Starting phenix.real_space_refine on Sun Sep 29 17:19:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/09_2024/8e7v_27941_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/09_2024/8e7v_27941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/09_2024/8e7v_27941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/09_2024/8e7v_27941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/09_2024/8e7v_27941_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/09_2024/8e7v_27941_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.026 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 P 16 5.49 5 Mg 3 5.21 5 S 198 5.16 5 C 23451 2.51 5 N 6391 2.21 5 O 7187 1.98 5 H 37552 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74798 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5424 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 14, 'TRANS': 335} Chain: "B" Number of atoms: 5445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 351, 5433 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 351, 5433 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} bond proxies already assigned to first conformer: 5456 Chain: "C" Number of atoms: 5434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5434 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "D" Number of atoms: 5434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5434 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "E" Number of atoms: 5435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5435 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "F" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5244 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Chain: "H" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "h" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "i" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "j" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3045 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "k" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "l" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "m" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "n" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "C" 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: "D" 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: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 197 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER B 197 " occ=0.50 Time building chain proxies: 30.89, per 1000 atoms: 0.41 Number of scatterers: 74798 At special positions: 0 Unit cell: (142.386, 142.386, 196.093, 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) S 198 16.00 P 16 15.00 Mg 3 11.99 O 7187 8.00 N 6391 7.00 C 23451 6.00 H 37552 1.00 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: 15.54 Conformation dependent library (CDL) restraints added in 5.3 seconds 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8792 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 68 sheets defined 52.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.78 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.780A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 101 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.757A pdb=" N SER A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN A 106 " --> pdb=" O ASP A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 106' Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.854A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.898A pdb=" N GLN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.618A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.987A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.506A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.749A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.673A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.698A pdb=" N ASP A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 4.179A pdb=" N ARG A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.613A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.555A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.321A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.539A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.646A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.297A pdb=" N PHE B 235 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.756A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.664A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.558A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.057A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.504A pdb=" N ARG B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.137A pdb=" N ARG B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 399 through 405 Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.921A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 124 through 135 removed outlier: 3.540A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.620A pdb=" N GLN C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.718A pdb=" N ARG C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 204 through 217 removed outlier: 4.630A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 removed outlier: 3.669A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 264 " --> pdb=" O HIS C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.816A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 301 through 308 Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.843A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.710A pdb=" N LYS C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.806A pdb=" N SER C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP C 382 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.713A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 4.100A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.614A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.518A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 204 through 217 removed outlier: 4.445A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.698A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 removed outlier: 3.718A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.601A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.923A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 345 removed outlier: 3.520A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 removed outlier: 3.612A pdb=" N LYS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 370 through 380 removed outlier: 3.884A pdb=" N SER D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 387 Processing helix chain 'D' and resid 399 through 405 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.595A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 101 Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 124 through 134 removed outlier: 3.609A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.942A pdb=" N GLN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS E 168 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 204 through 217 removed outlier: 4.705A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.578A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 288 Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.784A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.531A pdb=" N ILE E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 307 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 308 " --> pdb=" O PHE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.656A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 345 removed outlier: 3.552A pdb=" N GLU E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 Processing helix chain 'E' and resid 370 through 380 removed outlier: 4.438A pdb=" N SER E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 399 through 405 removed outlier: 3.618A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 Processing helix chain 'F' and resid 81 through 101 Processing helix chain 'F' and resid 124 through 136 removed outlier: 3.593A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 removed outlier: 4.254A pdb=" N GLU F 150 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.557A pdb=" N ASP F 157 " --> pdb=" O TYR F 153 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.665A pdb=" N ARG F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 removed outlier: 4.296A pdb=" N ILE F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 185 through 190' Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.526A pdb=" N GLN F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 243 No H-bonds generated for 'chain 'F' and resid 241 through 243' Processing helix chain 'F' and resid 253 through 263 removed outlier: 3.797A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.805A pdb=" N GLY F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.575A pdb=" N LEU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.531A pdb=" N ARG F 307 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 removed outlier: 3.712A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 345 Processing helix chain 'F' and resid 351 through 366 Processing helix chain 'F' and resid 369 through 387 removed outlier: 4.239A pdb=" N ARG F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 Processing helix chain 'H' and resid 18 through 26 removed outlier: 3.654A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.746A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 132 through 158 Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.512A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.620A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.531A pdb=" N GLY I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 132 through 158 Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 176 through 183 Processing helix chain 'J' and resid 19 through 25 Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.512A pdb=" N GLY J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 132 through 158 Processing helix chain 'J' and resid 160 through 169 Processing helix chain 'J' and resid 176 through 183 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.688A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.595A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 132 through 158 Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 176 through 183 Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.681A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 removed outlier: 3.559A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.612A pdb=" N GLY L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 105 Processing helix chain 'L' and resid 132 through 158 Processing helix chain 'L' and resid 160 through 168 Processing helix chain 'L' and resid 176 through 183 Processing helix chain 'M' and resid 18 through 26 removed outlier: 3.836A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.577A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 132 through 158 Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'N' and resid 19 through 25 Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.594A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 105 Processing helix chain 'N' and resid 132 through 158 Processing helix chain 'N' and resid 160 through 168 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'h' and resid 19 through 25 Processing helix chain 'h' and resid 36 through 54 Processing helix chain 'h' and resid 69 through 83 Processing helix chain 'h' and resid 96 through 105 Processing helix chain 'h' and resid 132 through 158 Processing helix chain 'h' and resid 160 through 169 Processing helix chain 'h' and resid 176 through 183 Processing helix chain 'i' and resid 18 through 25 Processing helix chain 'i' and resid 36 through 54 Processing helix chain 'i' and resid 69 through 83 removed outlier: 3.507A pdb=" N ILE i 76 " --> pdb=" O ALA i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 104 Processing helix chain 'i' and resid 132 through 158 Processing helix chain 'i' and resid 160 through 169 removed outlier: 3.551A pdb=" N GLU i 169 " --> pdb=" O GLU i 165 " (cutoff:3.500A) Processing helix chain 'i' and resid 176 through 182 Processing helix chain 'j' and resid 19 through 26 removed outlier: 3.875A pdb=" N GLU j 26 " --> pdb=" O ARG j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 54 Processing helix chain 'j' and resid 69 through 83 removed outlier: 3.620A pdb=" N GLY j 73 " --> pdb=" O VAL j 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE j 76 " --> pdb=" O ALA j 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 105 Processing helix chain 'j' and resid 132 through 158 Processing helix chain 'j' and resid 160 through 168 Processing helix chain 'j' and resid 176 through 183 Processing helix chain 'k' and resid 11 through 14 Processing helix chain 'k' and resid 19 through 25 removed outlier: 3.523A pdb=" N LYS k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 36 through 54 Processing helix chain 'k' and resid 69 through 83 removed outlier: 3.706A pdb=" N GLY k 73 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 105 Processing helix chain 'k' and resid 132 through 158 removed outlier: 3.502A pdb=" N ILE k 137 " --> pdb=" O THR k 133 " (cutoff:3.500A) Processing helix chain 'k' and resid 160 through 169 Processing helix chain 'k' and resid 176 through 182 Processing helix chain 'l' and resid 19 through 25 Processing helix chain 'l' and resid 36 through 54 Processing helix chain 'l' and resid 69 through 83 removed outlier: 3.686A pdb=" N GLY l 73 " --> pdb=" O VAL l 69 " (cutoff:3.500A) Processing helix chain 'l' and resid 96 through 105 Processing helix chain 'l' and resid 132 through 158 removed outlier: 3.590A pdb=" N ILE l 137 " --> pdb=" O THR l 133 " (cutoff:3.500A) Processing helix chain 'l' and resid 160 through 168 Processing helix chain 'l' and resid 176 through 183 Processing helix chain 'm' and resid 19 through 25 Processing helix chain 'm' and resid 36 through 54 Processing helix chain 'm' and resid 69 through 83 removed outlier: 3.659A pdb=" N GLY m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE m 76 " --> pdb=" O ALA m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 104 Processing helix chain 'm' and resid 132 through 158 Processing helix chain 'm' and resid 160 through 169 Processing helix chain 'm' and resid 175 through 183 Processing helix chain 'n' and resid 19 through 25 Processing helix chain 'n' and resid 36 through 54 Processing helix chain 'n' and resid 69 through 83 removed outlier: 3.563A pdb=" N ILE n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) Processing helix chain 'n' and resid 96 through 105 Processing helix chain 'n' and resid 132 through 158 Processing helix chain 'n' and resid 160 through 169 removed outlier: 3.509A pdb=" N GLU n 169 " --> pdb=" O GLU n 165 " (cutoff:3.500A) Processing helix chain 'n' and resid 176 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 144 removed outlier: 6.923A pdb=" N THR A 141 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP A 184 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 143 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.284A pdb=" N ASP A 347 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE A 398 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU A 349 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 144 removed outlier: 3.778A pdb=" N THR B 141 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 115 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY B 249 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 117 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 222 Processing sheet with id=AA5, first strand: chain 'B' and resid 348 through 350 removed outlier: 6.824A pdb=" N GLU B 349 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 247 through 249 removed outlier: 6.045A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 144 removed outlier: 7.002A pdb=" N THR C 141 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP C 184 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA C 143 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AA9, first strand: chain 'C' and resid 347 through 350 removed outlier: 4.163A pdb=" N LYS C 395 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 140 through 144 removed outlier: 6.460A pdb=" N THR D 141 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASP D 184 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA D 143 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU D 116 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 219 through 222 Processing sheet with id=AB3, first strand: chain 'D' and resid 347 through 350 removed outlier: 6.549A pdb=" N ASP D 347 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE D 398 " --> pdb=" O ASP D 347 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU D 349 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 144 removed outlier: 6.582A pdb=" N THR E 141 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASP E 184 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA E 143 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL E 181 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLY E 248 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE E 183 " --> pdb=" O GLY E 248 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE E 115 " --> pdb=" O CYS E 247 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY E 249 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU E 117 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 219 through 222 Processing sheet with id=AB6, first strand: chain 'E' and resid 347 through 350 removed outlier: 6.622A pdb=" N ASP E 347 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ILE E 398 " --> pdb=" O ASP E 347 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU E 349 " --> pdb=" O ILE E 398 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 115 through 118 removed outlier: 5.944A pdb=" N LEU F 116 " --> pdb=" O ALA F 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.492A pdb=" N THR F 141 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASP F 184 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA F 143 " --> pdb=" O ASP F 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 219 through 222 Processing sheet with id=AC1, first strand: chain 'F' and resid 347 through 350 removed outlier: 5.731A pdb=" N ASP F 347 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE F 398 " --> pdb=" O ASP F 347 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU F 349 " --> pdb=" O ILE F 398 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.723A pdb=" N THR H 10 " --> pdb=" O GLY H 13 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.175A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.175A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC6, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AC7, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.516A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER I 65 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.516A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER I 65 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 125 through 131 removed outlier: 3.518A pdb=" N TYR h 128 " --> pdb=" O TYR I 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AD2, first strand: chain 'J' and resid 28 through 32 removed outlier: 5.240A pdb=" N SER J 65 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN J 94 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 28 through 32 removed outlier: 5.240A pdb=" N SER J 65 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN J 94 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 125 through 131 removed outlier: 3.503A pdb=" N TYR i 128 " --> pdb=" O TYR J 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AD6, first strand: chain 'K' and resid 28 through 32 removed outlier: 5.144A pdb=" N SER K 65 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN K 94 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 118 through 121 Processing sheet with id=AD8, first strand: chain 'K' and resid 125 through 131 removed outlier: 3.525A pdb=" N TYR j 128 " --> pdb=" O TYR K 128 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AE1, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.257A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 94 through 95 removed outlier: 6.478A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 125 through 131 removed outlier: 3.540A pdb=" N TYR k 128 " --> pdb=" O TYR L 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 6 through 8 Processing sheet with id=AE5, first strand: chain 'M' and resid 28 through 32 removed outlier: 5.208A pdb=" N SER M 65 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN M 94 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG M 118 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY M 93 " --> pdb=" O ARG M 118 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N MET M 120 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA M 95 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 28 through 32 removed outlier: 5.208A pdb=" N SER M 65 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN M 94 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 125 through 131 removed outlier: 3.548A pdb=" N TYR M 128 " --> pdb=" O TYR l 128 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR l 128 " --> pdb=" O TYR M 128 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 5 through 9 Processing sheet with id=AE9, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.810A pdb=" N ILE N 29 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN N 64 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU N 31 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER N 65 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG N 118 " --> pdb=" O CYS N 91 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY N 93 " --> pdb=" O ARG N 118 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N MET N 120 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA N 95 " --> pdb=" O MET N 120 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE N 121 " --> pdb=" O ARG N 172 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.810A pdb=" N ILE N 29 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN N 64 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU N 31 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER N 65 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 125 through 131 Processing sheet with id=AF3, first strand: chain 'h' and resid 5 through 9 Processing sheet with id=AF4, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.422A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG h 118 " --> pdb=" O CYS h 91 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY h 93 " --> pdb=" O ARG h 118 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N MET h 120 " --> pdb=" O GLY h 93 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA h 95 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.422A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N PHE h 112 " --> pdb=" O VAL h 87 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR h 89 " --> pdb=" O PHE h 112 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER h 187 " --> pdb=" O ARG h 111 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'i' and resid 7 through 11 removed outlier: 3.897A pdb=" N GLU i 8 " --> pdb=" O ARG i 15 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ARG i 15 " --> pdb=" O GLU i 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.651A pdb=" N ILE i 29 " --> pdb=" O TYR i 62 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN i 64 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU i 31 " --> pdb=" O ASN i 64 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG i 118 " --> pdb=" O CYS i 91 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY i 93 " --> pdb=" O ARG i 118 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N MET i 120 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA i 95 " --> pdb=" O MET i 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 112 through 113 Processing sheet with id=AF9, first strand: chain 'j' and resid 5 through 6 Processing sheet with id=AG1, first strand: chain 'j' and resid 28 through 32 removed outlier: 5.317A pdb=" N SER j 65 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN j 94 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG j 118 " --> pdb=" O CYS j 91 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY j 93 " --> pdb=" O ARG j 118 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N MET j 120 " --> pdb=" O GLY j 93 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA j 95 " --> pdb=" O MET j 120 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 28 through 32 removed outlier: 5.317A pdb=" N SER j 65 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN j 94 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE j 112 " --> pdb=" O VAL j 87 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR j 89 " --> pdb=" O PHE j 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER j 187 " --> pdb=" O ARG j 111 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'k' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.382A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE k 112 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N THR k 89 " --> pdb=" O PHE k 112 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG k 111 " --> pdb=" O SER k 187 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'k' and resid 118 through 121 Processing sheet with id=AG6, first strand: chain 'l' and resid 5 through 8 removed outlier: 4.025A pdb=" N ARG l 15 " --> pdb=" O GLU l 8 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'l' and resid 28 through 32 removed outlier: 5.315A pdb=" N SER l 65 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLN l 94 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE l 112 " --> pdb=" O VAL l 87 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR l 89 " --> pdb=" O PHE l 112 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'l' and resid 118 through 121 Processing sheet with id=AG9, first strand: chain 'm' and resid 5 through 9 Processing sheet with id=AH1, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.620A pdb=" N ILE m 29 " --> pdb=" O TYR m 62 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASN m 64 " --> pdb=" O ILE m 29 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU m 31 " --> pdb=" O ASN m 64 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE m 59 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE m 90 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU m 61 " --> pdb=" O ILE m 90 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET m 92 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE m 63 " --> pdb=" O MET m 92 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN m 94 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE m 112 " --> pdb=" O VAL m 87 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR m 89 " --> pdb=" O PHE m 112 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'm' and resid 119 through 121 Processing sheet with id=AH3, first strand: chain 'n' and resid 5 through 9 Processing sheet with id=AH4, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.361A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG n 118 " --> pdb=" O CYS n 91 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY n 93 " --> pdb=" O ARG n 118 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N MET n 120 " --> pdb=" O GLY n 93 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA n 95 " --> pdb=" O MET n 120 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.361A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N PHE n 112 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR n 89 " --> pdb=" O PHE n 112 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG n 111 " --> pdb=" O SER n 187 " (cutoff:3.500A) 1897 hydrogen bonds defined for protein. 5514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 34.81 Time building geometry restraints manager: 19.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 37518 1.03 - 1.23: 38 1.23 - 1.42: 15052 1.42 - 1.62: 22388 1.62 - 1.81: 362 Bond restraints: 75358 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.36e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.19e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 75353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 136474 4.06 - 8.12: 204 8.12 - 12.17: 5 12.17 - 16.23: 0 16.23 - 20.29: 8 Bond angle restraints: 136691 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 119.58 20.29 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 119.63 20.24 1.00e+00 1.00e+00 4.10e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.85 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.02 18.85 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 119.22 17.61 1.00e+00 1.00e+00 3.10e+02 ... (remaining 136686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 33165 25.17 - 50.33: 1583 50.33 - 75.50: 338 75.50 - 100.67: 34 100.67 - 125.83: 2 Dihedral angle restraints: 35122 sinusoidal: 19820 harmonic: 15302 Sorted by residual: dihedral pdb=" O1B ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PB ADP F 600 " pdb=" PA ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 65.83 -125.83 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 49.88 -109.88 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA ASP C 347 " pdb=" CB ASP C 347 " pdb=" CG ASP C 347 " pdb=" OD1 ASP C 347 " ideal model delta sinusoidal sigma weight residual -30.00 -88.91 58.91 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 35119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4256 0.042 - 0.084: 1195 0.084 - 0.126: 348 0.126 - 0.168: 73 0.168 - 0.210: 1 Chirality restraints: 5873 Sorted by residual: chirality pdb=" CA GLN A 232 " pdb=" N GLN A 232 " pdb=" C GLN A 232 " pdb=" CB GLN A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO n 115 " pdb=" N PRO n 115 " pdb=" C PRO n 115 " pdb=" CB PRO n 115 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 5870 not shown) Planarity restraints: 11203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 195 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO D 196 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 230 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO E 231 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 231 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 231 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 231 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C PRO A 231 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO A 231 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 232 " 0.013 2.00e-02 2.50e+03 ... (remaining 11200 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 10250 2.27 - 2.85: 174143 2.85 - 3.43: 194680 3.43 - 4.02: 274479 4.02 - 4.60: 425044 Nonbonded interactions: 1078596 Sorted by model distance: nonbonded pdb=" OD1 ASP h 18 " pdb=" H SER h 21 " model vdw 1.683 2.450 nonbonded pdb=" HD1 HIS J 122 " pdb=" O GLN J 123 " model vdw 1.689 2.450 nonbonded pdb=" O ILE J 164 " pdb=" HG1 THR J 168 " model vdw 1.701 2.450 nonbonded pdb=" HG1 THR i 89 " pdb=" O LEU i 103 " model vdw 1.707 2.450 nonbonded pdb=" OD1 ASP m 18 " pdb=" H SER m 21 " model vdw 1.713 2.450 ... (remaining 1078591 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 64 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 127 through 191 or (resid 204 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 05 through 413)) selection = (chain 'B' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 413)) selection = (chain 'C' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 413)) selection = (chain 'D' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 413)) selection = (chain 'E' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 125 or (resid 126 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG2 \ 1 or name HG22 or name HG23)) or resid 127 through 191 or (resid 204 and (name N \ or name CA or name C or name O or name HA2 or name HA3)) or resid 205 through 4 \ 13)) selection = (chain 'F' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 125 or (resid 126 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG2 \ 1 or name HG22 or name HG23)) or resid 127 through 413)) } ncs_group { reference = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = (chain 'M' and resid 2 through 191) selection = (chain 'N' and resid 2 through 191) selection = (chain 'h' and resid 2 through 191) selection = (chain 'i' and resid 2 through 191) selection = (chain 'j' and resid 2 through 191) selection = (chain 'k' and resid 2 through 191) selection = (chain 'l' and resid 2 through 191) selection = (chain 'm' and resid 2 through 191) selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.050 Extract box with map and model: 2.310 Check model and map are aligned: 0.460 Set scattering table: 0.560 Process input model: 139.220 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 37806 Z= 0.332 Angle : 0.737 20.290 51070 Z= 0.461 Chirality : 0.044 0.210 5873 Planarity : 0.004 0.078 6624 Dihedral : 13.568 125.834 14448 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.11), residues: 4740 helix: 0.38 (0.10), residues: 2274 sheet: -0.78 (0.17), residues: 631 loop : -0.96 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS J 122 PHE 0.026 0.001 PHE I 17 TYR 0.017 0.001 TYR l 182 ARG 0.012 0.000 ARG k 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 772 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8807 (t80) cc_final: 0.8438 (t80) REVERT: A 247 CYS cc_start: 0.8329 (m) cc_final: 0.7799 (m) REVERT: B 82 GLU cc_start: 0.8336 (pm20) cc_final: 0.8066 (pp20) REVERT: B 94 ASN cc_start: 0.8843 (m-40) cc_final: 0.8619 (m110) REVERT: B 142 MET cc_start: 0.7909 (mtp) cc_final: 0.7477 (mtt) REVERT: B 195 ASN cc_start: 0.7838 (m110) cc_final: 0.7635 (m-40) REVERT: D 170 ASP cc_start: 0.8639 (t70) cc_final: 0.8256 (t0) REVERT: D 236 LEU cc_start: 0.8396 (mt) cc_final: 0.8174 (mt) REVERT: E 153 TYR cc_start: 0.7540 (m-80) cc_final: 0.7219 (m-80) REVERT: E 154 VAL cc_start: 0.7201 (p) cc_final: 0.6347 (p) REVERT: E 247 CYS cc_start: 0.9151 (m) cc_final: 0.8847 (m) REVERT: E 283 GLU cc_start: 0.7825 (tt0) cc_final: 0.7569 (mp0) REVERT: E 384 MET cc_start: 0.7107 (mtm) cc_final: 0.6901 (mtp) REVERT: F 159 GLU cc_start: 0.7370 (pp20) cc_final: 0.7050 (pp20) REVERT: F 160 ASN cc_start: 0.8879 (t0) cc_final: 0.8599 (t0) REVERT: F 266 SER cc_start: 0.7816 (p) cc_final: 0.7446 (t) REVERT: I 10 THR cc_start: 0.8577 (p) cc_final: 0.8055 (t) REVERT: M 34 GLN cc_start: 0.8149 (tp40) cc_final: 0.7935 (mm-40) REVERT: N 18 ASP cc_start: 0.7504 (p0) cc_final: 0.7231 (p0) REVERT: N 60 TYR cc_start: 0.8915 (m-80) cc_final: 0.8662 (m-80) REVERT: h 57 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8630 (mtpp) REVERT: n 78 ASP cc_start: 0.8271 (m-30) cc_final: 0.7911 (m-30) outliers start: 0 outliers final: 0 residues processed: 772 average time/residue: 1.0854 time to fit residues: 1312.7599 Evaluate side-chains 467 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 0.7980 chunk 359 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 371 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 324 GLN C 342 ASN D 73 HIS E 160 ASN E 233 GLN E 260 HIS E 406 GLN H 41 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN M 41 ASN N 41 ASN i 41 ASN k 41 ASN l 129 GLN m 41 ASN n 41 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37806 Z= 0.274 Angle : 0.556 6.220 51070 Z= 0.301 Chirality : 0.042 0.164 5873 Planarity : 0.004 0.048 6624 Dihedral : 6.510 114.712 5306 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.87 % Rotamer: Outliers : 0.55 % Allowed : 5.80 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.11), residues: 4740 helix: 1.27 (0.10), residues: 2368 sheet: -0.55 (0.18), residues: 620 loop : -0.77 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 73 PHE 0.013 0.001 PHE j 17 TYR 0.020 0.001 TYR F 96 ARG 0.007 0.000 ARG l 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 465 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8852 (t80) cc_final: 0.8488 (t80) REVERT: A 247 CYS cc_start: 0.8506 (m) cc_final: 0.8001 (m) REVERT: B 93 TYR cc_start: 0.8679 (t80) cc_final: 0.8324 (t80) REVERT: B 94 ASN cc_start: 0.8936 (m-40) cc_final: 0.8682 (m-40) REVERT: B 195 ASN cc_start: 0.7664 (m110) cc_final: 0.7436 (m110) REVERT: C 342 ASN cc_start: 0.8521 (m-40) cc_final: 0.8247 (m110) REVERT: D 160 ASN cc_start: 0.8760 (m110) cc_final: 0.8545 (m110) REVERT: D 170 ASP cc_start: 0.8740 (t70) cc_final: 0.8434 (t0) REVERT: E 153 TYR cc_start: 0.7700 (m-80) cc_final: 0.7269 (m-80) REVERT: E 154 VAL cc_start: 0.8044 (p) cc_final: 0.7823 (p) REVERT: E 247 CYS cc_start: 0.9098 (m) cc_final: 0.8829 (m) REVERT: E 283 GLU cc_start: 0.7919 (tt0) cc_final: 0.7581 (mp0) REVERT: F 160 ASN cc_start: 0.8796 (t0) cc_final: 0.8233 (t0) REVERT: F 266 SER cc_start: 0.7976 (p) cc_final: 0.7386 (t) REVERT: H 5 MET cc_start: 0.7833 (mmm) cc_final: 0.7531 (mmm) REVERT: H 136 GLU cc_start: 0.7348 (tp30) cc_final: 0.7079 (tp30) REVERT: K 78 ASP cc_start: 0.8067 (m-30) cc_final: 0.7810 (m-30) REVERT: M 78 ASP cc_start: 0.8236 (m-30) cc_final: 0.8010 (m-30) REVERT: M 144 LYS cc_start: 0.8908 (mttt) cc_final: 0.8681 (mtpt) REVERT: N 47 MET cc_start: 0.8739 (mtt) cc_final: 0.8160 (mtt) REVERT: N 60 TYR cc_start: 0.8962 (m-80) cc_final: 0.8692 (m-80) REVERT: k 84 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8256 (ttpp) REVERT: l 149 MET cc_start: 0.7890 (mmm) cc_final: 0.7303 (mmt) REVERT: n 78 ASP cc_start: 0.8360 (m-30) cc_final: 0.7915 (m-30) outliers start: 22 outliers final: 13 residues processed: 476 average time/residue: 1.0458 time to fit residues: 810.5876 Evaluate side-chains 424 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 410 time to evaluate : 4.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain k residue 84 LYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 431 optimal weight: 1.9990 chunk 465 optimal weight: 1.9990 chunk 384 optimal weight: 3.9990 chunk 427 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN D 225 GLN E 260 HIS F 94 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN K 123 GLN i 123 GLN l 159 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37806 Z= 0.254 Angle : 0.502 7.528 51070 Z= 0.266 Chirality : 0.041 0.151 5873 Planarity : 0.004 0.062 6624 Dihedral : 6.607 113.992 5306 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.75 % Allowed : 6.65 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 4740 helix: 1.61 (0.10), residues: 2383 sheet: -0.56 (0.17), residues: 672 loop : -0.56 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 122 PHE 0.019 0.001 PHE j 17 TYR 0.014 0.001 TYR l 182 ARG 0.006 0.000 ARG J 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 409 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8827 (t80) cc_final: 0.8431 (t80) REVERT: A 247 CYS cc_start: 0.8676 (m) cc_final: 0.8100 (m) REVERT: B 93 TYR cc_start: 0.8693 (t80) cc_final: 0.8488 (t80) REVERT: B 94 ASN cc_start: 0.8962 (m-40) cc_final: 0.8661 (m110) REVERT: B 195 ASN cc_start: 0.7634 (m110) cc_final: 0.7397 (m-40) REVERT: B 384 MET cc_start: 0.8736 (mtm) cc_final: 0.8077 (mtp) REVERT: C 342 ASN cc_start: 0.8729 (m-40) cc_final: 0.8422 (m-40) REVERT: E 153 TYR cc_start: 0.7737 (m-80) cc_final: 0.7256 (m-80) REVERT: E 154 VAL cc_start: 0.8251 (p) cc_final: 0.8039 (p) REVERT: E 247 CYS cc_start: 0.9079 (m) cc_final: 0.8797 (m) REVERT: E 283 GLU cc_start: 0.7765 (tt0) cc_final: 0.7455 (mp0) REVERT: F 160 ASN cc_start: 0.8804 (t0) cc_final: 0.8201 (t0) REVERT: F 266 SER cc_start: 0.8036 (p) cc_final: 0.7489 (t) REVERT: H 136 GLU cc_start: 0.7593 (tp30) cc_final: 0.7317 (tp30) REVERT: L 53 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: M 34 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: M 78 ASP cc_start: 0.8400 (m-30) cc_final: 0.8093 (m-30) REVERT: M 144 LYS cc_start: 0.9034 (mttt) cc_final: 0.8825 (mtpt) REVERT: N 47 MET cc_start: 0.8842 (mtt) cc_final: 0.8397 (mtt) REVERT: N 60 TYR cc_start: 0.8981 (m-80) cc_final: 0.8767 (m-80) REVERT: k 84 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8329 (ttpp) REVERT: l 149 MET cc_start: 0.7999 (mmm) cc_final: 0.7512 (mmt) REVERT: n 78 ASP cc_start: 0.8433 (m-30) cc_final: 0.7964 (m-30) outliers start: 30 outliers final: 18 residues processed: 428 average time/residue: 0.9839 time to fit residues: 688.0128 Evaluate side-chains 402 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 381 time to evaluate : 4.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain k residue 84 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain l residue 89 THR Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 432 optimal weight: 2.9990 chunk 458 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 410 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 163 GLN C 406 GLN E 160 ASN E 163 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 HIS ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 37806 Z= 0.231 Angle : 0.481 6.357 51070 Z= 0.254 Chirality : 0.041 0.153 5873 Planarity : 0.003 0.041 6624 Dihedral : 6.551 109.282 5306 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.72 % Allowed : 7.62 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.12), residues: 4740 helix: 1.76 (0.10), residues: 2387 sheet: -0.42 (0.18), residues: 655 loop : -0.43 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 260 PHE 0.012 0.001 PHE L 17 TYR 0.012 0.001 TYR F 153 ARG 0.003 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 420 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 391 time to evaluate : 4.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8816 (t80) cc_final: 0.8431 (t80) REVERT: A 247 CYS cc_start: 0.8648 (m) cc_final: 0.8041 (m) REVERT: B 93 TYR cc_start: 0.8686 (t80) cc_final: 0.8472 (t80) REVERT: B 94 ASN cc_start: 0.8892 (m-40) cc_final: 0.8548 (m110) REVERT: B 195 ASN cc_start: 0.7623 (m110) cc_final: 0.7230 (m110) REVERT: B 384 MET cc_start: 0.8717 (mtm) cc_final: 0.8083 (mtp) REVERT: C 182 TYR cc_start: 0.8428 (t80) cc_final: 0.8110 (t80) REVERT: C 342 ASN cc_start: 0.8675 (m-40) cc_final: 0.8317 (m-40) REVERT: E 153 TYR cc_start: 0.7748 (m-80) cc_final: 0.7262 (m-80) REVERT: E 247 CYS cc_start: 0.9101 (m) cc_final: 0.8842 (m) REVERT: F 96 TYR cc_start: 0.8239 (m-80) cc_final: 0.7746 (m-80) REVERT: F 160 ASN cc_start: 0.8806 (t0) cc_final: 0.8209 (t0) REVERT: F 266 SER cc_start: 0.8028 (p) cc_final: 0.7517 (t) REVERT: H 5 MET cc_start: 0.7884 (mmm) cc_final: 0.7665 (mmm) REVERT: I 15 ARG cc_start: 0.7607 (mtt180) cc_final: 0.6889 (mtt180) REVERT: L 18 ASP cc_start: 0.8667 (p0) cc_final: 0.8396 (p0) REVERT: L 53 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: M 34 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: M 78 ASP cc_start: 0.8417 (m-30) cc_final: 0.8013 (m-30) REVERT: M 144 LYS cc_start: 0.9035 (mttt) cc_final: 0.8833 (mtpt) REVERT: i 41 ASN cc_start: 0.8820 (t0) cc_final: 0.8446 (t0) REVERT: l 149 MET cc_start: 0.8209 (mmm) cc_final: 0.7763 (mmt) REVERT: m 141 GLU cc_start: 0.8559 (tp30) cc_final: 0.8091 (tp30) outliers start: 29 outliers final: 18 residues processed: 410 average time/residue: 0.9669 time to fit residues: 655.0320 Evaluate side-chains 399 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 379 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 149 MET Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain i residue 43 ILE Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 89 THR Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 341 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 390 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 0.5980 chunk 411 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN E 160 ASN E 163 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN i 41 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37806 Z= 0.195 Angle : 0.461 6.412 51070 Z= 0.242 Chirality : 0.040 0.150 5873 Planarity : 0.003 0.049 6624 Dihedral : 6.438 107.793 5306 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.65 % Allowed : 7.67 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.12), residues: 4740 helix: 1.95 (0.11), residues: 2378 sheet: -0.45 (0.18), residues: 685 loop : -0.34 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 122 PHE 0.011 0.001 PHE L 17 TYR 0.012 0.001 TYR N 60 ARG 0.003 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 384 time to evaluate : 4.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8804 (t80) cc_final: 0.8426 (t80) REVERT: A 218 THR cc_start: 0.6575 (OUTLIER) cc_final: 0.6040 (p) REVERT: A 247 CYS cc_start: 0.8687 (m) cc_final: 0.8081 (m) REVERT: A 392 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7228 (p0) REVERT: B 93 TYR cc_start: 0.8681 (t80) cc_final: 0.8452 (t80) REVERT: B 94 ASN cc_start: 0.8884 (m-40) cc_final: 0.8528 (m110) REVERT: B 195 ASN cc_start: 0.7645 (m110) cc_final: 0.7245 (m110) REVERT: B 384 MET cc_start: 0.8787 (mtm) cc_final: 0.8082 (mtp) REVERT: C 182 TYR cc_start: 0.8481 (t80) cc_final: 0.8143 (t80) REVERT: C 342 ASN cc_start: 0.8653 (m-40) cc_final: 0.8369 (m-40) REVERT: E 153 TYR cc_start: 0.7721 (m-80) cc_final: 0.7226 (m-80) REVERT: E 247 CYS cc_start: 0.9094 (m) cc_final: 0.8826 (m) REVERT: F 96 TYR cc_start: 0.8187 (m-80) cc_final: 0.7702 (m-80) REVERT: F 160 ASN cc_start: 0.8793 (t0) cc_final: 0.8200 (t0) REVERT: L 18 ASP cc_start: 0.8654 (p0) cc_final: 0.8385 (p0) REVERT: L 53 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: M 34 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: M 78 ASP cc_start: 0.8572 (m-30) cc_final: 0.8143 (m-30) REVERT: l 149 MET cc_start: 0.8208 (mmm) cc_final: 0.7786 (mmt) REVERT: m 141 GLU cc_start: 0.8591 (tp30) cc_final: 0.8092 (tp30) outliers start: 26 outliers final: 18 residues processed: 403 average time/residue: 0.9412 time to fit residues: 627.4488 Evaluate side-chains 392 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 370 time to evaluate : 4.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 149 MET Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 6.9990 chunk 412 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 269 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 458 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN D 237 GLN E 160 ASN E 163 GLN E 260 HIS H 131 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN i 41 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37806 Z= 0.282 Angle : 0.490 6.433 51070 Z= 0.261 Chirality : 0.041 0.151 5873 Planarity : 0.003 0.042 6624 Dihedral : 6.468 106.616 5306 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.72 % Allowed : 8.12 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.12), residues: 4740 helix: 1.97 (0.11), residues: 2371 sheet: -0.35 (0.18), residues: 676 loop : -0.37 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 260 PHE 0.011 0.001 PHE L 17 TYR 0.011 0.001 TYR F 153 ARG 0.007 0.000 ARG H 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 381 time to evaluate : 4.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8791 (t80) cc_final: 0.8437 (t80) REVERT: A 218 THR cc_start: 0.6800 (OUTLIER) cc_final: 0.6244 (p) REVERT: A 247 CYS cc_start: 0.8740 (m) cc_final: 0.8090 (m) REVERT: B 94 ASN cc_start: 0.8867 (m-40) cc_final: 0.8529 (m110) REVERT: B 195 ASN cc_start: 0.7612 (m110) cc_final: 0.7226 (m110) REVERT: C 342 ASN cc_start: 0.8658 (m-40) cc_final: 0.8387 (m-40) REVERT: E 153 TYR cc_start: 0.7728 (m-80) cc_final: 0.7218 (m-80) REVERT: E 247 CYS cc_start: 0.9025 (m) cc_final: 0.8696 (m) REVERT: F 96 TYR cc_start: 0.7931 (m-80) cc_final: 0.7440 (m-80) REVERT: F 160 ASN cc_start: 0.8797 (t0) cc_final: 0.8215 (t0) REVERT: L 18 ASP cc_start: 0.8714 (p0) cc_final: 0.8440 (p0) REVERT: L 53 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: M 34 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: M 36 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7114 (pp20) REVERT: M 78 ASP cc_start: 0.8596 (m-30) cc_final: 0.8142 (m-30) REVERT: N 2 LEU cc_start: 0.7625 (tp) cc_final: 0.7284 (tt) REVERT: N 47 MET cc_start: 0.8889 (mtt) cc_final: 0.8571 (mtt) REVERT: N 60 TYR cc_start: 0.9058 (m-80) cc_final: 0.8579 (m-80) REVERT: m 141 GLU cc_start: 0.8653 (tp30) cc_final: 0.8178 (tp30) outliers start: 29 outliers final: 22 residues processed: 398 average time/residue: 0.9612 time to fit residues: 631.3055 Evaluate side-chains 398 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 372 time to evaluate : 4.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain K residue 149 MET Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain i residue 113 CYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 334 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 386 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 456 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN E 160 ASN E 163 GLN E 260 HIS I 41 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 41 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37806 Z= 0.225 Angle : 0.470 7.635 51070 Z= 0.247 Chirality : 0.040 0.148 5873 Planarity : 0.003 0.051 6624 Dihedral : 6.352 106.590 5306 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.60 % Allowed : 8.59 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 4740 helix: 2.06 (0.11), residues: 2372 sheet: -0.36 (0.18), residues: 684 loop : -0.30 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 260 PHE 0.014 0.001 PHE l 101 TYR 0.011 0.001 TYR B 171 ARG 0.007 0.000 ARG J 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 405 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 381 time to evaluate : 4.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8788 (t80) cc_final: 0.8423 (t80) REVERT: A 218 THR cc_start: 0.6871 (OUTLIER) cc_final: 0.6344 (p) REVERT: A 247 CYS cc_start: 0.8746 (m) cc_final: 0.8114 (m) REVERT: B 94 ASN cc_start: 0.8854 (m-40) cc_final: 0.8644 (m110) REVERT: B 195 ASN cc_start: 0.7626 (m110) cc_final: 0.7240 (m110) REVERT: E 153 TYR cc_start: 0.7751 (m-80) cc_final: 0.7238 (m-80) REVERT: E 247 CYS cc_start: 0.9014 (m) cc_final: 0.8731 (m) REVERT: F 96 TYR cc_start: 0.7759 (m-80) cc_final: 0.7296 (m-80) REVERT: F 160 ASN cc_start: 0.8789 (t0) cc_final: 0.8208 (t0) REVERT: L 18 ASP cc_start: 0.8694 (p0) cc_final: 0.8428 (p0) REVERT: L 53 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: M 34 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: N 2 LEU cc_start: 0.7619 (tp) cc_final: 0.7314 (tt) REVERT: N 47 MET cc_start: 0.8884 (mtt) cc_final: 0.8565 (mtt) REVERT: N 60 TYR cc_start: 0.9054 (m-80) cc_final: 0.8590 (m-80) REVERT: l 41 ASN cc_start: 0.8707 (t0) cc_final: 0.8492 (t0) REVERT: m 141 GLU cc_start: 0.8632 (tp30) cc_final: 0.8101 (tp30) outliers start: 24 outliers final: 20 residues processed: 397 average time/residue: 0.9787 time to fit residues: 640.8932 Evaluate side-chains 390 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 367 time to evaluate : 4.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 149 MET Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain k residue 149 MET Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 359 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN C 230 HIS E 260 HIS ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37806 Z= 0.248 Angle : 0.476 10.547 51070 Z= 0.250 Chirality : 0.040 0.146 5873 Planarity : 0.003 0.059 6624 Dihedral : 6.310 107.075 5306 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.70 % Allowed : 8.69 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 4740 helix: 2.02 (0.11), residues: 2390 sheet: -0.27 (0.18), residues: 677 loop : -0.32 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS n 38 PHE 0.013 0.001 PHE B 235 TYR 0.009 0.001 TYR k 182 ARG 0.010 0.000 ARG J 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 398 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 370 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8784 (t80) cc_final: 0.8444 (t80) REVERT: A 218 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6350 (p) REVERT: A 247 CYS cc_start: 0.8766 (m) cc_final: 0.8136 (m) REVERT: B 94 ASN cc_start: 0.8855 (m-40) cc_final: 0.8644 (m110) REVERT: B 195 ASN cc_start: 0.7629 (m110) cc_final: 0.7241 (m110) REVERT: E 153 TYR cc_start: 0.7758 (m-80) cc_final: 0.7255 (m-80) REVERT: E 247 CYS cc_start: 0.9007 (m) cc_final: 0.8722 (m) REVERT: F 96 TYR cc_start: 0.7474 (m-80) cc_final: 0.7068 (m-80) REVERT: F 160 ASN cc_start: 0.8789 (t0) cc_final: 0.8278 (t0) REVERT: L 18 ASP cc_start: 0.8701 (p0) cc_final: 0.8436 (p0) REVERT: L 53 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: M 34 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: M 36 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7100 (pp20) REVERT: M 78 ASP cc_start: 0.8268 (m-30) cc_final: 0.7816 (m-30) REVERT: N 2 LEU cc_start: 0.7594 (tp) cc_final: 0.7298 (tt) REVERT: N 47 MET cc_start: 0.8890 (mtt) cc_final: 0.8626 (mtt) REVERT: N 60 TYR cc_start: 0.9070 (m-80) cc_final: 0.8622 (m-80) REVERT: N 80 MET cc_start: 0.8994 (mtp) cc_final: 0.8696 (mtp) REVERT: l 41 ASN cc_start: 0.8700 (t0) cc_final: 0.8460 (t0) REVERT: m 141 GLU cc_start: 0.8640 (tp30) cc_final: 0.8145 (tp30) outliers start: 28 outliers final: 22 residues processed: 389 average time/residue: 0.9258 time to fit residues: 594.4032 Evaluate side-chains 392 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 366 time to evaluate : 4.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 149 MET Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain k residue 149 MET Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 0.8980 chunk 437 optimal weight: 0.6980 chunk 399 optimal weight: 5.9990 chunk 425 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 334 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 384 optimal weight: 0.2980 chunk 402 optimal weight: 1.9990 chunk 424 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37806 Z= 0.157 Angle : 0.451 6.301 51070 Z= 0.235 Chirality : 0.040 0.144 5873 Planarity : 0.003 0.042 6624 Dihedral : 6.181 107.197 5306 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.50 % Allowed : 8.89 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 4740 helix: 2.15 (0.11), residues: 2384 sheet: -0.29 (0.18), residues: 690 loop : -0.25 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS F 68 PHE 0.036 0.001 PHE B 235 TYR 0.010 0.001 TYR E 385 ARG 0.008 0.000 ARG J 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 377 time to evaluate : 4.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8771 (t80) cc_final: 0.8475 (t80) REVERT: A 218 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6254 (p) REVERT: A 247 CYS cc_start: 0.8776 (m) cc_final: 0.8115 (m) REVERT: B 94 ASN cc_start: 0.8843 (m-40) cc_final: 0.8627 (m110) REVERT: B 195 ASN cc_start: 0.7694 (m110) cc_final: 0.7292 (m110) REVERT: B 384 MET cc_start: 0.8713 (mtm) cc_final: 0.8179 (mtp) REVERT: C 94 ASN cc_start: 0.8915 (m-40) cc_final: 0.8678 (m-40) REVERT: E 153 TYR cc_start: 0.7735 (m-80) cc_final: 0.7231 (m-80) REVERT: E 247 CYS cc_start: 0.9002 (m) cc_final: 0.8714 (m) REVERT: F 96 TYR cc_start: 0.7718 (m-10) cc_final: 0.7307 (m-80) REVERT: F 160 ASN cc_start: 0.8803 (t0) cc_final: 0.8308 (t0) REVERT: L 18 ASP cc_start: 0.8751 (p0) cc_final: 0.8485 (p0) REVERT: M 34 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: M 78 ASP cc_start: 0.8235 (m-30) cc_final: 0.7747 (m-30) REVERT: N 2 LEU cc_start: 0.7558 (tp) cc_final: 0.7260 (tt) REVERT: N 47 MET cc_start: 0.8913 (mtt) cc_final: 0.8649 (mtt) REVERT: N 80 MET cc_start: 0.8943 (mtp) cc_final: 0.8678 (mtp) REVERT: h 74 MET cc_start: 0.8156 (mmm) cc_final: 0.7913 (mmm) REVERT: l 34 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8190 (mm-40) REVERT: l 41 ASN cc_start: 0.8732 (t0) cc_final: 0.8502 (t0) REVERT: m 98 MET cc_start: 0.8355 (tpp) cc_final: 0.8071 (tpt) REVERT: m 189 LEU cc_start: 0.8314 (mt) cc_final: 0.8051 (mt) REVERT: n 78 ASP cc_start: 0.8332 (m-30) cc_final: 0.8000 (m-30) outliers start: 20 outliers final: 15 residues processed: 391 average time/residue: 0.9924 time to fit residues: 647.0421 Evaluate side-chains 382 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 365 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 149 MET Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 2.9990 chunk 450 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 472 optimal weight: 0.9990 chunk 434 optimal weight: 0.7980 chunk 376 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 290 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN E 260 HIS ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37806 Z= 0.225 Angle : 0.467 6.769 51070 Z= 0.245 Chirality : 0.040 0.145 5873 Planarity : 0.003 0.041 6624 Dihedral : 6.135 108.217 5306 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.50 % Allowed : 8.99 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.12), residues: 4740 helix: 2.20 (0.11), residues: 2377 sheet: -0.24 (0.18), residues: 690 loop : -0.29 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 68 PHE 0.024 0.001 PHE B 235 TYR 0.018 0.001 TYR E 385 ARG 0.006 0.000 ARG J 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 395 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 375 time to evaluate : 4.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8768 (t80) cc_final: 0.8479 (t80) REVERT: A 218 THR cc_start: 0.6784 (OUTLIER) cc_final: 0.6264 (p) REVERT: A 247 CYS cc_start: 0.8864 (m) cc_final: 0.8247 (m) REVERT: B 94 ASN cc_start: 0.8849 (m-40) cc_final: 0.8622 (m110) REVERT: B 195 ASN cc_start: 0.7633 (m110) cc_final: 0.7234 (m110) REVERT: B 384 MET cc_start: 0.8691 (mtm) cc_final: 0.8143 (mtp) REVERT: C 94 ASN cc_start: 0.8908 (m-40) cc_final: 0.8678 (m-40) REVERT: E 153 TYR cc_start: 0.7749 (m-80) cc_final: 0.7248 (m-80) REVERT: E 247 CYS cc_start: 0.8990 (m) cc_final: 0.8723 (m) REVERT: F 96 TYR cc_start: 0.7163 (m-10) cc_final: 0.6801 (m-80) REVERT: F 160 ASN cc_start: 0.8804 (t0) cc_final: 0.8311 (t0) REVERT: L 18 ASP cc_start: 0.8770 (p0) cc_final: 0.8500 (p0) REVERT: M 34 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: M 36 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7119 (pp20) REVERT: M 78 ASP cc_start: 0.8266 (m-30) cc_final: 0.7833 (m-30) REVERT: N 2 LEU cc_start: 0.7553 (tp) cc_final: 0.7261 (tt) REVERT: N 47 MET cc_start: 0.8938 (mtt) cc_final: 0.8677 (mtt) REVERT: N 60 TYR cc_start: 0.9039 (m-80) cc_final: 0.8655 (m-80) REVERT: N 80 MET cc_start: 0.8947 (mtp) cc_final: 0.8687 (mtp) REVERT: h 74 MET cc_start: 0.8229 (mmm) cc_final: 0.7972 (mmm) REVERT: l 41 ASN cc_start: 0.8756 (t0) cc_final: 0.8525 (t0) REVERT: m 47 MET cc_start: 0.8971 (mtt) cc_final: 0.8709 (mtt) REVERT: m 141 GLU cc_start: 0.8627 (tp30) cc_final: 0.8103 (tp30) outliers start: 20 outliers final: 16 residues processed: 390 average time/residue: 0.9618 time to fit residues: 620.1805 Evaluate side-chains 388 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 369 time to evaluate : 4.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 149 MET Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 1.9990 chunk 400 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 346 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 376 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 386 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.126109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079983 restraints weight = 187650.181| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.28 r_work: 0.2967 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37806 Z= 0.182 Angle : 0.454 6.239 51070 Z= 0.237 Chirality : 0.040 0.143 5873 Planarity : 0.003 0.042 6624 Dihedral : 6.060 108.389 5306 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.50 % Allowed : 8.99 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.12), residues: 4740 helix: 2.23 (0.11), residues: 2383 sheet: -0.36 (0.18), residues: 730 loop : -0.19 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 68 PHE 0.023 0.001 PHE B 235 TYR 0.016 0.001 TYR E 385 ARG 0.004 0.000 ARG J 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14986.38 seconds wall clock time: 256 minutes 13.10 seconds (15373.10 seconds total)