Starting phenix.real_space_refine on Sun Feb 8 10:13:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mse_48586/02_2026/9mse_48586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mse_48586/02_2026/9mse_48586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mse_48586/02_2026/9mse_48586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mse_48586/02_2026/9mse_48586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mse_48586/02_2026/9mse_48586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mse_48586/02_2026/9mse_48586.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 112 5.49 5 Mg 3 5.21 5 S 143 5.16 5 C 26906 2.51 5 N 7503 2.21 5 O 9141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43810 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "B" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "C" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "D" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1972 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "E" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "F" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "G" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2347 Classifications: {'peptide': 302} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 287} Chain breaks: 2 Chain: "H" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 10523 Classifications: {'peptide': 1352} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1296} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "M" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3371 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "S" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 217 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "U" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "V" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} 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: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 296 Classifications: {'water': 296} Link IDs: {None: 295} Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 205 Classifications: {'water': 205} Link IDs: {None: 204} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "U" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "V" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27064 SG CYS J 70 51.266 69.663 129.820 1.00 88.52 S ATOM 27078 SG CYS J 72 53.109 70.541 132.949 1.00100.09 S ATOM 27186 SG CYS J 85 49.630 71.555 132.832 1.00100.27 S ATOM 27210 SG CYS J 88 52.310 73.358 130.749 1.00 85.82 S ATOM 32898 SG CYS J 814 33.731 98.719 69.000 1.00102.89 S ATOM 33463 SG CYS J 888 36.926 98.111 71.043 1.00 78.86 S ATOM 33514 SG CYS J 895 35.260 95.428 69.111 1.00 87.16 S ATOM 33535 SG CYS J 898 36.980 98.007 67.185 1.00101.51 S Time building chain proxies: 9.82, per 1000 atoms: 0.22 Number of scatterers: 43810 At special positions: 0 Unit cell: (160.82, 171.14, 239.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 143 16.00 P 112 15.00 Mg 3 11.99 O 9141 8.00 N 7503 7.00 C 26906 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: 3.83 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9640 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 71 sheets defined 45.4% alpha, 14.8% beta 44 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 5.90 Creating SS restraints... Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.527A pdb=" N ILE A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.553A pdb=" N LYS A 188 " --> pdb=" O ASP A 185 " (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 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 243 removed outlier: 3.918A pdb=" N LEU A 243 " --> pdb=" O ILE A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.540A pdb=" N VAL A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 309 through 315 removed outlier: 4.569A pdb=" N LYS A 314 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU A 315 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.546A pdb=" N ARG A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.574A pdb=" N GLU A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.504A pdb=" N LEU A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.519A pdb=" N ILE B 203 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 204 " --> pdb=" O ARG B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 204' Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 247 through 250 removed outlier: 3.682A pdb=" N LYS B 250 " --> pdb=" O ALA B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.644A pdb=" N ILE B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.553A pdb=" N TYR B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 316 through 332 Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 354 through 369 removed outlier: 3.524A pdb=" N GLU B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.957A pdb=" N LEU B 380 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 156 removed outlier: 3.717A pdb=" N GLU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE C 149 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 150 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 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 203 through 210 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.777A pdb=" N ALA C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 4.326A pdb=" N GLU C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.546A pdb=" N LYS C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 301 removed outlier: 3.539A pdb=" N TYR C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 354 through 369 removed outlier: 3.568A pdb=" N GLU C 358 " --> pdb=" O GLY C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.561A pdb=" N GLU D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 149 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 240 through 243 removed outlier: 3.667A pdb=" N LEU D 243 " --> pdb=" O ILE D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.610A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 290 Processing helix chain 'D' and resid 293 through 301 removed outlier: 3.610A pdb=" N TYR D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 333 Processing helix chain 'D' and resid 340 through 348 Processing helix chain 'D' and resid 354 through 369 removed outlier: 3.567A pdb=" N GLU D 358 " --> pdb=" O GLY D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'E' and resid 143 through 156 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 172 through 183 Processing helix chain 'E' and resid 203 through 209 removed outlier: 3.538A pdb=" N LEU E 208 " --> pdb=" O PHE E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 251 through 257 removed outlier: 3.835A pdb=" N ILE E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 290 Processing helix chain 'E' and resid 293 through 301 removed outlier: 3.611A pdb=" N TYR E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR E 298 " --> pdb=" O GLU E 294 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 316 through 333 removed outlier: 3.702A pdb=" N LEU E 320 " --> pdb=" O ASP E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 350 Processing helix chain 'E' and resid 354 through 370 Processing helix chain 'F' and resid 143 through 156 Processing helix chain 'F' and resid 157 through 159 No H-bonds generated for 'chain 'F' and resid 157 through 159' Processing helix chain 'F' and resid 172 through 184 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 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 203 through 210 removed outlier: 3.633A pdb=" N LEU F 208 " --> pdb=" O PHE F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.969A pdb=" N ALA F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 257 removed outlier: 3.606A pdb=" N ILE F 255 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 289 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 316 through 333 Processing helix chain 'F' and resid 340 through 350 removed outlier: 3.542A pdb=" N GLN F 344 " --> pdb=" O THR F 340 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU F 345 " --> pdb=" O LYS F 341 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F 347 " --> pdb=" O ALA F 343 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU F 348 " --> pdb=" O GLN F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 370 removed outlier: 3.593A pdb=" N GLU F 358 " --> pdb=" O GLY F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 4.113A pdb=" N LEU F 380 " --> pdb=" O ASP F 376 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.649A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.680A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 158 Processing helix chain 'G' and resid 212 through 233 removed outlier: 4.438A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.803A pdb=" N LEU G 254 " --> pdb=" O ASP G 250 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG G 255 " --> pdb=" O PRO G 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 250 through 255' Processing helix chain 'G' and resid 256 through 260 Processing helix chain 'G' and resid 263 through 273 Processing helix chain 'G' and resid 277 through 282 Processing helix chain 'G' and resid 285 through 291 Processing helix chain 'G' and resid 296 through 310 removed outlier: 3.878A pdb=" N ARG G 310 " --> pdb=" O VAL G 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.563A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.567A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 159 removed outlier: 3.665A pdb=" N THR H 157 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE H 159 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.582A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.599A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.911A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 removed outlier: 4.251A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.029A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.541A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 359 through 371 removed outlier: 4.339A pdb=" N LEU I 363 " --> pdb=" O ARG I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.925A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 479 removed outlier: 3.592A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.689A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 545 through 549 removed outlier: 3.512A pdb=" N ASP I 549 " --> pdb=" O GLU I 546 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.619A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.565A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.673A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 906 Processing helix chain 'I' and resid 908 through 911 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.662A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU I 963 " --> pdb=" O ASP I 959 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 986 through 992 Processing helix chain 'I' and resid 993 through 999 Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.775A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU I1011 " --> pdb=" O LYS I1007 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.502A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.536A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.558A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.848A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.731A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.755A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 11 removed outlier: 3.807A pdb=" N GLN J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.773A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.593A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 removed outlier: 4.002A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.623A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 removed outlier: 3.522A pdb=" N ARG J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.155A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.850A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.838A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.971A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.592A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.698A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 4.292A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.630A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.706A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.513A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.808A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.528A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1374 removed outlier: 3.741A pdb=" N ALA J1374 " --> pdb=" O MET J1370 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.521A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 4.277A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 28 removed outlier: 4.327A pdb=" N GLN M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 23 through 28' Processing helix chain 'M' and resid 29 through 44 removed outlier: 3.612A pdb=" N SER M 43 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.521A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 148 Processing helix chain 'M' and resid 157 through 166 removed outlier: 3.507A pdb=" N ILE M 161 " --> pdb=" O PRO M 157 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.803A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 removed outlier: 3.710A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.500A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU M 248 " --> pdb=" O ASP M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 265 removed outlier: 3.641A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE M 264 " --> pdb=" O GLY M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 306 Processing helix chain 'M' and resid 312 through 351 removed outlier: 3.648A pdb=" N PHE M 318 " --> pdb=" O GLY M 314 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.844A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 400 through 403 removed outlier: 3.686A pdb=" N PHE M 403 " --> pdb=" O LYS M 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 400 through 403' Processing helix chain 'M' and resid 417 through 430 Processing helix chain 'M' and resid 438 through 448 removed outlier: 3.921A pdb=" N GLU M 448 " --> pdb=" O SER M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 465 Processing helix chain 'M' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 195 removed outlier: 6.526A pdb=" N VAL A 192 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP A 238 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 194 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 279 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 339 removed outlier: 7.451A pdb=" N GLY A 338 " --> pdb=" O ILE A 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 195 removed outlier: 6.515A pdb=" N VAL B 192 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP B 238 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 194 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 167 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 260 Processing sheet with id=AA7, first strand: chain 'B' and resid 338 through 339 removed outlier: 7.057A pdb=" N GLY B 338 " --> pdb=" O ILE B 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 191 through 195 removed outlier: 3.548A pdb=" N GLY C 167 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 259 through 261 Processing sheet with id=AB1, first strand: chain 'C' and resid 338 through 339 removed outlier: 7.451A pdb=" N GLY C 338 " --> pdb=" O ILE C 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 191 through 195 removed outlier: 3.590A pdb=" N ALA D 278 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU D 164 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AB4, first strand: chain 'D' and resid 259 through 260 Processing sheet with id=AB5, first strand: chain 'E' and resid 191 through 195 removed outlier: 6.317A pdb=" N LEU E 164 " --> pdb=" O ILE E 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 210 through 211 Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AB8, first strand: chain 'E' and resid 338 through 339 removed outlier: 6.890A pdb=" N GLY E 338 " --> pdb=" O ILE E 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 191 through 195 removed outlier: 6.716A pdb=" N VAL F 192 " --> pdb=" O PHE F 236 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASP F 238 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU F 194 " --> pdb=" O ASP F 238 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU F 235 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA F 278 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU F 237 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL F 163 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR F 279 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE F 165 " --> pdb=" O THR F 279 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'F' and resid 338 through 339 removed outlier: 7.451A pdb=" N GLY F 338 " --> pdb=" O ILE F 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.049A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU G 198 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA G 189 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.512A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC6, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.526A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'H' and resid 13 through 20 removed outlier: 6.487A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP H 197 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA H 190 " --> pdb=" O ASP H 197 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP H 199 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU H 188 " --> pdb=" O ASP H 199 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU H 201 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN H 186 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE H 203 " --> pdb=" O ALA H 184 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA H 184 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET H 205 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG H 182 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR H 207 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL H 180 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.973A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AD2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.659A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.452A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AD6, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.590A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.308A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 227 through 230 Processing sheet with id=AD9, first strand: chain 'I' and resid 239 through 240 removed outlier: 3.604A pdb=" N MET I 239 " --> pdb=" O ILE I 285 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 255 through 256 Processing sheet with id=AE2, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.718A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.471A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 580 through 581 removed outlier: 7.126A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AE6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.421A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.757A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AE9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AF1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.140A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.556A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AF4, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.833A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AF6, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.867A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.677A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.058A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.863A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AG2, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AG3, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AG4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AG5, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.379A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.570A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.551A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 991 through 997 removed outlier: 6.456A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS J 996 " --> pdb=" O THR J 980 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR J 980 " --> pdb=" O LYS J 996 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.390A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AH2, first strand: chain 'J' and resid 1046 through 1050 Processing sheet with id=AH3, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.310A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AH5, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.836A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AH7, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.637A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 414 through 416 removed outlier: 4.062A pdb=" N ASN M 408 " --> pdb=" O MET M 452 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET M 452 " --> pdb=" O ASN M 408 " (cutoff:3.500A) 1742 hydrogen bonds defined for protein. 4896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 13.43 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11886 1.33 - 1.45: 6830 1.45 - 1.57: 24808 1.57 - 1.69: 212 1.69 - 1.81: 236 Bond restraints: 43972 Sorted by residual: bond pdb=" O POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 1.661 1.610 0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" O POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.660 1.610 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" O1 POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.531 1.508 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" O2 POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.531 1.509 0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" O5 POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 1.530 1.509 0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 43967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 59689 3.51 - 7.03: 39 7.03 - 10.54: 2 10.54 - 14.05: 0 14.05 - 17.56: 1 Bond angle restraints: 59731 Sorted by residual: angle pdb=" P1 POP I1401 " pdb=" O POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 139.66 122.10 17.56 3.00e+00 1.11e-01 3.43e+01 angle pdb=" N GLU E 371 " pdb=" CA GLU E 371 " pdb=" C GLU E 371 " ideal model delta sigma weight residual 114.56 110.62 3.94 1.27e+00 6.20e-01 9.62e+00 angle pdb=" C LEU M 19 " pdb=" N GLN M 20 " pdb=" CA GLN M 20 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.59e+00 angle pdb=" N ILE J 490 " pdb=" CA ILE J 490 " pdb=" C ILE J 490 " ideal model delta sigma weight residual 111.90 109.61 2.29 8.10e-01 1.52e+00 7.96e+00 angle pdb=" N GLY J1182 " pdb=" CA GLY J1182 " pdb=" C GLY J1182 " ideal model delta sigma weight residual 111.20 114.64 -3.44 1.39e+00 5.18e-01 6.11e+00 ... (remaining 59726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 24721 17.14 - 34.28: 1496 34.28 - 51.42: 508 51.42 - 68.57: 167 68.57 - 85.71: 14 Dihedral angle restraints: 26906 sinusoidal: 11941 harmonic: 14965 Sorted by residual: dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU J 701 " pdb=" C LEU J 701 " pdb=" N GLN J 702 " pdb=" CA GLN J 702 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N VAL H 192 " pdb=" CA VAL H 192 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 26903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 4399 0.032 - 0.063: 1671 0.063 - 0.095: 413 0.095 - 0.127: 256 0.127 - 0.158: 21 Chirality restraints: 6760 Sorted by residual: chirality pdb=" CB VAL J1255 " pdb=" CA VAL J1255 " pdb=" CG1 VAL J1255 " pdb=" CG2 VAL J1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ILE I 734 " pdb=" N ILE I 734 " pdb=" C ILE I 734 " pdb=" CB ILE I 734 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 6757 not shown) Planarity restraints: 7407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 823 " -0.035 5.00e-02 4.00e+02 5.41e-02 4.67e+00 pdb=" N PRO J 824 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO J 824 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 824 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO I 698 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO I 590 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.021 5.00e-02 4.00e+02 ... (remaining 7404 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 497 2.61 - 3.18: 35262 3.18 - 3.75: 64287 3.75 - 4.33: 94082 4.33 - 4.90: 155784 Nonbonded interactions: 349912 Sorted by model distance: nonbonded pdb="MG MG J1501 " pdb=" O HOH J1729 " model vdw 2.033 2.170 nonbonded pdb=" O2B ATP E 401 " pdb="MG MG E 402 " model vdw 2.142 2.170 nonbonded pdb="MG MG J1501 " pdb=" O HOH J1747 " model vdw 2.181 2.170 nonbonded pdb=" OG SER I 318 " pdb=" OD1 ASP I 320 " model vdw 2.182 3.040 nonbonded pdb=" O GLU G 72 " pdb=" O HOH G 401 " model vdw 2.191 3.040 ... (remaining 349907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 138 through 383) selection = (chain 'B' and resid 138 through 383) selection = (chain 'C' and resid 138 through 383) selection = (chain 'D' and resid 138 through 383) selection = (chain 'E' and resid 138 through 383) selection = (chain 'F' and resid 138 through 383) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 53.280 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 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 0.224 43980 Z= 0.130 Angle : 0.467 17.563 59743 Z= 0.256 Chirality : 0.040 0.158 6760 Planarity : 0.004 0.054 7407 Dihedral : 13.188 85.708 17266 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 1.10 % Allowed : 4.64 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.58 (0.12), residues: 5164 helix: 1.24 (0.12), residues: 2029 sheet: 0.93 (0.20), residues: 657 loop : -0.45 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I1246 TYR 0.014 0.001 TYR J 631 PHE 0.014 0.001 PHE J1319 TRP 0.007 0.001 TRP J 409 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00261 (43972) covalent geometry : angle 0.46685 (59731) hydrogen bonds : bond 0.14616 ( 1844) hydrogen bonds : angle 5.40872 ( 5104) metal coordination : bond 0.11855 ( 8) metal coordination : angle 0.04724 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 349 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8837 (mt) REVERT: A 294 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: A 298 TYR cc_start: 0.8381 (m-10) cc_final: 0.7887 (m-80) REVERT: A 350 TYR cc_start: 0.8872 (t80) cc_final: 0.8493 (t80) REVERT: B 146 MET cc_start: 0.8998 (mmm) cc_final: 0.8796 (mmm) REVERT: F 282 ASN cc_start: 0.8966 (t0) cc_final: 0.8584 (t0) REVERT: F 340 THR cc_start: 0.8394 (p) cc_final: 0.8018 (p) REVERT: F 344 GLN cc_start: 0.8945 (mt0) cc_final: 0.8739 (mm110) REVERT: G 268 ASN cc_start: 0.9093 (m110) cc_final: 0.8826 (m110) REVERT: G 294 ASN cc_start: 0.8860 (m110) cc_final: 0.8559 (t0) REVERT: H 212 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8058 (t0) REVERT: I 369 MET cc_start: 0.8835 (tmm) cc_final: 0.8634 (ppp) REVERT: J 975 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6289 (mp) REVERT: J 1020 TRP cc_start: 0.7112 (p90) cc_final: 0.6648 (p90) REVERT: J 1095 MET cc_start: 0.7517 (ttm) cc_final: 0.7072 (tmt) REVERT: J 1189 MET cc_start: 0.8248 (ttp) cc_final: 0.7414 (tmm) REVERT: J 1373 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7859 (mmp80) REVERT: K 36 ASP cc_start: 0.8868 (m-30) cc_final: 0.8548 (p0) REVERT: K 72 GLN cc_start: 0.9043 (tt0) cc_final: 0.8578 (tm-30) REVERT: M 238 VAL cc_start: 0.9479 (t) cc_final: 0.9272 (m) outliers start: 49 outliers final: 16 residues processed: 389 average time/residue: 0.9056 time to fit residues: 425.1760 Evaluate side-chains 265 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 265 optimal weight: 4.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 516 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 649 GLN I 659 GLN I 686 GLN I 922 ASN I1220 GLN J 206 ASN J 651 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN M 3 GLN M 282 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.086217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052338 restraints weight = 108459.798| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.77 r_work: 0.2705 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 43980 Z= 0.217 Angle : 0.545 11.249 59743 Z= 0.291 Chirality : 0.042 0.199 6760 Planarity : 0.004 0.046 7407 Dihedral : 13.781 97.645 6951 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 1.77 % Allowed : 7.80 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.69 (0.12), residues: 5164 helix: 1.38 (0.12), residues: 2093 sheet: 0.95 (0.20), residues: 643 loop : -0.46 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 996 TYR 0.019 0.001 TYR F 350 PHE 0.015 0.001 PHE J1319 TRP 0.013 0.001 TRP F 352 HIS 0.011 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00522 (43972) covalent geometry : angle 0.54424 (59731) hydrogen bonds : bond 0.04941 ( 1844) hydrogen bonds : angle 4.38534 ( 5104) metal coordination : bond 0.00874 ( 8) metal coordination : angle 2.35480 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 261 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.8003 (mm) REVERT: A 294 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: A 298 TYR cc_start: 0.8717 (m-10) cc_final: 0.8185 (m-10) REVERT: A 350 TYR cc_start: 0.8993 (t80) cc_final: 0.8512 (t80) REVERT: D 295 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8955 (m-30) REVERT: E 238 ASP cc_start: 0.9065 (t0) cc_final: 0.8796 (t0) REVERT: E 376 ASP cc_start: 0.9037 (p0) cc_final: 0.8501 (p0) REVERT: F 282 ASN cc_start: 0.9080 (t0) cc_final: 0.8537 (t0) REVERT: F 340 THR cc_start: 0.8578 (p) cc_final: 0.8165 (p) REVERT: F 344 GLN cc_start: 0.8823 (mt0) cc_final: 0.8613 (mm110) REVERT: F 350 TYR cc_start: 0.7896 (t80) cc_final: 0.7636 (t80) REVERT: G 268 ASN cc_start: 0.9115 (m110) cc_final: 0.8797 (m110) REVERT: G 294 ASN cc_start: 0.9063 (m110) cc_final: 0.8575 (t0) REVERT: H 95 LYS cc_start: 0.8872 (pmtt) cc_final: 0.8572 (pmmt) REVERT: H 212 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7619 (t0) REVERT: I 165 HIS cc_start: 0.8924 (t-90) cc_final: 0.8682 (t-90) REVERT: I 200 ARG cc_start: 0.8275 (mtm180) cc_final: 0.8037 (mtm180) REVERT: I 239 MET cc_start: 0.7323 (tmm) cc_final: 0.6868 (ppp) REVERT: I 319 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7462 (mm) REVERT: I 369 MET cc_start: 0.9077 (tmm) cc_final: 0.8771 (ppp) REVERT: I 394 ARG cc_start: 0.8981 (mtt180) cc_final: 0.8467 (mmm-85) REVERT: I 488 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8261 (mmp) REVERT: J 314 ARG cc_start: 0.8290 (mmp-170) cc_final: 0.7928 (mmm160) REVERT: J 322 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8478 (mtm-85) REVERT: J 1095 MET cc_start: 0.7495 (ttm) cc_final: 0.7221 (tmt) REVERT: J 1189 MET cc_start: 0.8380 (ttp) cc_final: 0.7295 (tmm) REVERT: J 1373 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7766 (mmp80) REVERT: K 36 ASP cc_start: 0.8947 (m-30) cc_final: 0.8247 (p0) REVERT: K 61 ASN cc_start: 0.7505 (t0) cc_final: 0.7271 (t0) REVERT: K 69 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7746 (mmm160) outliers start: 79 outliers final: 32 residues processed: 314 average time/residue: 0.7173 time to fit residues: 280.7862 Evaluate side-chains 281 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 344 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 221 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 418 optimal weight: 0.9990 chunk 363 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 477 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 922 ASN J 320 ASN J 651 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN J1098 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.087620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.053721 restraints weight = 105937.250| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.68 r_work: 0.2661 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43980 Z= 0.102 Angle : 0.464 10.733 59743 Z= 0.248 Chirality : 0.039 0.170 6760 Planarity : 0.003 0.047 7407 Dihedral : 13.646 95.394 6949 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 1.26 % Allowed : 8.68 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.91 (0.12), residues: 5164 helix: 1.60 (0.12), residues: 2107 sheet: 0.96 (0.20), residues: 634 loop : -0.35 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 473 TYR 0.017 0.001 TYR F 350 PHE 0.014 0.001 PHE J1319 TRP 0.017 0.001 TRP J1020 HIS 0.008 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00228 (43972) covalent geometry : angle 0.46352 (59731) hydrogen bonds : bond 0.03616 ( 1844) hydrogen bonds : angle 4.02081 ( 5104) metal coordination : bond 0.00399 ( 8) metal coordination : angle 1.87510 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASN cc_start: 0.8482 (t0) cc_final: 0.8271 (t0) REVERT: A 294 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: A 298 TYR cc_start: 0.8693 (m-10) cc_final: 0.8080 (m-10) REVERT: A 316 ASP cc_start: 0.8715 (m-30) cc_final: 0.8423 (m-30) REVERT: A 350 TYR cc_start: 0.9068 (t80) cc_final: 0.8592 (t80) REVERT: E 238 ASP cc_start: 0.8944 (t0) cc_final: 0.8615 (t0) REVERT: E 316 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8872 (t0) REVERT: E 374 PHE cc_start: 0.9375 (m-10) cc_final: 0.9169 (m-10) REVERT: F 282 ASN cc_start: 0.9051 (t0) cc_final: 0.8496 (t0) REVERT: F 340 THR cc_start: 0.8525 (p) cc_final: 0.8093 (p) REVERT: G 268 ASN cc_start: 0.9162 (m110) cc_final: 0.8876 (m110) REVERT: G 294 ASN cc_start: 0.8990 (m110) cc_final: 0.8596 (t0) REVERT: H 95 LYS cc_start: 0.8901 (pmtt) cc_final: 0.8634 (pmmt) REVERT: H 212 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7750 (t0) REVERT: I 165 HIS cc_start: 0.8862 (t-90) cc_final: 0.8525 (t70) REVERT: I 200 ARG cc_start: 0.8235 (mtm180) cc_final: 0.7910 (mtm-85) REVERT: I 239 MET cc_start: 0.7233 (tmm) cc_final: 0.6968 (tmm) REVERT: I 369 MET cc_start: 0.9085 (tmm) cc_final: 0.8698 (ppp) REVERT: I 394 ARG cc_start: 0.8958 (mtt180) cc_final: 0.8461 (mmm-85) REVERT: I 439 LYS cc_start: 0.8827 (tptp) cc_final: 0.8442 (tptp) REVERT: I 488 MET cc_start: 0.8540 (mmp) cc_final: 0.8301 (mmp) REVERT: I 996 ARG cc_start: 0.8874 (mmm160) cc_final: 0.8666 (mmp80) REVERT: J 314 ARG cc_start: 0.8462 (mmp-170) cc_final: 0.7755 (mmm160) REVERT: J 322 ARG cc_start: 0.8927 (ttm110) cc_final: 0.8529 (mtm-85) REVERT: J 905 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8651 (mmt180) REVERT: J 1095 MET cc_start: 0.7512 (ttm) cc_final: 0.7238 (tmt) REVERT: J 1189 MET cc_start: 0.8413 (ttp) cc_final: 0.7373 (tmm) REVERT: J 1373 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7848 (mmp80) REVERT: K 7 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8058 (mm-40) REVERT: K 36 ASP cc_start: 0.8982 (m-30) cc_final: 0.8378 (p0) REVERT: K 69 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7679 (mmm160) REVERT: K 72 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8358 (tm-30) outliers start: 56 outliers final: 18 residues processed: 292 average time/residue: 0.7034 time to fit residues: 255.2832 Evaluate side-chains 257 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 905 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 14 optimal weight: 9.9990 chunk 320 optimal weight: 2.9990 chunk 416 optimal weight: 10.0000 chunk 486 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 290 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN I 922 ASN J 651 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.086985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.053174 restraints weight = 106285.413| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.66 r_work: 0.2648 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43980 Z= 0.124 Angle : 0.465 10.754 59743 Z= 0.248 Chirality : 0.039 0.148 6760 Planarity : 0.003 0.041 7407 Dihedral : 13.498 76.250 6930 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 1.64 % Allowed : 9.17 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.97 (0.12), residues: 5164 helix: 1.67 (0.12), residues: 2108 sheet: 0.94 (0.20), residues: 643 loop : -0.33 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 8 TYR 0.019 0.001 TYR F 350 PHE 0.014 0.001 PHE J1319 TRP 0.016 0.001 TRP J1193 HIS 0.008 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00287 (43972) covalent geometry : angle 0.46471 (59731) hydrogen bonds : bond 0.03715 ( 1844) hydrogen bonds : angle 3.91948 ( 5104) metal coordination : bond 0.00473 ( 8) metal coordination : angle 1.90040 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 246 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8536 (t0) cc_final: 0.8185 (p0) REVERT: A 294 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8168 (tp30) REVERT: A 298 TYR cc_start: 0.8720 (m-10) cc_final: 0.8164 (m-10) REVERT: A 316 ASP cc_start: 0.8700 (m-30) cc_final: 0.8459 (m-30) REVERT: A 350 TYR cc_start: 0.9085 (t80) cc_final: 0.8543 (t80) REVERT: F 282 ASN cc_start: 0.9028 (t0) cc_final: 0.8489 (t0) REVERT: F 350 TYR cc_start: 0.7882 (t80) cc_final: 0.7623 (t80) REVERT: G 268 ASN cc_start: 0.9184 (m110) cc_final: 0.8904 (m110) REVERT: G 294 ASN cc_start: 0.8976 (m110) cc_final: 0.8583 (t0) REVERT: H 95 LYS cc_start: 0.8901 (pmtt) cc_final: 0.8635 (pmmt) REVERT: H 212 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7768 (t0) REVERT: H 231 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: I 165 HIS cc_start: 0.8845 (t-90) cc_final: 0.8461 (t70) REVERT: I 200 ARG cc_start: 0.8246 (mtm180) cc_final: 0.7925 (mtm-85) REVERT: I 341 LEU cc_start: 0.8380 (pp) cc_final: 0.7882 (mm) REVERT: I 369 MET cc_start: 0.9088 (tmm) cc_final: 0.8724 (ppp) REVERT: I 394 ARG cc_start: 0.8959 (mtt180) cc_final: 0.8457 (mmm-85) REVERT: I 439 LYS cc_start: 0.8847 (tptp) cc_final: 0.8402 (tptp) REVERT: I 488 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8248 (mmp) REVERT: I 742 TYR cc_start: 0.8526 (m-80) cc_final: 0.8281 (m-80) REVERT: J 314 ARG cc_start: 0.8470 (mmp-170) cc_final: 0.7793 (mmm160) REVERT: J 322 ARG cc_start: 0.8923 (ttm110) cc_final: 0.8420 (mtm-85) REVERT: J 905 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8632 (mmt180) REVERT: J 1095 MET cc_start: 0.7556 (ttm) cc_final: 0.7246 (tmt) REVERT: J 1189 MET cc_start: 0.8460 (ttp) cc_final: 0.7494 (tmm) REVERT: J 1295 ASN cc_start: 0.9103 (t0) cc_final: 0.8819 (t0) REVERT: K 7 GLN cc_start: 0.8364 (tp-100) cc_final: 0.8111 (mm-40) REVERT: K 36 ASP cc_start: 0.8977 (m-30) cc_final: 0.8349 (p0) REVERT: K 61 ASN cc_start: 0.7587 (t0) cc_final: 0.7336 (t0) REVERT: K 69 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7590 (mmm160) REVERT: K 72 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8325 (tm-30) outliers start: 73 outliers final: 28 residues processed: 294 average time/residue: 0.7076 time to fit residues: 260.1766 Evaluate side-chains 265 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 905 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 383 optimal weight: 0.9980 chunk 330 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 411 optimal weight: 0.7980 chunk 333 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS I 922 ASN J 651 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.085644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.051366 restraints weight = 106280.478| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.68 r_work: 0.2606 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 43980 Z= 0.207 Angle : 0.513 11.523 59743 Z= 0.273 Chirality : 0.042 0.183 6760 Planarity : 0.004 0.046 7407 Dihedral : 13.546 77.258 6928 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 1.66 % Allowed : 9.51 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.83 (0.12), residues: 5164 helix: 1.55 (0.12), residues: 2129 sheet: 0.87 (0.20), residues: 640 loop : -0.42 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 473 TYR 0.016 0.001 TYR J 631 PHE 0.015 0.001 PHE J1319 TRP 0.018 0.001 TRP J1193 HIS 0.008 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00497 (43972) covalent geometry : angle 0.51240 (59731) hydrogen bonds : bond 0.04502 ( 1844) hydrogen bonds : angle 4.03354 ( 5104) metal coordination : bond 0.00786 ( 8) metal coordination : angle 2.07456 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 240 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: A 298 TYR cc_start: 0.8739 (m-10) cc_final: 0.8218 (m-10) REVERT: A 316 ASP cc_start: 0.8726 (m-30) cc_final: 0.8470 (m-30) REVERT: A 350 TYR cc_start: 0.9092 (t80) cc_final: 0.8566 (t80) REVERT: E 238 ASP cc_start: 0.9083 (t0) cc_final: 0.8648 (t0) REVERT: F 282 ASN cc_start: 0.9002 (t0) cc_final: 0.8448 (t0) REVERT: F 350 TYR cc_start: 0.7927 (t80) cc_final: 0.7623 (t80) REVERT: G 268 ASN cc_start: 0.9192 (m110) cc_final: 0.8910 (m110) REVERT: G 294 ASN cc_start: 0.8982 (m110) cc_final: 0.8566 (t0) REVERT: H 95 LYS cc_start: 0.8957 (pmtt) cc_final: 0.8666 (pmmt) REVERT: H 212 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7812 (t0) REVERT: H 231 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.8850 (m-80) REVERT: I 165 HIS cc_start: 0.8820 (t-90) cc_final: 0.8461 (t-90) REVERT: I 200 ARG cc_start: 0.8239 (mtm180) cc_final: 0.7912 (mtm-85) REVERT: I 369 MET cc_start: 0.9074 (tmm) cc_final: 0.8717 (ppp) REVERT: I 394 ARG cc_start: 0.8992 (mtt180) cc_final: 0.8661 (mtp-110) REVERT: I 439 LYS cc_start: 0.8831 (tptp) cc_final: 0.8354 (tptp) REVERT: I 742 TYR cc_start: 0.8564 (m-80) cc_final: 0.8285 (m-80) REVERT: J 314 ARG cc_start: 0.8485 (mmp-170) cc_final: 0.7787 (mmm160) REVERT: J 905 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8663 (mmt180) REVERT: J 1095 MET cc_start: 0.7548 (ttm) cc_final: 0.7270 (tmt) REVERT: J 1174 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5517 (mpp80) REVERT: J 1189 MET cc_start: 0.8514 (ttp) cc_final: 0.7423 (tmm) REVERT: J 1295 ASN cc_start: 0.9130 (t0) cc_final: 0.8822 (t0) REVERT: K 7 GLN cc_start: 0.8442 (tp-100) cc_final: 0.8186 (mm-40) REVERT: K 69 ARG cc_start: 0.8070 (mmm160) cc_final: 0.7684 (mmm160) REVERT: K 72 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8330 (tm-30) REVERT: M 8 ARG cc_start: 0.9003 (ptp-110) cc_final: 0.8390 (ptp90) outliers start: 74 outliers final: 32 residues processed: 290 average time/residue: 0.6559 time to fit residues: 238.4443 Evaluate side-chains 267 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 905 ARG Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 109 optimal weight: 3.9990 chunk 426 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 517 optimal weight: 4.9990 chunk 318 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 446 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 441 optimal weight: 8.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS H 75 GLN I 922 ASN J 320 ASN J 651 HIS J1010 GLN K 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.085496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.051282 restraints weight = 106429.096| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.69 r_work: 0.2605 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 43980 Z= 0.186 Angle : 0.509 12.352 59743 Z= 0.270 Chirality : 0.041 0.175 6760 Planarity : 0.003 0.041 7407 Dihedral : 13.568 77.470 6928 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.32 % Favored : 97.66 % Rotamer: Outliers : 1.55 % Allowed : 9.98 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.85 (0.12), residues: 5164 helix: 1.59 (0.12), residues: 2104 sheet: 0.90 (0.21), residues: 621 loop : -0.40 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 240 TYR 0.017 0.001 TYR A 139 PHE 0.015 0.001 PHE J1319 TRP 0.021 0.001 TRP J1193 HIS 0.008 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00447 (43972) covalent geometry : angle 0.50857 (59731) hydrogen bonds : bond 0.04347 ( 1844) hydrogen bonds : angle 4.02459 ( 5104) metal coordination : bond 0.00710 ( 8) metal coordination : angle 1.88858 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8241 (tp30) REVERT: A 298 TYR cc_start: 0.8786 (m-10) cc_final: 0.8247 (m-10) REVERT: A 316 ASP cc_start: 0.8719 (m-30) cc_final: 0.8483 (m-30) REVERT: A 350 TYR cc_start: 0.9082 (t80) cc_final: 0.8679 (t80) REVERT: E 238 ASP cc_start: 0.9056 (t0) cc_final: 0.8622 (t0) REVERT: F 282 ASN cc_start: 0.9001 (t0) cc_final: 0.8373 (t0) REVERT: G 268 ASN cc_start: 0.9186 (m110) cc_final: 0.8894 (m110) REVERT: G 294 ASN cc_start: 0.9040 (m110) cc_final: 0.8598 (t0) REVERT: H 95 LYS cc_start: 0.9023 (pmtt) cc_final: 0.8783 (pmmt) REVERT: H 212 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7806 (t0) REVERT: H 231 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8855 (m-80) REVERT: I 165 HIS cc_start: 0.8845 (t-90) cc_final: 0.8456 (t-90) REVERT: I 200 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7997 (mtm180) REVERT: I 341 LEU cc_start: 0.8273 (pp) cc_final: 0.7807 (mm) REVERT: I 369 MET cc_start: 0.9059 (tmm) cc_final: 0.8707 (ppp) REVERT: I 394 ARG cc_start: 0.9006 (mtt180) cc_final: 0.8671 (mtp-110) REVERT: I 439 LYS cc_start: 0.8822 (tptp) cc_final: 0.8324 (tptp) REVERT: I 742 TYR cc_start: 0.8575 (m-80) cc_final: 0.8294 (m-80) REVERT: J 314 ARG cc_start: 0.8477 (mmp-170) cc_final: 0.7777 (mmm160) REVERT: J 322 ARG cc_start: 0.8959 (ttm110) cc_final: 0.8520 (ptp-110) REVERT: J 905 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8665 (mmt180) REVERT: J 1095 MET cc_start: 0.7624 (ttm) cc_final: 0.7391 (tmt) REVERT: J 1189 MET cc_start: 0.8512 (ttp) cc_final: 0.7548 (tmm) REVERT: J 1295 ASN cc_start: 0.9148 (t0) cc_final: 0.8825 (t0) REVERT: K 7 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8164 (mm-40) REVERT: K 69 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7780 (mmm160) REVERT: K 72 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8383 (tm-30) REVERT: M 8 ARG cc_start: 0.9030 (ptp-110) cc_final: 0.8399 (ptp90) outliers start: 69 outliers final: 36 residues processed: 290 average time/residue: 0.6080 time to fit residues: 220.9345 Evaluate side-chains 271 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 905 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 344 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 403 optimal weight: 0.9990 chunk 100 optimal weight: 0.0570 chunk 426 optimal weight: 20.0000 chunk 365 optimal weight: 0.0270 chunk 474 optimal weight: 9.9990 chunk 460 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 470 optimal weight: 0.0040 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN J 651 HIS J1010 GLN K 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053584 restraints weight = 105917.494| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.68 r_work: 0.2666 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 43980 Z= 0.089 Angle : 0.467 17.873 59743 Z= 0.247 Chirality : 0.039 0.146 6760 Planarity : 0.003 0.086 7407 Dihedral : 13.468 76.064 6928 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.05 % Favored : 97.93 % Rotamer: Outliers : 0.94 % Allowed : 10.94 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.12), residues: 5164 helix: 1.78 (0.12), residues: 2102 sheet: 0.96 (0.20), residues: 631 loop : -0.29 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 473 TYR 0.019 0.001 TYR F 350 PHE 0.014 0.001 PHE J1319 TRP 0.024 0.001 TRP F 352 HIS 0.009 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00192 (43972) covalent geometry : angle 0.46617 (59731) hydrogen bonds : bond 0.03194 ( 1844) hydrogen bonds : angle 3.79036 ( 5104) metal coordination : bond 0.00261 ( 8) metal coordination : angle 1.60131 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8558 (t0) cc_final: 0.8183 (p0) REVERT: A 294 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: A 298 TYR cc_start: 0.8809 (m-10) cc_final: 0.8230 (m-10) REVERT: A 316 ASP cc_start: 0.8647 (m-30) cc_final: 0.8422 (m-30) REVERT: A 350 TYR cc_start: 0.9119 (t80) cc_final: 0.8735 (t80) REVERT: E 238 ASP cc_start: 0.8999 (t0) cc_final: 0.8567 (t0) REVERT: F 282 ASN cc_start: 0.9020 (t0) cc_final: 0.8445 (t0) REVERT: G 268 ASN cc_start: 0.9198 (m110) cc_final: 0.8973 (m110) REVERT: G 271 LYS cc_start: 0.9363 (ttpt) cc_final: 0.9148 (mtmm) REVERT: G 294 ASN cc_start: 0.9048 (m110) cc_final: 0.8635 (t0) REVERT: H 95 LYS cc_start: 0.9001 (pmtt) cc_final: 0.8696 (pmmt) REVERT: H 212 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7766 (t0) REVERT: H 231 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8836 (m-80) REVERT: I 39 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8428 (tp) REVERT: I 165 HIS cc_start: 0.8824 (t-90) cc_final: 0.8475 (t-90) REVERT: I 200 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7989 (mtm180) REVERT: I 239 MET cc_start: 0.6889 (tmm) cc_final: 0.6615 (tmm) REVERT: I 341 LEU cc_start: 0.8271 (pp) cc_final: 0.7755 (mm) REVERT: I 369 MET cc_start: 0.9078 (tmm) cc_final: 0.8704 (ppp) REVERT: I 394 ARG cc_start: 0.8987 (mtt180) cc_final: 0.8677 (mtp-110) REVERT: I 439 LYS cc_start: 0.8828 (tptp) cc_final: 0.8274 (tptp) REVERT: I 742 TYR cc_start: 0.8538 (m-80) cc_final: 0.8303 (m-80) REVERT: J 314 ARG cc_start: 0.8483 (mmp-170) cc_final: 0.8019 (mtp-110) REVERT: J 322 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8589 (mtm-85) REVERT: J 1095 MET cc_start: 0.7623 (ttm) cc_final: 0.7383 (tmt) REVERT: J 1189 MET cc_start: 0.8512 (ttp) cc_final: 0.7434 (tmm) REVERT: J 1295 ASN cc_start: 0.9184 (t0) cc_final: 0.8846 (t0) REVERT: K 7 GLN cc_start: 0.8414 (tp-100) cc_final: 0.8174 (mm-40) REVERT: K 69 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7884 (mmm160) REVERT: K 72 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8385 (tm-30) outliers start: 42 outliers final: 21 residues processed: 273 average time/residue: 0.6755 time to fit residues: 229.9431 Evaluate side-chains 255 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 66 optimal weight: 2.9990 chunk 469 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 228 optimal weight: 30.0000 chunk 320 optimal weight: 1.9990 chunk 341 optimal weight: 0.6980 chunk 330 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 409 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 282 ASN H 66 HIS I 235 ASN I 922 ASN J 651 HIS J 951 GLN J1010 GLN K 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.051363 restraints weight = 107460.881| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.67 r_work: 0.2605 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 43980 Z= 0.188 Angle : 0.513 15.063 59743 Z= 0.271 Chirality : 0.041 0.170 6760 Planarity : 0.004 0.068 7407 Dihedral : 13.520 77.375 6926 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.60 % Rotamer: Outliers : 1.05 % Allowed : 11.17 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.99 (0.12), residues: 5164 helix: 1.69 (0.12), residues: 2113 sheet: 0.94 (0.20), residues: 647 loop : -0.33 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 473 TYR 0.019 0.001 TYR F 350 PHE 0.021 0.001 PHE B 236 TRP 0.023 0.001 TRP J1193 HIS 0.009 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00454 (43972) covalent geometry : angle 0.51266 (59731) hydrogen bonds : bond 0.04280 ( 1844) hydrogen bonds : angle 3.94001 ( 5104) metal coordination : bond 0.00744 ( 8) metal coordination : angle 1.98113 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8308 (tp30) REVERT: A 298 TYR cc_start: 0.8781 (m-10) cc_final: 0.8237 (m-10) REVERT: A 350 TYR cc_start: 0.9123 (t80) cc_final: 0.8735 (t80) REVERT: C 376 ASP cc_start: 0.9071 (t0) cc_final: 0.8533 (t0) REVERT: E 238 ASP cc_start: 0.9026 (t0) cc_final: 0.8578 (t0) REVERT: F 282 ASN cc_start: 0.8994 (t0) cc_final: 0.8433 (t0) REVERT: G 268 ASN cc_start: 0.9211 (m110) cc_final: 0.8987 (m110) REVERT: G 294 ASN cc_start: 0.9030 (m110) cc_final: 0.8604 (t0) REVERT: H 95 LYS cc_start: 0.9031 (pmtt) cc_final: 0.8777 (pmmt) REVERT: H 127 GLN cc_start: 0.8974 (mp10) cc_final: 0.8728 (pm20) REVERT: H 212 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7826 (t0) REVERT: H 231 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8849 (m-80) REVERT: I 165 HIS cc_start: 0.8833 (t-90) cc_final: 0.8463 (t-90) REVERT: I 200 ARG cc_start: 0.8216 (mtm180) cc_final: 0.7998 (mtm180) REVERT: I 341 LEU cc_start: 0.8312 (pp) cc_final: 0.7781 (mm) REVERT: I 369 MET cc_start: 0.9075 (tmm) cc_final: 0.8735 (ppp) REVERT: I 394 ARG cc_start: 0.9003 (mtt180) cc_final: 0.8697 (mtp-110) REVERT: I 439 LYS cc_start: 0.8840 (tptp) cc_final: 0.8317 (tptp) REVERT: I 742 TYR cc_start: 0.8576 (m-80) cc_final: 0.8331 (m-80) REVERT: I 994 ARG cc_start: 0.8784 (mtm110) cc_final: 0.8469 (ttm170) REVERT: J 314 ARG cc_start: 0.8482 (mmp-170) cc_final: 0.7808 (mmm160) REVERT: J 322 ARG cc_start: 0.8984 (ttm110) cc_final: 0.8640 (ptp-110) REVERT: J 905 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8656 (mmt180) REVERT: J 1095 MET cc_start: 0.7641 (ttm) cc_final: 0.7372 (tmt) REVERT: J 1189 MET cc_start: 0.8561 (ttp) cc_final: 0.7490 (tmm) REVERT: K 7 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8171 (mm-40) REVERT: K 69 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7865 (mmm160) REVERT: K 72 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8371 (tm-30) outliers start: 47 outliers final: 26 residues processed: 268 average time/residue: 0.4369 time to fit residues: 147.9032 Evaluate side-chains 260 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 905 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 114 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 363 optimal weight: 0.0970 chunk 28 optimal weight: 0.0070 chunk 413 optimal weight: 5.9990 chunk 313 optimal weight: 0.9980 chunk 332 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS I 235 ASN I 922 ASN J 651 HIS J1010 GLN K 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.087422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053892 restraints weight = 107480.776| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.70 r_work: 0.2744 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 43980 Z= 0.093 Angle : 0.473 16.101 59743 Z= 0.249 Chirality : 0.039 0.158 6760 Planarity : 0.003 0.066 7407 Dihedral : 13.451 76.240 6926 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.90 % Allowed : 11.48 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 1.12 (0.12), residues: 5164 helix: 1.82 (0.12), residues: 2102 sheet: 0.97 (0.20), residues: 652 loop : -0.25 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 473 TYR 0.020 0.001 TYR F 350 PHE 0.018 0.001 PHE B 236 TRP 0.028 0.001 TRP F 352 HIS 0.011 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00208 (43972) covalent geometry : angle 0.47245 (59731) hydrogen bonds : bond 0.03230 ( 1844) hydrogen bonds : angle 3.76255 ( 5104) metal coordination : bond 0.00274 ( 8) metal coordination : angle 1.65801 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8552 (t0) cc_final: 0.8179 (p0) REVERT: A 294 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: A 298 TYR cc_start: 0.8866 (m-10) cc_final: 0.8311 (m-10) REVERT: A 316 ASP cc_start: 0.8801 (m-30) cc_final: 0.8307 (m-30) REVERT: A 350 TYR cc_start: 0.9112 (t80) cc_final: 0.8667 (t80) REVERT: B 274 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8050 (ttt90) REVERT: C 376 ASP cc_start: 0.9029 (t0) cc_final: 0.8495 (t0) REVERT: D 189 GLU cc_start: 0.8665 (mp0) cc_final: 0.8421 (pm20) REVERT: E 238 ASP cc_start: 0.9031 (t0) cc_final: 0.8530 (t0) REVERT: F 282 ASN cc_start: 0.8994 (t0) cc_final: 0.8400 (t0) REVERT: G 268 ASN cc_start: 0.9217 (m110) cc_final: 0.8981 (m110) REVERT: G 294 ASN cc_start: 0.9087 (m110) cc_final: 0.8628 (t0) REVERT: H 95 LYS cc_start: 0.8994 (pmtt) cc_final: 0.8729 (pmmt) REVERT: H 212 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7622 (t0) REVERT: H 231 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8623 (m-80) REVERT: I 39 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (tp) REVERT: I 165 HIS cc_start: 0.8876 (t-90) cc_final: 0.8484 (t-90) REVERT: I 200 ARG cc_start: 0.8214 (mtm180) cc_final: 0.8000 (mtm180) REVERT: I 341 LEU cc_start: 0.8321 (pp) cc_final: 0.7781 (OUTLIER) REVERT: I 369 MET cc_start: 0.9126 (tmm) cc_final: 0.8802 (ppp) REVERT: I 394 ARG cc_start: 0.9051 (mtt180) cc_final: 0.8676 (mtp-110) REVERT: I 439 LYS cc_start: 0.8863 (tptp) cc_final: 0.8321 (tptp) REVERT: I 742 TYR cc_start: 0.8541 (m-80) cc_final: 0.8288 (m-80) REVERT: I 996 ARG cc_start: 0.8813 (mmp80) cc_final: 0.8549 (mmp80) REVERT: J 314 ARG cc_start: 0.8377 (mmp-170) cc_final: 0.7691 (mmm160) REVERT: J 322 ARG cc_start: 0.8976 (ttm110) cc_final: 0.8585 (ptp-110) REVERT: J 822 MET cc_start: 0.8146 (tpt) cc_final: 0.7807 (tpt) REVERT: J 1095 MET cc_start: 0.7642 (ttm) cc_final: 0.7386 (tmt) REVERT: J 1189 MET cc_start: 0.8571 (ttp) cc_final: 0.7504 (tmm) REVERT: J 1295 ASN cc_start: 0.9183 (t0) cc_final: 0.8931 (t0) REVERT: K 7 GLN cc_start: 0.8280 (tp-100) cc_final: 0.8024 (mm-40) REVERT: K 69 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7843 (mmm160) REVERT: K 72 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8363 (tm-30) outliers start: 40 outliers final: 27 residues processed: 265 average time/residue: 0.4434 time to fit residues: 148.4532 Evaluate side-chains 264 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 474 optimal weight: 10.0000 chunk 455 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 364 optimal weight: 0.9990 chunk 429 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 458 optimal weight: 3.9990 chunk 471 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS I 922 ASN J 651 HIS J1010 GLN K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.087387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053816 restraints weight = 108369.027| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.71 r_work: 0.2743 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 43980 Z= 0.101 Angle : 0.482 16.460 59743 Z= 0.252 Chirality : 0.039 0.174 6760 Planarity : 0.003 0.063 7407 Dihedral : 13.422 76.405 6926 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.83 % Allowed : 11.57 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 5164 helix: 1.86 (0.12), residues: 2106 sheet: 1.09 (0.20), residues: 645 loop : -0.21 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG I 473 TYR 0.020 0.001 TYR A 139 PHE 0.019 0.001 PHE B 236 TRP 0.039 0.001 TRP F 352 HIS 0.019 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00233 (43972) covalent geometry : angle 0.48172 (59731) hydrogen bonds : bond 0.03269 ( 1844) hydrogen bonds : angle 3.73508 ( 5104) metal coordination : bond 0.00355 ( 8) metal coordination : angle 1.71897 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8166 (ppp) REVERT: A 231 ASP cc_start: 0.8543 (t0) cc_final: 0.8175 (p0) REVERT: A 294 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: A 298 TYR cc_start: 0.8869 (m-10) cc_final: 0.8333 (m-10) REVERT: A 316 ASP cc_start: 0.8873 (m-30) cc_final: 0.8324 (m-30) REVERT: A 350 TYR cc_start: 0.9133 (t80) cc_final: 0.8700 (t80) REVERT: B 274 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8048 (ttt90) REVERT: C 376 ASP cc_start: 0.9033 (t0) cc_final: 0.8496 (t0) REVERT: D 189 GLU cc_start: 0.8655 (mp0) cc_final: 0.8308 (pm20) REVERT: E 238 ASP cc_start: 0.9025 (t0) cc_final: 0.8514 (t0) REVERT: F 282 ASN cc_start: 0.8996 (t0) cc_final: 0.8406 (t0) REVERT: G 268 ASN cc_start: 0.9257 (m110) cc_final: 0.9023 (m110) REVERT: G 271 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8632 (pttp) REVERT: G 294 ASN cc_start: 0.9082 (m110) cc_final: 0.8628 (t0) REVERT: H 95 LYS cc_start: 0.8999 (pmtt) cc_final: 0.8732 (pmmt) REVERT: H 212 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7615 (t0) REVERT: I 165 HIS cc_start: 0.8865 (t-90) cc_final: 0.8481 (t-90) REVERT: I 200 ARG cc_start: 0.8231 (mtm180) cc_final: 0.8025 (mtm180) REVERT: I 239 MET cc_start: 0.6688 (tmm) cc_final: 0.6415 (tmm) REVERT: I 341 LEU cc_start: 0.8334 (pp) cc_final: 0.7787 (OUTLIER) REVERT: I 369 MET cc_start: 0.9155 (tmm) cc_final: 0.8831 (ppp) REVERT: I 394 ARG cc_start: 0.9048 (mtt180) cc_final: 0.8680 (mtp-110) REVERT: I 439 LYS cc_start: 0.8872 (tptp) cc_final: 0.8322 (tptp) REVERT: I 742 TYR cc_start: 0.8553 (m-80) cc_final: 0.8291 (m-80) REVERT: J 314 ARG cc_start: 0.8372 (mmp-170) cc_final: 0.7688 (mmm160) REVERT: J 322 ARG cc_start: 0.8976 (ttm110) cc_final: 0.8585 (ptp-110) REVERT: J 822 MET cc_start: 0.8176 (tpt) cc_final: 0.7851 (tpt) REVERT: J 1095 MET cc_start: 0.7632 (ttm) cc_final: 0.7375 (tmt) REVERT: J 1189 MET cc_start: 0.8565 (ttp) cc_final: 0.7504 (tmm) REVERT: J 1295 ASN cc_start: 0.9215 (t0) cc_final: 0.8946 (t0) REVERT: K 7 GLN cc_start: 0.8288 (tp-100) cc_final: 0.8033 (mm-40) REVERT: K 69 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7822 (mmm160) REVERT: K 72 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8343 (tm-30) REVERT: M 8 ARG cc_start: 0.8917 (ptp-110) cc_final: 0.8330 (ptp90) outliers start: 37 outliers final: 26 residues processed: 263 average time/residue: 0.4446 time to fit residues: 147.6235 Evaluate side-chains 262 residues out of total 4461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 284 HIS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 120 optimal weight: 10.0000 chunk 367 optimal weight: 1.9990 chunk 202 optimal weight: 0.0040 chunk 456 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 513 optimal weight: 0.0060 chunk 305 optimal weight: 0.6980 chunk 502 optimal weight: 0.8980 chunk 466 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 overall best weight: 0.7210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS I 922 ASN J 651 HIS J1010 GLN K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054465 restraints weight = 108673.118| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.70 r_work: 0.2760 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 43980 Z= 0.092 Angle : 0.464 16.492 59743 Z= 0.243 Chirality : 0.039 0.174 6760 Planarity : 0.003 0.058 7407 Dihedral : 13.366 76.173 6926 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.74 % Allowed : 11.71 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 1.27 (0.12), residues: 5164 helix: 1.92 (0.12), residues: 2099 sheet: 1.14 (0.20), residues: 638 loop : -0.17 (0.12), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I 473 TYR 0.018 0.001 TYR A 139 PHE 0.016 0.001 PHE B 236 TRP 0.026 0.001 TRP J1193 HIS 0.012 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00211 (43972) covalent geometry : angle 0.46362 (59731) hydrogen bonds : bond 0.03015 ( 1844) hydrogen bonds : angle 3.65966 ( 5104) metal coordination : bond 0.00301 ( 8) metal coordination : angle 1.71825 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14457.39 seconds wall clock time: 245 minutes 49.73 seconds (14749.73 seconds total)