 0.8695 (t0) cc_final: 0.8239 (t0) REVERT: b 1 MET cc_start: 0.4931 (OUTLIER) cc_final: 0.3831 (mtt) REVERT: b 8 ASP cc_start: 0.8591 (t0) cc_final: 0.8054 (t0) REVERT: c 6 LYS cc_start: 0.9085 (mttt) cc_final: 0.8346 (tttt) REVERT: c 65 LYS cc_start: 0.8099 (mmtp) cc_final: 0.6825 (tptt) REVERT: d 8 ASP cc_start: 0.8592 (t70) cc_final: 0.8330 (t70) REVERT: d 65 LYS cc_start: 0.8517 (mppt) cc_final: 0.7336 (tptt) REVERT: d 115 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8735 (ttp-170) REVERT: e 13 ASN cc_start: 0.8970 (m-40) cc_final: 0.8764 (m-40) REVERT: e 16 ASP cc_start: 0.8345 (m-30) cc_final: 0.8066 (m-30) REVERT: e 136 ASP cc_start: 0.8902 (m-30) cc_final: 0.8298 (m-30) REVERT: e 138 ASP cc_start: 0.7450 (t70) cc_final: 0.7175 (t0) REVERT: f 73 ASP cc_start: 0.8050 (t0) cc_final: 0.7282 (m-30) outliers start: 65 outliers final: 27 residues processed: 328 average time/residue: 0.7179 time to fit residues: 286.8568 Evaluate side-chains 308 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain X residue 445 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 445 VAL Chi-restraints excluded: chain Y residue 536 THR Chi-restraints excluded: chain Y residue 581 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain d residue 115 ARG Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 106 ARG Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [458, 280, 455, 462, 268, 233, 257, 361, 203, 24, 319] chunk 458 optimal weight: 2.9990 chunk 280 optimal weight: 8.9990 chunk 455 optimal weight: 3.9990 chunk 462 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 361 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 319 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 HIS C 14 ASN F 43 GLN G 89 HIS H 163 HIS Y 26 ASN c 34 ASN d 128 GLN e 23 GLN e 128 GLN f 20 ASN f 23 GLN f 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061350 restraints weight = 488098.664| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 6.04 r_work: 0.2708 rms_B_bonded: 5.00 restraints_weight: 2.0000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41394 Z= 0.163 Angle : 0.573 10.763 56356 Z= 0.288 Chirality : 0.047 0.188 6354 Planarity : 0.004 0.057 7236 Dihedral : 5.713 81.050 5842 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.47 % Rotamer: Outliers : 2.11 % Allowed : 9.15 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.12), residues: 5184 helix: 0.91 (0.13), residues: 1606 sheet: 0.18 (0.14), residues: 1260 loop : 0.67 (0.14), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG f 115 TYR 0.019 0.001 TYR Y 217 PHE 0.017 0.001 PHE b 29 TRP 0.014 0.002 TRP F 342 HIS 0.006 0.001 HIS G 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (41394) covalent geometry : angle 0.57312 / 0.29 (56356) hydrogen bonds : bond 0.03654 / 2.40 ( 1798) hydrogen bonds : angle 4.88266 / 3.46 ( 4727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.1057 (OUTLIER) cc_final: -0.2343 (mmt) REVERT: A 366 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8344 (mm-30) REVERT: B 49 MET cc_start: -0.0409 (mmt) cc_final: -0.0664 (mpm) REVERT: B 70 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8239 (mtpp) REVERT: C 49 MET cc_start: 0.4465 (ppp) cc_final: 0.4207 (ppp) REVERT: C 357 MET cc_start: 0.9024 (mmm) cc_final: 0.8714 (mtp) REVERT: D 49 MET cc_start: 0.3277 (ptp) cc_final: 0.2604 (ttt) REVERT: E 46 MET cc_start: 0.2180 (mtm) cc_final: 0.1668 (mmm) REVERT: E 49 MET cc_start: 0.6377 (pmm) cc_final: 0.5420 (ptm) REVERT: E 62 SER cc_start: 0.7677 (m) cc_final: 0.7433 (p) REVERT: F 49 MET cc_start: 0.5196 (pmm) cc_final: 0.4454 (tpt) REVERT: G 12 CYS cc_start: 0.8407 (t) cc_final: 0.8125 (t) REVERT: G 46 MET cc_start: 0.4791 (mpt) cc_final: 0.2644 (mmp) REVERT: G 285 MET cc_start: 0.7182 (mmm) cc_final: 0.6831 (mmm) REVERT: G 357 MET cc_start: 0.6867 (mtt) cc_final: 0.6662 (mtp) REVERT: G 362 GLN cc_start: 0.8614 (mp10) cc_final: 0.8255 (pm20) REVERT: H 84 MET cc_start: 0.6298 (tpt) cc_final: 0.6068 (tpp) REVERT: H 113 ASN cc_start: 0.3223 (OUTLIER) cc_final: 0.2641 (t0) REVERT: H 361 LYS cc_start: 0.3999 (OUTLIER) cc_final: 0.3280 (mttm) REVERT: Y 20 THR cc_start: 0.8094 (m) cc_final: 0.7530 (p) REVERT: Y 581 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8529 (mtt) REVERT: a 8 ASP cc_start: 0.8739 (t70) cc_final: 0.7867 (p0) REVERT: a 138 ASP cc_start: 0.8686 (t0) cc_final: 0.8226 (t0) REVERT: b 1 MET cc_start: 0.4767 (OUTLIER) cc_final: 0.3662 (mtt) REVERT: b 8 ASP cc_start: 0.8559 (t0) cc_final: 0.7988 (t0) REVERT: c 6 LYS cc_start: 0.9039 (mttt) cc_final: 0.8315 (tttt) REVERT: c 65 LYS cc_start: 0.8027 (mmtp) cc_final: 0.6739 (tptt) REVERT: d 8 ASP cc_start: 0.8581 (t70) cc_final: 0.8307 (t70) REVERT: d 65 LYS cc_start: 0.8465 (mppt) cc_final: 0.7227 (tptt) REVERT: d 115 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8740 (ttp-170) REVERT: e 13 ASN cc_start: 0.8943 (m-40) cc_final: 0.8739 (m-40) REVERT: e 16 ASP cc_start: 0.8298 (m-30) cc_final: 0.8035 (m-30) REVERT: e 136 ASP cc_start: 0.8883 (m-30) cc_final: 0.8256 (m-30) REVERT: e 138 ASP cc_start: 0.7494 (t70) cc_final: 0.7221 (t0) REVERT: f 73 ASP cc_start: 0.8001 (t0) cc_final: 0.7362 (m-30) outliers start: 60 outliers final: 25 residues processed: 318 average time/residue: 0.7274 time to fit residues: 282.8335 Evaluate side-chains 305 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 102 PHE Chi-restraints excluded: chain X residue 445 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 270 THR Chi-restraints excluded: chain Y residue 400 VAL Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 445 VAL Chi-restraints excluded: chain Y residue 536 THR Chi-restraints excluded: chain Y residue 581 MET Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain d residue 115 ARG Chi-restraints excluded: chain e residue 8 ASP Chi-restraints excluded: chain f residue 106 ARG Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [319, 450, 150, 117, 406, 500, 455, 232, 372, 347, 11] chunk 319 optimal weight: 10.0000 chunk 450 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 406 optimal weight: 8.9990 chunk 500 optimal weight: 0.0070 chunk 455 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 372 optimal weight: 0.0170 chunk 347 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.9438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 HIS C 14 ASN H 163 HIS H 265 GLN X 6 GLN ** Y 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 23 GLN f 23 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.062703 restraints weight = 485723.185| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 6.14 r_work: 0.2737 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 41394 Z= 0.110 Angle : 0.549 11.266 56356 Z= 0.274 Chirality : 0.045 0.179 6354 Planarity : 0.004 0.052 7236 Dihedral : 5.489 80.500 5842 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer: Outliers : 1.87 % Allowed : 9.72 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.12), residues: 5184 helix: 1.07 (0.14), residues: 1606 sheet: 0.25 (0.14), residues: 1258 loop : 0.72 (0.14), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 374 TYR 0.029 0.001 TYR E 168 PHE 0.042 0.001 PHE H 225 TRP 0.014 0.001 TRP F 342 HIS 0.003 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (41394) covalent geometry : angle 0.54877 / 0.27 (56356) hydrogen bonds : bond 0.03243 / 2.13 ( 1798) hydrogen bonds : angle 4.73819 / 3.35 ( 4727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 289 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.0954 (OUTLIER) cc_final: -0.2284 (mmt) REVERT: B 49 MET cc_start: -0.0389 (mmt) cc_final: -0.0652 (mpm) REVERT: B 70 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: C 49 MET cc_start: 0.4390 (ppp) cc_final: 0.4080 (ppp) REVERT: C 357 MET cc_start: 0.9011 (mmm) cc_final: 0.8661 (mtp) REVERT: D 49 MET cc_start: 0.3225 (ptp) cc_final: 0.2623 (ttt) REVERT: E 46 MET cc_start: 0.2249 (mtm) cc_final: 0.1706 (mmm) REVERT: E 49 MET cc_start: 0.6322 (pmm) cc_final: 0.5396 (ptm) REVERT: F 49 MET cc_start: 0.5232 (pmm) cc_final: 0.4470 (tpt) REVERT: F 84 MET cc_start: 0.9015 (tpt) cc_final: 0.8729 (mmm) REVERT: G 12 CYS cc_start: 0.8377 (t) cc_final: 0.8069 (t) REVERT: G 46 MET cc_start: 0.4716 (mpt) cc_final: 0.2572 (mmp) REVERT: G 285 MET cc_start: 0.7151 (mmm) cc_final: 0.6821 (mmm) REVERT: G 357 MET cc_start: 0.7035 (mtt) cc_final: 0.6820 (mtp) REVERT: G 362 GLN cc_start: 0.8598 (mp10) cc_final: 0.8265 (pm20) REVERT: H 113 ASN cc_start: 0.3109 (OUTLIER) cc_final: 0.2582 (t0) REVERT: H 361 LYS cc_start: 0.4353 (OUTLIER) cc_final: 0.3652 (mttm) REVERT: X 63 THR cc_start: 0.9348 (m) cc_final: 0.9057 (p) REVERT: Y 20 THR cc_start: 0.8054 (m) cc_final: 0.7467 (p) REVERT: Y 79 VAL cc_start: 0.7779 (p) cc_final: 0.7501 (m) REVERT: Y 126 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: Y 369 MET cc_start: 0.9096 (tpp) cc_final: 0.8845 (ttm) REVERT: Y 581 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8544 (mtt) REVERT: a 8 ASP cc_start: 0.8717 (t70) cc_final: 0.7892 (p0) REVERT: a 138 ASP cc_start: 0.8683 (t0) cc_final: 0.8219 (t0) REVERT: b 1 MET cc_start: 0.4791 (OUTLIER) cc_final: 0.3700 (mtt) REVERT: b 8 ASP cc_start: 0.8531 (t0) cc_final: 0.7931 (t0) REVERT: c 6 LYS cc_start: 0.9042 (mttt) cc_final: 0.8309 (tttt) REVERT: c 65 LYS cc_start: 0.7982 (mmtp) cc_final: 0.6697 (tptt) REVERT: d 8 ASP cc_start: 0.8556 (t70) cc_final: 0.8266 (t70) REVERT: d 65 LYS cc_start: 0.8424 (mppt) cc_final: 0.7154 (tptt) REVERT: d 115 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8681 (ttp-170) REVERT: e 16 ASP cc_start: 0.8315 (m-30) cc_final: 0.8075 (m-30) REVERT: e 136 ASP cc_start: 0.8874 (m-30) cc_final: 0.8229 (m-30) REVERT: e 138 ASP cc_start: 0.7453 (t70) cc_final: 0.7173 (t0) REVERT: e 150 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7112 (OUTLIER) REVERT: f 47 ASN cc_start: 0.8401 (m110) cc_final: 0.7931 (p0) REVERT: f 73 ASP cc_start: 0.7992 (t0) cc_final: 0.7439 (m-30) REVERT: f 151 ARG cc_start: 0.6678 (mtt90) cc_final: 0.6282 (mtt90) outliers start: 47 outliers final: 18 residues processed: 318 average time/residue: 0.7374 time to fit residues: 285.9135 Evaluate side-chains 303 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 102 PHE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 445 VAL Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Y residue 400 VAL Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 445 VAL Chi-restraints excluded: chain Y residue 581 MET Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain d residue 115 ARG Chi-restraints excluded: chain e residue 150 GLN Chi-restraints excluded: chain f residue 81 GLN Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [159, 466, 202, 386, 214, 357, 58, 107, 66, 11, 394] chunk 159 optimal weight: 3.9990 chunk 466 optimal weight: 0.0980 chunk 202 optimal weight: 6.9990 chunk 386 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 357 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 107 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 394 optimal weight: 10.0000 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN H 163 HIS ** Y 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 23 GLN e 128 GLN f 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062394 restraints weight = 500173.894| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 6.03 r_work: 0.2743 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41394 Z= 0.119 Angle : 0.553 12.028 56356 Z= 0.274 Chirality : 0.046 0.191 6354 Planarity : 0.004 0.052 7236 Dihedral : 5.406 78.848 5842 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.43 % Favored : 97.53 % Rotamer: Outliers : 1.87 % Allowed : 9.90 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.12), residues: 5184 helix: 1.11 (0.14), residues: 1606 sheet: 0.29 (0.14), residues: 1258 loop : 0.75 (0.14), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 374 TYR 0.022 0.001 TYR Y 217 PHE 0.015 0.001 PHE b 29 TRP 0.017 0.001 TRP H 88 HIS 0.003 0.001 HIS G 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (41394) covalent geometry : angle 0.55318 / 0.27 (56356) hydrogen bonds : bond 0.03241 / 2.12 ( 1798) hydrogen bonds : angle 4.68677 / 3.31 ( 4727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: -0.1056 (OUTLIER) cc_final: -0.2372 (mmt) REVERT: B 49 MET cc_start: -0.0391 (mmt) cc_final: -0.0633 (mpm) REVERT: B 70 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: C 49 MET cc_start: 0.4424 (ppp) cc_final: 0.4115 (ppp) REVERT: C 357 MET cc_start: 0.9017 (mmm) cc_final: 0.8682 (mtp) REVERT: D 49 MET cc_start: 0.3258 (ptp) cc_final: 0.2496 (ttt) REVERT: D 66 ILE cc_start: 0.8531 (pt) cc_final: 0.8031 (tp) REVERT: E 46 MET cc_start: 0.2261 (mtm) cc_final: 0.1726 (mmm) REVERT: E 49 MET cc_start: 0.6312 (pmm) cc_final: 0.5402 (ptm) REVERT: F 49 MET cc_start: 0.5221 (pmm) cc_final: 0.4456 (tpt) REVERT: F 84 MET cc_start: 0.9017 (tpt) cc_final: 0.8728 (mmm) REVERT: G 12 CYS cc_start: 0.8367 (t) cc_final: 0.8037 (t) REVERT: G 46 MET cc_start: 0.4694 (mpt) cc_final: 0.2563 (mmp) REVERT: G 49 MET cc_start: 0.1969 (OUTLIER) cc_final: 0.0088 (ttm) REVERT: G 285 MET cc_start: 0.7166 (mmm) cc_final: 0.6845 (mmm) REVERT: G 362 GLN cc_start: 0.8625 (mp10) cc_final: 0.8277 (pm20) REVERT: H 113 ASN cc_start: 0.3117 (OUTLIER) cc_final: 0.2600 (t0) REVERT: H 361 LYS cc_start: 0.4363 (OUTLIER) cc_final: 0.3713 (mttm) REVERT: X 63 THR cc_start: 0.9357 (m) cc_final: 0.9044 (p) REVERT: Y 20 THR cc_start: 0.8002 (m) cc_final: 0.7436 (p) REVERT: Y 79 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7502 (m) REVERT: Y 126 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: Y 369 MET cc_start: 0.9110 (tpp) cc_final: 0.8892 (ttm) REVERT: Y 581 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8582 (mtt) REVERT: a 8 ASP cc_start: 0.8699 (t70) cc_final: 0.7902 (p0) REVERT: b 1 MET cc_start: 0.4791 (OUTLIER) cc_final: 0.3720 (mtt) REVERT: b 8 ASP cc_start: 0.8540 (t0) cc_final: 0.7957 (t0) REVERT: c 6 LYS cc_start: 0.9044 (mttt) cc_final: 0.8314 (tttt) REVERT: c 65 LYS cc_start: 0.7966 (mmtp) cc_final: 0.6667 (tptt) REVERT: d 8 ASP cc_start: 0.8555 (t70) cc_final: 0.8235 (t70) REVERT: d 65 LYS cc_start: 0.8417 (mppt) cc_final: 0.7153 (tptt) REVERT: d 115 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8677 (ttp-170) REVERT: e 16 ASP cc_start: 0.8319 (m-30) cc_final: 0.8066 (m-30) REVERT: e 115 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8244 (tmm-80) REVERT: e 136 ASP cc_start: 0.8871 (m-30) cc_final: 0.8244 (m-30) REVERT: e 138 ASP cc_start: 0.7433 (t70) cc_final: 0.7085 (t0) REVERT: f 47 ASN cc_start: 0.8418 (m110) cc_final: 0.7934 (p0) REVERT: f 73 ASP cc_start: 0.7980 (t0) cc_final: 0.7436 (m-30) REVERT: f 151 ARG cc_start: 0.6668 (mtt90) cc_final: 0.6286 (mtt90) outliers start: 45 outliers final: 20 residues processed: 311 average time/residue: 0.7260 time to fit residues: 276.2698 Evaluate side-chains 306 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 102 PHE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain X residue 445 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Y residue 400 VAL Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 445 VAL Chi-restraints excluded: chain Y residue 581 MET Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain d residue 115 ARG Chi-restraints excluded: chain e residue 8 ASP Chi-restraints excluded: chain f residue 81 GLN Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [22, 194, 366, 203, 314, 276, 0, 283, 169, 23, 36] chunk 22 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 366 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 314 optimal weight: 0.9980 chunk 276 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 283 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN H 163 HIS ** Y 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 23 GLN e 128 GLN f 23 GLN f 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.061243 restraints weight = 504654.655| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 6.13 r_work: 0.2705 rms_B_bonded: 5.00 restraints_weight: 2.0000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 41394 Z= 0.209 Angle : 0.594 12.423 56356 Z= 0.296 Chirality : 0.048 0.206 6354 Planarity : 0.004 0.053 7236 Dihedral : 5.518 75.799 5842 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.71 % Allowed : 10.30 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 5184 helix: 1.02 (0.13), residues: 1606 sheet: 0.25 (0.14), residues: 1258 loop : 0.70 (0.14), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 374 TYR 0.024 0.001 TYR Y 217 PHE 0.026 0.001 PHE H 225 TRP 0.017 0.001 TRP H 88 HIS 0.004 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (41394) covalent geometry : angle 0.59428 / 0.30 (56356) hydrogen bonds : bond 0.03686 / 2.42 ( 1798) hydrogen bonds : angle 4.77960 / 3.37 ( 4727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: -0.0481 (mmt) cc_final: -0.0716 (mpm) REVERT: B 70 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8230 (mtpp) REVERT: C 49 MET cc_start: 0.4407 (ppp) cc_final: 0.4126 (ppp) REVERT: C 357 MET cc_start: 0.9057 (mmm) cc_final: 0.8733 (mtp) REVERT: D 49 MET cc_start: 0.3286 (ptp) cc_final: 0.2475 (ttt) REVERT: D 66 ILE cc_start: 0.8532 (pt) cc_final: 0.8039 (tp) REVERT: E 46 MET cc_start: 0.2283 (mtm) cc_final: 0.1745 (mmm) REVERT: E 49 MET cc_start: 0.6327 (pmm) cc_final: 0.5415 (ptm) REVERT: F 49 MET cc_start: 0.5263 (pmm) cc_final: 0.4520 (tpt) REVERT: G 12 CYS cc_start: 0.8414 (t) cc_final: 0.8079 (t) REVERT: G 46 MET cc_start: 0.4654 (mpt) cc_final: 0.2446 (mmp) REVERT: G 49 MET cc_start: 0.1957 (OUTLIER) cc_final: 0.0108 (mtt) REVERT: G 84 MET cc_start: 0.7952 (mmm) cc_final: 0.7478 (tpt) REVERT: G 285 MET cc_start: 0.7160 (mmm) cc_final: 0.6796 (mmm) REVERT: G 315 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5979 (mpp) REVERT: G 362 GLN cc_start: 0.8655 (mp10) cc_final: 0.8302 (pm20) REVERT: H 113 ASN cc_start: 0.2953 (OUTLIER) cc_final: 0.2405 (t0) REVERT: H 225 PHE cc_start: 0.6275 (t80) cc_final: 0.5569 (t80) REVERT: H 229 MET cc_start: 0.7799 (mpp) cc_final: 0.7394 (mpp) REVERT: H 361 LYS cc_start: 0.4454 (OUTLIER) cc_final: 0.3782 (mttm) REVERT: Y 20 THR cc_start: 0.8128 (m) cc_final: 0.7542 (p) REVERT: Y 79 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7638 (m) REVERT: Y 369 MET cc_start: 0.9129 (tpp) cc_final: 0.8908 (ttm) REVERT: a 8 ASP cc_start: 0.8733 (t70) cc_final: 0.7875 (p0) REVERT: b 1 MET cc_start: 0.4859 (OUTLIER) cc_final: 0.3812 (mtt) REVERT: b 8 ASP cc_start: 0.8582 (t0) cc_final: 0.7998 (t0) REVERT: c 6 LYS cc_start: 0.9056 (mttt) cc_final: 0.8315 (tttt) REVERT: d 8 ASP cc_start: 0.8582 (t70) cc_final: 0.8300 (t70) REVERT: d 65 LYS cc_start: 0.8467 (mppt) cc_final: 0.7189 (tptt) REVERT: e 16 ASP cc_start: 0.8316 (m-30) cc_final: 0.8073 (m-30) REVERT: e 136 ASP cc_start: 0.8871 (m-30) cc_final: 0.8214 (m-30) REVERT: e 138 ASP cc_start: 0.7454 (t70) cc_final: 0.7160 (t0) REVERT: f 73 ASP cc_start: 0.8016 (t0) cc_final: 0.7388 (m-30) REVERT: f 151 ARG cc_start: 0.6735 (mtt90) cc_final: 0.6317 (mtt90) outliers start: 37 outliers final: 18 residues processed: 302 average time/residue: 0.7108 time to fit residues: 263.3152 Evaluate side-chains 299 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 315 MET Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 102 PHE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain X residue 445 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 400 VAL Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 445 VAL Chi-restraints excluded: chain Y residue 536 THR Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [48, 161, 209, 415, 461, 494, 149, 342, 489, 123, 47] chunk 48 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 415 optimal weight: 2.9990 chunk 461 optimal weight: 3.9990 chunk 494 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 chunk 489 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN H 163 HIS ** Y 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 23 GLN e 128 GLN f 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.097267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.062246 restraints weight = 466492.443| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 5.71 r_work: 0.2734 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41394 Z= 0.144 Angle : 0.571 12.474 56356 Z= 0.283 Chirality : 0.046 0.189 6354 Planarity : 0.004 0.053 7236 Dihedral : 5.461 73.680 5842 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 1.71 % Allowed : 10.44 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.12), residues: 5184 helix: 1.05 (0.13), residues: 1606 sheet: 0.27 (0.14), residues: 1258 loop : 0.71 (0.14), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 374 TYR 0.023 0.001 TYR Y 217 PHE 0.022 0.001 PHE H 225 TRP 0.018 0.001 TRP H 88 HIS 0.003 0.001 HIS G 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (41394) covalent geometry : angle 0.57096 / 0.28 (56356) hydrogen bonds : bond 0.03414 / 2.23 ( 1798) hydrogen bonds : angle 4.72339 / 3.33 ( 4727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7664 (mmt) REVERT: B 49 MET cc_start: -0.0681 (mmt) cc_final: -0.0895 (mpm) REVERT: B 70 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8420 (mtpp) REVERT: C 49 MET cc_start: 0.4475 (ppp) cc_final: 0.4199 (ppp) REVERT: C 357 MET cc_start: 0.9023 (mmm) cc_final: 0.8700 (mtp) REVERT: D 49 MET cc_start: 0.3282 (ptp) cc_final: 0.2495 (ttt) REVERT: D 66 ILE cc_start: 0.8524 (pt) cc_final: 0.8029 (tp) REVERT: E 46 MET cc_start: 0.2279 (mtm) cc_final: 0.1720 (mmm) REVERT: E 49 MET cc_start: 0.6354 (pmm) cc_final: 0.5488 (ptm) REVERT: E 84 MET cc_start: 0.9083 (tpt) cc_final: 0.8741 (tpt) REVERT: F 49 MET cc_start: 0.5267 (pmm) cc_final: 0.4540 (tpt) REVERT: G 46 MET cc_start: 0.4692 (mpt) cc_final: 0.2536 (mmp) REVERT: G 49 MET cc_start: 0.1952 (OUTLIER) cc_final: 0.0315 (mtt) REVERT: G 84 MET cc_start: 0.7880 (mmm) cc_final: 0.7565 (tpt) REVERT: G 285 MET cc_start: 0.7130 (mmm) cc_final: 0.6752 (mmm) REVERT: G 327 MET cc_start: 0.3354 (tpt) cc_final: 0.1548 (tmt) REVERT: G 362 GLN cc_start: 0.8662 (mp10) cc_final: 0.8296 (pm20) REVERT: H 113 ASN cc_start: 0.2817 (OUTLIER) cc_final: 0.2264 (t0) REVERT: H 225 PHE cc_start: 0.5967 (t80) cc_final: 0.5757 (t80) REVERT: H 229 MET cc_start: 0.7779 (mpp) cc_final: 0.7577 (mpt) REVERT: H 361 LYS cc_start: 0.4533 (OUTLIER) cc_final: 0.3852 (mttm) REVERT: Y 20 THR cc_start: 0.8061 (m) cc_final: 0.7493 (p) REVERT: Y 79 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7649 (m) REVERT: Y 369 MET cc_start: 0.9110 (tpp) cc_final: 0.8906 (ttm) REVERT: a 8 ASP cc_start: 0.8700 (t70) cc_final: 0.7905 (p0) REVERT: b 1 MET cc_start: 0.4874 (OUTLIER) cc_final: 0.3786 (mtt) REVERT: b 8 ASP cc_start: 0.8559 (t0) cc_final: 0.7974 (t0) REVERT: c 6 LYS cc_start: 0.9052 (mttt) cc_final: 0.8307 (tttt) REVERT: c 65 LYS cc_start: 0.8034 (mmtp) cc_final: 0.6753 (tptt) REVERT: d 8 ASP cc_start: 0.8559 (t70) cc_final: 0.8272 (t70) REVERT: d 65 LYS cc_start: 0.8408 (mppt) cc_final: 0.7135 (tptt) REVERT: d 115 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8720 (ttp-170) REVERT: e 16 ASP cc_start: 0.8320 (m-30) cc_final: 0.8057 (m-30) REVERT: e 136 ASP cc_start: 0.8878 (m-30) cc_final: 0.8234 (m-30) REVERT: e 138 ASP cc_start: 0.7485 (t70) cc_final: 0.7165 (t0) REVERT: f 73 ASP cc_start: 0.7994 (t0) cc_final: 0.7414 (m-30) REVERT: f 151 ARG cc_start: 0.6776 (mtt90) cc_final: 0.6420 (mtt90) outliers start: 37 outliers final: 23 residues processed: 307 average time/residue: 0.7226 time to fit residues: 272.1931 Evaluate side-chains 306 residues out of total 4198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 102 PHE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 445 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 400 VAL Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 445 VAL Chi-restraints excluded: chain Y residue 536 THR Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain d residue 115 ARG Chi-restraints excluded: chain e residue 8 ASP Chi-restraints excluded: chain f residue 138 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: [341, 481, 186, 237, 502, 274, 423, 369, 175, 433, 32] chunk 341 optimal weight: 9.9990 chunk 481 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 502 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 423 optimal weight: 0.9980 chunk 369 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 433 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN ** F 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 HIS ** Y 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 ASN e 23 GLN e 128 GLN f 23 GLN f 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.060188 restraints weight = 475624.577| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 5.40 r_work: 0.2716 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 41394 Z= 0.234 Angle : 0.693 43.021 56356 Z= 0.337 Chirality : 0.049 0.216 6354 Planarity : 0.004 0.067 7236 Dihedral : 5.617 77.332 5842 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.20 % Favored : 96.78 % Rotamer: Outliers : 1.73 % Allowed : 10.46 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.12), residues: 5184 helix: 0.93 (0.13), residues: 1606 sheet: 0.21 (0.14), residues: 1260 loop : 0.65 (0.14), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 374 TYR 0.033 0.002 TYR E 168 PHE 0.033 0.002 PHE H 225 TRP 0.030 0.002 TRP H 88 HIS 0.005 0.001 HIS H 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.23 (41394) covalent geometry : angle 0.69310 / 0.34 (56356) hydrogen bonds : bond 0.03993 / 2.62 ( 1798) hydrogen bonds : angle 4.86421 / 3.43 ( 4727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13992.33 seconds wall clock time: 239 minutes 1.21 seconds (14341.21 seconds total)