Starting phenix.real_space_refine on Sun Sep 29 15:47:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/09_2024/8e91_27952_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/09_2024/8e91_27952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/09_2024/8e91_27952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/09_2024/8e91_27952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/09_2024/8e91_27952_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/09_2024/8e91_27952_trim.cif" } resolution = 2.57 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= 0.001 sd= 0.034 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 208 5.16 5 C 23462 2.51 5 N 6399 2.21 5 O 7180 1.98 5 H 37574 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.44s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74842 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: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "D" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "E" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5442 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} 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: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} 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: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 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, 'AGS': 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, 'AGS': 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, 'AGS': 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: 29.76, per 1000 atoms: 0.40 Number of scatterers: 74842 At special positions: 0 Unit cell: (148.368, 136.004, 193.328, 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 208 16.00 P 16 15.00 Mg 3 11.99 O 7180 8.00 N 6399 7.00 C 23462 6.00 H 37574 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: 15.38 Conformation dependent library (CDL) restraints added in 4.9 seconds 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8794 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 69 sheets defined 51.9% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.823A 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: 4.138A pdb=" N ASN A 106 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.516A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.846A pdb=" N GLN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 168 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.827A pdb=" N ARG A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.610A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 4.326A pdb=" N GLY A 226 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.902A 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: 3.526A 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: 3.741A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.820A pdb=" N ASP A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 4.271A pdb=" N ARG A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.785A 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: 3.581A 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 124 through 136 removed outlier: 3.506A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.279A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.566A pdb=" N ARG B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.521A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.642A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.273A pdb=" N PHE B 235 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.808A 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: 3.639A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.562A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.535A pdb=" N LEU B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.048A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.853A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.619A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 380 removed outlier: 4.160A pdb=" N LEU B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.734A 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 removed outlier: 3.519A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.500A pdb=" N HIS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.868A 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: 3.541A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.688A pdb=" N GLN C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.635A 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: 4.116A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 removed outlier: 3.590A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 264 " --> pdb=" O HIS C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.667A 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: 3.756A 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: 3.542A pdb=" N ASP C 356 " --> pdb=" O ASP C 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 4.164A pdb=" N ARG C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.826A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 4.064A 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 124 through 134 removed outlier: 3.593A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.651A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.572A pdb=" N ARG D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 204 through 217 removed outlier: 3.646A pdb=" N GLN D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.686A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (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 removed outlier: 3.540A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.747A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.792A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 removed outlier: 3.517A pdb=" N LEU D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 removed outlier: 3.556A pdb=" N ALA D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 4.301A pdb=" N ARG D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 3.913A 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 removed outlier: 3.519A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY D 405 " --> pdb=" O SER D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 399 through 405' Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.514A 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 124 through 134 removed outlier: 3.692A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.788A 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: 3.512A pdb=" N GLN E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 264 Processing helix chain 'E' and resid 282 through 288 Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.729A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.595A pdb=" N ILE E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG E 307 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 308 " --> pdb=" O PHE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.774A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 343 Processing helix chain 'E' and resid 351 through 366 removed outlier: 3.588A pdb=" N ALA E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 380 removed outlier: 4.393A 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: 3.721A pdb=" N ILE E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.867A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 101 Processing helix chain 'F' and resid 124 through 136 removed outlier: 3.536A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 169 removed outlier: 4.033A pdb=" N ASP F 157 " --> pdb=" O TYR F 153 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 179 Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.541A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.675A 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: 3.701A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.898A pdb=" N GLY F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.711A pdb=" N LEU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.541A pdb=" N ARG F 307 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 removed outlier: 3.806A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 345 removed outlier: 3.621A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 366 removed outlier: 3.618A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 387 removed outlier: 4.307A pdb=" N ARG F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 removed outlier: 3.519A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 25 Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.742A 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 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.651A 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: 3.588A 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 26 removed outlier: 3.777A 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: 3.608A 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: 3.663A 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: 3.592A 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: 3.640A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 removed outlier: 3.650A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.553A pdb=" N GLY L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.813A 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: 3.543A 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: 3.654A 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 26 removed outlier: 3.760A 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: 3.661A pdb=" N GLY h 73 " --> pdb=" O VAL h 69 " (cutoff:3.500A) removed outlier: 3.643A 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 169 Processing helix chain 'h' and resid 176 through 183 Processing helix chain 'i' and resid 19 through 26 removed outlier: 3.923A 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: 3.674A pdb=" N GLY i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.553A 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 182 Processing helix chain 'j' and resid 19 through 26 removed outlier: 3.739A 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: 3.595A pdb=" N GLY j 73 " --> pdb=" O VAL j 69 " (cutoff:3.500A) removed outlier: 3.607A 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: 3.945A 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: 3.663A pdb=" N GLY k 73 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 3.589A 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 182 Processing helix chain 'l' and resid 19 through 26 removed outlier: 3.779A pdb=" N GLU l 26 " --> pdb=" O ARG l 22 " (cutoff:3.500A) 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 Processing helix chain 'l' and resid 160 through 169 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: 3.702A pdb=" N GLY m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.517A 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 26 removed outlier: 3.534A pdb=" N LEU n 23 " --> pdb=" O ILE n 19 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU n 26 " --> pdb=" O ARG n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 54 Processing helix chain 'n' and resid 69 through 83 removed outlier: 3.690A pdb=" N GLY n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) removed outlier: 3.535A 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 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: 6.907A pdb=" N THR A 141 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP A 184 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 143 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 115 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N GLY A 249 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 117 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA3, 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: 7.977A pdb=" N ILE A 398 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU A 349 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 144 removed outlier: 3.766A pdb=" N THR B 141 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 115 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY B 249 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B 117 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 222 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350 removed outlier: 6.090A pdb=" N ASP B 347 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE B 398 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU B 349 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 247 through 249 removed outlier: 6.096A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 140 through 144 removed outlier: 7.093A pdb=" N THR C 141 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASP C 184 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA C 143 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 219 through 220 removed outlier: 3.668A pdb=" N VAL C 238 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.887A pdb=" N GLU C 349 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS C 395 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 140 through 144 removed outlier: 3.593A pdb=" N THR D 141 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D 181 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLY D 248 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE D 183 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU D 116 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 219 through 222 Processing sheet with id=AB4, first strand: chain 'D' and resid 347 through 350 removed outlier: 6.697A pdb=" N ASP D 347 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE D 398 " --> pdb=" O ASP D 347 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLU D 349 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 395 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 140 through 144 removed outlier: 6.589A pdb=" N THR E 141 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASP E 184 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA E 143 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL E 181 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY E 248 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE E 183 " --> pdb=" O GLY E 248 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE E 115 " --> pdb=" O CYS E 247 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLY E 249 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU E 117 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 219 through 222 Processing sheet with id=AB7, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.613A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 115 through 118 Processing sheet with id=AB9, first strand: chain 'F' and resid 140 through 144 removed outlier: 3.728A pdb=" N THR F 141 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 219 through 222 Processing sheet with id=AC2, first strand: chain 'F' and resid 347 through 350 removed outlier: 6.462A pdb=" N ASP F 347 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE F 398 " --> pdb=" O ASP F 347 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLU F 349 " --> pdb=" O ILE F 398 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 6 through 9 Processing sheet with id=AC4, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.206A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.206A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC7, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AC8, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.541A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER I 65 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.332A 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=AC9, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.541A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER I 65 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 125 through 131 Processing sheet with id=AD2, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AD3, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.556A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER J 65 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.556A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER J 65 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 125 through 131 Processing sheet with id=AD6, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AD7, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.492A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER K 65 " --> pdb=" O GLN K 94 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG K 118 " --> pdb=" O CYS K 91 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY K 93 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N MET K 120 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.492A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER K 65 " --> pdb=" O GLN K 94 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 125 through 131 Processing sheet with id=AE1, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.712A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.350A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 94 through 95 removed outlier: 6.536A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 125 through 131 removed outlier: 3.503A pdb=" N TYR k 128 " --> pdb=" O TYR L 128 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 6 through 8 Processing sheet with id=AE6, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.434A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG M 118 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY M 93 " --> pdb=" O ARG M 118 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N MET M 120 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA M 95 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.434A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 125 through 131 removed outlier: 3.538A pdb=" N TYR l 128 " --> pdb=" O TYR M 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 5 through 9 Processing sheet with id=AF1, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.386A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER N 65 " --> pdb=" O GLN N 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.386A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER N 65 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 125 through 131 Processing sheet with id=AF4, first strand: chain 'h' and resid 5 through 9 Processing sheet with id=AF5, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.417A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG h 118 " --> pdb=" O CYS h 91 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY h 93 " --> pdb=" O ARG h 118 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N MET h 120 " --> pdb=" O GLY h 93 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA h 95 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.417A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE h 112 " --> pdb=" O VAL h 87 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR h 89 " --> pdb=" O PHE h 112 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'i' and resid 5 through 9 Processing sheet with id=AF8, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.373A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG i 118 " --> pdb=" O CYS i 91 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY i 93 " --> pdb=" O ARG i 118 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N MET i 120 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA i 95 " --> pdb=" O MET i 120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.373A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE i 112 " --> pdb=" O VAL i 87 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR i 89 " --> pdb=" O PHE i 112 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 5 through 9 Processing sheet with id=AG2, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.426A pdb=" N ILE j 59 " --> pdb=" O SER j 88 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE j 90 " --> pdb=" O ILE j 59 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU j 61 " --> pdb=" O ILE j 90 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET j 92 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE j 63 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLN j 94 " --> pdb=" O ILE j 63 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE j 112 " --> pdb=" O VAL j 87 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR j 89 " --> pdb=" O PHE j 112 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'j' and resid 118 through 121 Processing sheet with id=AG4, first strand: chain 'k' and resid 5 through 9 Processing sheet with id=AG5, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.430A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER k 65 " --> pdb=" O GLN k 94 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG k 118 " --> pdb=" O CYS k 91 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY k 93 " --> pdb=" O ARG k 118 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N MET k 120 " --> pdb=" O GLY k 93 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA k 95 " --> pdb=" O MET k 120 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.430A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER k 65 " --> pdb=" O GLN k 94 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE k 112 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR k 89 " --> pdb=" O PHE k 112 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'l' and resid 5 through 9 Processing sheet with id=AG8, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.550A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG l 118 " --> pdb=" O CYS l 91 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY l 93 " --> pdb=" O ARG l 118 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N MET l 120 " --> pdb=" O GLY l 93 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA l 95 " --> pdb=" O MET l 120 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.550A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE l 112 " --> pdb=" O VAL l 87 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR l 89 " --> pdb=" O PHE l 112 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'm' and resid 5 through 9 Processing sheet with id=AH2, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.491A pdb=" N ILE m 59 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE m 90 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU m 61 " --> pdb=" O ILE m 90 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET m 92 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE m 63 " --> pdb=" O MET m 92 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLN m 94 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER m 65 " --> pdb=" O GLN m 94 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE m 112 " --> pdb=" O VAL m 87 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR m 89 " --> pdb=" O PHE m 112 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'm' and resid 118 through 121 Processing sheet with id=AH4, first strand: chain 'n' and resid 5 through 9 Processing sheet with id=AH5, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.390A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG n 118 " --> pdb=" O CYS n 91 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY n 93 " --> pdb=" O ARG n 118 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N MET n 120 " --> pdb=" O GLY n 93 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA n 95 " --> pdb=" O MET n 120 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.390A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE n 112 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR n 89 " --> pdb=" O PHE n 112 " (cutoff:3.500A) 1890 hydrogen bonds defined for protein. 5505 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: 33.51 Time building geometry restraints manager: 18.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 37534 1.06 - 1.28: 6513 1.28 - 1.50: 15124 1.50 - 1.73: 15859 1.73 - 1.95: 372 Bond restraints: 75402 Sorted by residual: bond pdb=" C HIS A 230 " pdb=" N PRO A 231 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.30e-02 5.92e+03 1.93e+00 bond pdb=" CB PRO J 85 " pdb=" CG PRO J 85 " ideal model delta sigma weight residual 1.492 1.423 0.069 5.00e-02 4.00e+02 1.91e+00 bond pdb=" CB GLU D 234 " pdb=" CG GLU D 234 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB PRO I 85 " pdb=" CG PRO I 85 " ideal model delta sigma weight residual 1.492 1.430 0.062 5.00e-02 4.00e+02 1.56e+00 bond pdb=" CA ARG L 12 " pdb=" CB ARG L 12 " ideal model delta sigma weight residual 1.531 1.550 -0.019 1.51e-02 4.39e+03 1.53e+00 ... (remaining 75397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 128656 1.23 - 2.46: 7258 2.46 - 3.68: 602 3.68 - 4.91: 203 4.91 - 6.14: 47 Bond angle restraints: 136766 Sorted by residual: angle pdb=" CA GLU D 234 " pdb=" CB GLU D 234 " pdb=" CG GLU D 234 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.42e+00 angle pdb=" N ILE B 198 " pdb=" CA ILE B 198 " pdb=" C ILE B 198 " ideal model delta sigma weight residual 112.96 109.90 3.06 1.00e+00 1.00e+00 9.35e+00 angle pdb=" CA ARG L 12 " pdb=" CB ARG L 12 " pdb=" CG ARG L 12 " ideal model delta sigma weight residual 114.10 119.96 -5.86 2.00e+00 2.50e-01 8.58e+00 angle pdb=" CA GLN D 232 " pdb=" CB GLN D 232 " pdb=" CG GLN D 232 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.39e+00 angle pdb=" CA GLN F 225 " pdb=" CB GLN F 225 " pdb=" CG GLN F 225 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.35e+00 ... (remaining 136761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 33158 23.98 - 47.95: 1506 47.95 - 71.93: 395 71.93 - 95.90: 24 95.90 - 119.88: 2 Dihedral angle restraints: 35085 sinusoidal: 19777 harmonic: 15308 Sorted by residual: 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 -179.88 119.88 1 2.00e+01 2.50e-03 3.60e+01 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 48.59 -108.59 1 2.00e+01 2.50e-03 3.17e+01 dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -142.34 82.34 1 2.00e+01 2.50e-03 2.08e+01 ... (remaining 35082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3894 0.035 - 0.069: 1232 0.069 - 0.104: 534 0.104 - 0.138: 194 0.138 - 0.173: 28 Chirality restraints: 5882 Sorted by residual: 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 2.61 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA ASP A 170 " pdb=" N ASP A 170 " pdb=" C ASP A 170 " pdb=" CB ASP A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA VAL F 222 " pdb=" N VAL F 222 " pdb=" C VAL F 222 " pdb=" CB VAL F 222 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 5879 not shown) Planarity restraints: 11212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 230 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO E 231 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 231 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 231 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 223 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B 224 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 224 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 224 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 155 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C GLY A 155 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY A 155 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 156 " -0.012 2.00e-02 2.50e+03 ... (remaining 11209 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 7057 2.24 - 2.83: 172296 2.83 - 3.42: 196039 3.42 - 4.01: 277821 4.01 - 4.60: 431859 Nonbonded interactions: 1085072 Sorted by model distance: nonbonded pdb=" OG1 THR E 149 " pdb=" H GLU E 156 " model vdw 1.650 2.450 nonbonded pdb=" OG1 THR B 149 " pdb=" H GLU B 156 " model vdw 1.677 2.450 nonbonded pdb=" OD1 ASP m 18 " pdb=" H SER m 21 " model vdw 1.699 2.450 nonbonded pdb=" H GLU A 291 " pdb=" OD2 ASP A 294 " model vdw 1.701 2.450 nonbonded pdb=" O ASP F 144 " pdb=" HG1 THR F 147 " model vdw 1.702 2.450 ... (remaining 1085067 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.030 Extract box with map and model: 2.300 Check model and map are aligned: 0.450 Set scattering table: 0.580 Process input model: 133.190 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.430 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37828 Z= 0.285 Angle : 0.650 6.139 51098 Z= 0.356 Chirality : 0.044 0.173 5882 Planarity : 0.004 0.054 6629 Dihedral : 12.111 119.879 14400 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -0.18 (0.11), residues: 4744 helix: 0.57 (0.10), residues: 2271 sheet: -0.46 (0.17), residues: 727 loop : -0.74 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 122 PHE 0.019 0.001 PHE N 17 TYR 0.010 0.001 TYR C 153 ARG 0.007 0.001 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 914 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 914 time to evaluate : 4.700 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 73 HIS cc_start: 0.7995 (t-90) cc_final: 0.7784 (t-170) REVERT: A 182 TYR cc_start: 0.8176 (t80) cc_final: 0.7944 (t80) REVERT: B 94 ASN cc_start: 0.9280 (m-40) cc_final: 0.9073 (m-40) REVERT: B 171 TYR cc_start: 0.8196 (m-10) cc_final: 0.7945 (m-10) REVERT: B 294 ASP cc_start: 0.8028 (m-30) cc_final: 0.7693 (m-30) REVERT: C 160 ASN cc_start: 0.9036 (m110) cc_final: 0.8055 (m110) REVERT: C 283 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7801 (tm-30) REVERT: C 352 ASP cc_start: 0.8263 (m-30) cc_final: 0.8037 (t0) REVERT: D 72 ASN cc_start: 0.8515 (m-40) cc_final: 0.8249 (m-40) REVERT: D 73 HIS cc_start: 0.8675 (t70) cc_final: 0.8473 (t-90) REVERT: D 115 ILE cc_start: 0.9431 (mt) cc_final: 0.9223 (mp) REVERT: D 142 MET cc_start: 0.8271 (mtp) cc_final: 0.7853 (mpt) REVERT: D 205 GLU cc_start: 0.8476 (tt0) cc_final: 0.7923 (tt0) REVERT: D 297 LYS cc_start: 0.9047 (mttt) cc_final: 0.8547 (tptp) REVERT: E 77 TYR cc_start: 0.8487 (m-80) cc_final: 0.8188 (m-80) REVERT: E 96 TYR cc_start: 0.8719 (m-80) cc_final: 0.8359 (m-80) REVERT: E 301 ILE cc_start: 0.8870 (mm) cc_final: 0.8208 (tt) REVERT: F 94 ASN cc_start: 0.9273 (m-40) cc_final: 0.9012 (m-40) REVERT: F 95 HIS cc_start: 0.8924 (t70) cc_final: 0.8714 (t-90) REVERT: F 256 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8685 (tptt) REVERT: F 293 GLU cc_start: 0.8019 (pm20) cc_final: 0.7795 (mp0) REVERT: I 10 THR cc_start: 0.8716 (p) cc_final: 0.8397 (p) REVERT: h 18 ASP cc_start: 0.7101 (p0) cc_final: 0.6897 (p0) REVERT: i 17 PHE cc_start: 0.7332 (m-80) cc_final: 0.7073 (m-80) REVERT: l 7 ILE cc_start: 0.9212 (mm) cc_final: 0.9008 (mm) REVERT: l 57 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8056 (mtmm) REVERT: m 110 LYS cc_start: 0.8861 (mttt) cc_final: 0.8527 (mttt) REVERT: n 60 TYR cc_start: 0.8689 (m-80) cc_final: 0.8482 (m-80) outliers start: 0 outliers final: 3 residues processed: 914 average time/residue: 2.8365 time to fit residues: 3113.8048 Evaluate side-chains 528 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 525 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain l residue 17 PHE Chi-restraints excluded: chain l residue 92 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 199 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 371 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 430 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 72 ASN B 160 ASN C 94 ASN C 342 ASN E 101 ASN F 72 ASN F 324 GLN F 342 ASN H 129 GLN I 34 GLN J 159 GLN K 9 GLN M 41 ASN N 41 ASN h 9 GLN h 34 GLN h 41 ASN h 81 GLN ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 129 GLN j 9 GLN j 41 ASN k 191 HIS l 41 ASN m 9 GLN m 41 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37828 Z= 0.244 Angle : 0.571 6.519 51098 Z= 0.305 Chirality : 0.042 0.156 5882 Planarity : 0.004 0.069 6629 Dihedral : 5.962 111.788 5263 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.67 % Allowed : 8.81 % Favored : 89.52 % 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: 0.59 (0.12), residues: 4744 helix: 1.38 (0.10), residues: 2362 sheet: -0.38 (0.18), residues: 687 loop : -0.60 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 260 PHE 0.016 0.001 PHE E 350 TYR 0.013 0.001 TYR F 96 ARG 0.014 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 625 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 558 time to evaluate : 4.791 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 140 PHE cc_start: 0.7930 (t80) cc_final: 0.7695 (t80) REVERT: A 160 ASN cc_start: 0.8463 (t0) cc_final: 0.8109 (t0) REVERT: A 182 TYR cc_start: 0.8114 (t80) cc_final: 0.7481 (t80) REVERT: B 148 LEU cc_start: 0.8584 (mt) cc_final: 0.8363 (mt) REVERT: B 294 ASP cc_start: 0.8253 (m-30) cc_final: 0.7960 (m-30) REVERT: C 160 ASN cc_start: 0.8473 (m110) cc_final: 0.8069 (m110) REVERT: D 142 MET cc_start: 0.8354 (mtp) cc_final: 0.8051 (mpt) REVERT: D 205 GLU cc_start: 0.8337 (tt0) cc_final: 0.7951 (tt0) REVERT: D 297 LYS cc_start: 0.9088 (mttt) cc_final: 0.8759 (tptp) REVERT: E 384 MET cc_start: 0.9063 (mtt) cc_final: 0.8850 (mtt) REVERT: F 94 ASN cc_start: 0.9403 (m-40) cc_final: 0.8853 (m110) REVERT: F 256 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8843 (mmmt) REVERT: F 293 GLU cc_start: 0.8264 (pm20) cc_final: 0.8014 (mp0) REVERT: I 17 PHE cc_start: 0.8521 (m-80) cc_final: 0.8201 (m-80) REVERT: J 18 ASP cc_start: 0.7402 (p0) cc_final: 0.7028 (p0) REVERT: M 17 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: h 47 MET cc_start: 0.9122 (mtt) cc_final: 0.8846 (mtt) REVERT: i 17 PHE cc_start: 0.7783 (m-80) cc_final: 0.7452 (m-80) REVERT: l 57 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8387 (mtmm) REVERT: l 129 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7688 (tp40) REVERT: m 144 LYS cc_start: 0.8596 (mttt) cc_final: 0.8387 (mttp) REVERT: n 60 TYR cc_start: 0.8803 (m-80) cc_final: 0.8566 (m-80) outliers start: 67 outliers final: 15 residues processed: 590 average time/residue: 2.6012 time to fit residues: 1895.5255 Evaluate side-chains 512 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 495 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 17 PHE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain h residue 117 SER Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain m residue 187 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 0.3980 chunk 133 optimal weight: 40.0000 chunk 358 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 431 optimal weight: 2.9990 chunk 465 optimal weight: 2.9990 chunk 384 optimal weight: 5.9990 chunk 427 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN E 94 ASN E 101 ASN E 331 ASN H 46 GLN ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN K 9 GLN K 41 ASN M 41 ASN h 41 ASN i 41 ASN m 9 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37828 Z= 0.281 Angle : 0.531 7.703 51098 Z= 0.279 Chirality : 0.042 0.157 5882 Planarity : 0.003 0.046 6629 Dihedral : 5.760 108.604 5255 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.52 % Allowed : 10.01 % Favored : 88.47 % 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: 0.91 (0.12), residues: 4744 helix: 1.65 (0.11), residues: 2358 sheet: -0.24 (0.17), residues: 769 loop : -0.45 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS F 95 PHE 0.039 0.001 PHE C 235 TYR 0.014 0.001 TYR E 96 ARG 0.005 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 560 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 499 time to evaluate : 4.706 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: A 140 PHE cc_start: 0.7604 (t80) cc_final: 0.7386 (t80) REVERT: B 160 ASN cc_start: 0.9133 (m110) cc_final: 0.8533 (m110) REVERT: B 294 ASP cc_start: 0.8344 (m-30) cc_final: 0.8081 (m-30) REVERT: C 160 ASN cc_start: 0.8437 (m110) cc_final: 0.8095 (m110) REVERT: C 283 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7209 (tm-30) REVERT: D 191 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7514 (mtm110) REVERT: D 205 GLU cc_start: 0.8346 (tt0) cc_final: 0.7991 (tt0) REVERT: D 297 LYS cc_start: 0.9179 (mttt) cc_final: 0.8779 (tptp) REVERT: F 77 TYR cc_start: 0.8616 (m-10) cc_final: 0.8394 (m-80) REVERT: F 256 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8859 (mmmt) REVERT: J 34 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: K 9 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.7921 (mp-120) REVERT: K 41 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7869 (m-40) REVERT: h 98 MET cc_start: 0.8429 (tpt) cc_final: 0.8021 (tpt) REVERT: i 17 PHE cc_start: 0.8330 (m-80) cc_final: 0.8048 (m-80) REVERT: i 36 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: j 36 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: l 15 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7287 (ttp-170) REVERT: l 57 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8590 (mtmm) REVERT: l 92 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8374 (ptp) REVERT: l 129 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7643 (tp40) REVERT: m 60 TYR cc_start: 0.8731 (m-80) cc_final: 0.8446 (m-80) REVERT: n 25 LYS cc_start: 0.9187 (mtpp) cc_final: 0.8881 (mtmt) REVERT: n 60 TYR cc_start: 0.8949 (m-80) cc_final: 0.8679 (m-80) outliers start: 61 outliers final: 12 residues processed: 527 average time/residue: 2.7489 time to fit residues: 1802.8922 Evaluate side-chains 482 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 462 time to evaluate : 4.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain K residue 9 GLN Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain i residue 5 MET Chi-restraints excluded: chain i residue 36 GLU Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain l residue 15 ARG Chi-restraints excluded: chain l residue 92 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 6.9990 chunk 324 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 289 optimal weight: 2.9990 chunk 432 optimal weight: 2.9990 chunk 458 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 410 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 342 ASN E 94 ASN E 101 ASN E 260 HIS E 331 ASN F 209 GLN H 131 GLN I 9 GLN M 41 ASN N 159 GLN h 41 ASN i 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN m 41 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 37828 Z= 0.298 Angle : 0.520 7.474 51098 Z= 0.273 Chirality : 0.042 0.143 5882 Planarity : 0.003 0.034 6629 Dihedral : 5.744 109.724 5255 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.22 % Allowed : 10.90 % Favored : 87.88 % 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: 1.03 (0.12), residues: 4744 helix: 1.80 (0.11), residues: 2342 sheet: -0.20 (0.17), residues: 768 loop : -0.45 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 95 PHE 0.013 0.001 PHE N 17 TYR 0.017 0.001 TYR F 182 ARG 0.004 0.000 ARG h 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 521 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 472 time to evaluate : 4.778 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: B 160 ASN cc_start: 0.9076 (m110) cc_final: 0.8489 (m110) REVERT: C 283 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7250 (tm-30) REVERT: D 191 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7580 (mtm110) REVERT: D 205 GLU cc_start: 0.8318 (tt0) cc_final: 0.7915 (tt0) REVERT: D 297 LYS cc_start: 0.9188 (mttt) cc_final: 0.8800 (tptp) REVERT: E 73 HIS cc_start: 0.8556 (t70) cc_final: 0.8355 (t-90) REVERT: E 118 ILE cc_start: 0.8984 (mt) cc_final: 0.8660 (mm) REVERT: F 142 MET cc_start: 0.7370 (tmt) cc_final: 0.7016 (tmt) REVERT: F 256 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8856 (mmmt) REVERT: K 15 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7625 (ptp-170) REVERT: h 36 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7650 (pp20) REVERT: i 36 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7222 (pt0) REVERT: j 36 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: l 36 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: l 129 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7647 (tp40) REVERT: m 60 TYR cc_start: 0.8827 (m-80) cc_final: 0.8547 (m-80) REVERT: n 25 LYS cc_start: 0.9207 (mtpp) cc_final: 0.8961 (mtmt) REVERT: n 60 TYR cc_start: 0.9012 (m-80) cc_final: 0.8766 (m-80) outliers start: 49 outliers final: 15 residues processed: 499 average time/residue: 2.5834 time to fit residues: 1581.2733 Evaluate side-chains 473 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 452 time to evaluate : 4.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 117 SER Chi-restraints excluded: chain i residue 36 GLU Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 36 GLU Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 341 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 390 optimal weight: 0.6980 chunk 316 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN E 101 ASN E 260 HIS I 9 GLN J 41 ASN M 41 ASN h 41 ASN i 41 ASN m 9 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37828 Z= 0.272 Angle : 0.505 6.471 51098 Z= 0.265 Chirality : 0.041 0.142 5882 Planarity : 0.003 0.040 6629 Dihedral : 5.704 107.547 5255 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.17 % Allowed : 11.48 % Favored : 87.35 % 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: 1.15 (0.12), residues: 4744 helix: 1.90 (0.11), residues: 2344 sheet: -0.14 (0.18), residues: 684 loop : -0.40 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 122 PHE 0.013 0.001 PHE N 17 TYR 0.013 0.001 TYR A 77 ARG 0.004 0.000 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 505 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 458 time to evaluate : 4.807 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: B 160 ASN cc_start: 0.9064 (m110) cc_final: 0.8476 (m110) REVERT: C 283 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 337 TYR cc_start: 0.8058 (m-80) cc_final: 0.6581 (m-80) REVERT: D 191 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7611 (mtm110) REVERT: D 205 GLU cc_start: 0.8315 (tt0) cc_final: 0.7924 (tt0) REVERT: D 235 PHE cc_start: 0.8447 (m-10) cc_final: 0.7873 (m-80) REVERT: D 297 LYS cc_start: 0.9164 (mttt) cc_final: 0.8842 (tptp) REVERT: E 118 ILE cc_start: 0.8866 (mt) cc_final: 0.8556 (mm) REVERT: F 165 LEU cc_start: 0.9444 (tp) cc_final: 0.9243 (tm) REVERT: F 331 ASN cc_start: 0.8442 (p0) cc_final: 0.8155 (p0) REVERT: J 34 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: h 92 MET cc_start: 0.8566 (mtm) cc_final: 0.8319 (ptp) REVERT: i 36 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: j 36 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7527 (pt0) REVERT: l 129 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7613 (tp40) REVERT: m 60 TYR cc_start: 0.8860 (m-80) cc_final: 0.8646 (m-80) REVERT: n 60 TYR cc_start: 0.9049 (m-80) cc_final: 0.8821 (m-80) outliers start: 47 outliers final: 20 residues processed: 487 average time/residue: 2.6194 time to fit residues: 1565.8018 Evaluate side-chains 470 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 446 time to evaluate : 4.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 390 MET Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain h residue 117 SER Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 36 GLU Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 15 ARG Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 9.9990 chunk 412 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 458 optimal weight: 2.9990 chunk 380 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN C 163 GLN C 233 GLN C 342 ASN E 94 ASN E 101 ASN E 260 HIS I 9 GLN J 41 ASN M 41 ASN h 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN n 41 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37828 Z= 0.278 Angle : 0.505 6.350 51098 Z= 0.265 Chirality : 0.041 0.142 5882 Planarity : 0.003 0.058 6629 Dihedral : 5.665 104.315 5255 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.15 % Allowed : 11.65 % Favored : 87.20 % 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: 1.21 (0.12), residues: 4744 helix: 1.97 (0.11), residues: 2347 sheet: 0.22 (0.20), residues: 544 loop : -0.51 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS m 122 PHE 0.014 0.001 PHE N 17 TYR 0.016 0.001 TYR C 337 ARG 0.007 0.000 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 501 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 455 time to evaluate : 4.715 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: B 160 ASN cc_start: 0.9070 (m110) cc_final: 0.8470 (m110) REVERT: C 283 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7303 (tm-30) REVERT: C 331 ASN cc_start: 0.8525 (m-40) cc_final: 0.8208 (m-40) REVERT: D 191 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7635 (mtm110) REVERT: D 205 GLU cc_start: 0.8300 (tt0) cc_final: 0.7882 (tt0) REVERT: D 235 PHE cc_start: 0.8481 (m-10) cc_final: 0.7935 (m-80) REVERT: D 297 LYS cc_start: 0.9167 (mttt) cc_final: 0.8856 (tptp) REVERT: E 118 ILE cc_start: 0.8857 (mt) cc_final: 0.8546 (mm) REVERT: F 142 MET cc_start: 0.7276 (tmt) cc_final: 0.6898 (tmt) REVERT: F 165 LEU cc_start: 0.9445 (tp) cc_final: 0.9216 (tm) REVERT: F 331 ASN cc_start: 0.8470 (p0) cc_final: 0.8216 (p0) REVERT: J 34 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: K 15 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7639 (ptp-170) REVERT: h 92 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8330 (ptp) REVERT: i 36 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: j 36 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: l 129 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7627 (tp40) REVERT: m 60 TYR cc_start: 0.8896 (m-80) cc_final: 0.8681 (m-80) REVERT: n 25 LYS cc_start: 0.9225 (mtpp) cc_final: 0.8998 (mtmt) REVERT: n 60 TYR cc_start: 0.9062 (m-80) cc_final: 0.8852 (m-80) outliers start: 46 outliers final: 21 residues processed: 480 average time/residue: 2.6103 time to fit residues: 1539.9282 Evaluate side-chains 460 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 433 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 36 GLU Chi-restraints excluded: chain j residue 25 LYS Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 15 ARG Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 261 optimal weight: 0.3980 chunk 334 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 456 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN E 94 ASN E 101 ASN E 260 HIS E 331 ASN I 9 GLN M 41 ASN h 41 ASN i 41 ASN m 9 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37828 Z= 0.219 Angle : 0.489 6.330 51098 Z= 0.255 Chirality : 0.041 0.141 5882 Planarity : 0.003 0.048 6629 Dihedral : 5.591 97.618 5255 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.97 % Allowed : 11.92 % Favored : 87.10 % 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: 1.27 (0.12), residues: 4744 helix: 2.03 (0.11), residues: 2342 sheet: 0.28 (0.20), residues: 558 loop : -0.50 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS m 122 PHE 0.014 0.001 PHE L 17 TYR 0.014 0.001 TYR C 337 ARG 0.005 0.000 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 483 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 444 time to evaluate : 4.774 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: B 160 ASN cc_start: 0.9068 (m110) cc_final: 0.8463 (m110) REVERT: C 283 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7297 (tm-30) REVERT: C 331 ASN cc_start: 0.8442 (m-40) cc_final: 0.8158 (m-40) REVERT: D 191 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7627 (mtm110) REVERT: D 205 GLU cc_start: 0.8278 (tt0) cc_final: 0.7866 (tt0) REVERT: D 235 PHE cc_start: 0.8493 (m-10) cc_final: 0.7941 (m-80) REVERT: D 297 LYS cc_start: 0.9163 (mttt) cc_final: 0.8911 (tptp) REVERT: E 118 ILE cc_start: 0.8845 (mt) cc_final: 0.8533 (mm) REVERT: F 142 MET cc_start: 0.7240 (tmt) cc_final: 0.6671 (tmt) REVERT: F 331 ASN cc_start: 0.8443 (p0) cc_final: 0.8195 (p0) REVERT: J 34 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: K 15 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7692 (ptp-170) REVERT: i 36 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: j 36 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: l 129 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7619 (tp40) REVERT: m 60 TYR cc_start: 0.8895 (m-80) cc_final: 0.8681 (m-80) REVERT: n 25 LYS cc_start: 0.9220 (mtpp) cc_final: 0.8985 (mtmt) REVERT: n 60 TYR cc_start: 0.9065 (m-80) cc_final: 0.8848 (m-80) outliers start: 39 outliers final: 17 residues processed: 464 average time/residue: 2.5328 time to fit residues: 1449.9348 Evaluate side-chains 460 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 438 time to evaluate : 4.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain i residue 36 GLU Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain m residue 32 THR Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 0.5980 chunk 182 optimal weight: 7.9990 chunk 272 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 359 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 342 ASN D 83 GLN E 94 ASN E 101 ASN E 260 HIS E 331 ASN I 9 GLN M 41 ASN h 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 41 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37828 Z= 0.254 Angle : 0.498 6.629 51098 Z= 0.260 Chirality : 0.041 0.143 5882 Planarity : 0.003 0.038 6629 Dihedral : 5.523 87.759 5255 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.05 % Allowed : 12.05 % Favored : 86.91 % 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: 1.31 (0.12), residues: 4744 helix: 2.06 (0.11), residues: 2344 sheet: 0.35 (0.20), residues: 558 loop : -0.51 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS m 122 PHE 0.016 0.001 PHE F 140 TYR 0.014 0.001 TYR F 182 ARG 0.004 0.000 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 490 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 448 time to evaluate : 4.731 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 142 MET cc_start: 0.8731 (tpp) cc_final: 0.8497 (mmm) REVERT: B 160 ASN cc_start: 0.9063 (m110) cc_final: 0.8456 (m110) REVERT: C 283 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 331 ASN cc_start: 0.8457 (m-40) cc_final: 0.8192 (m-40) REVERT: D 191 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7635 (mtm110) REVERT: D 205 GLU cc_start: 0.8262 (tt0) cc_final: 0.7845 (tt0) REVERT: D 235 PHE cc_start: 0.8494 (m-10) cc_final: 0.7892 (m-80) REVERT: D 297 LYS cc_start: 0.9176 (mttt) cc_final: 0.8930 (tptp) REVERT: E 118 ILE cc_start: 0.8840 (mt) cc_final: 0.8540 (mm) REVERT: F 331 ASN cc_start: 0.8458 (p0) cc_final: 0.8215 (p0) REVERT: J 34 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: K 15 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7659 (ptp-170) REVERT: i 36 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: j 36 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: l 15 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7502 (mtm180) REVERT: l 129 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: m 60 TYR cc_start: 0.8893 (m-80) cc_final: 0.8679 (m-80) REVERT: n 25 LYS cc_start: 0.9230 (mtpp) cc_final: 0.8986 (mtmt) REVERT: n 60 TYR cc_start: 0.9075 (m-80) cc_final: 0.8871 (m-80) outliers start: 42 outliers final: 23 residues processed: 468 average time/residue: 2.6260 time to fit residues: 1543.4539 Evaluate side-chains 462 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 434 time to evaluate : 4.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain i residue 36 GLU Chi-restraints excluded: chain j residue 17 PHE Chi-restraints excluded: chain j residue 25 LYS Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain m residue 32 THR Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 53 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 2.9990 chunk 437 optimal weight: 0.6980 chunk 399 optimal weight: 2.9990 chunk 425 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 334 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 384 optimal weight: 0.4980 chunk 402 optimal weight: 2.9990 chunk 424 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 342 ASN E 94 ASN E 101 ASN E 331 ASN F 260 HIS M 41 ASN h 41 ASN m 9 GLN n 41 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37828 Z= 0.197 Angle : 0.482 6.537 51098 Z= 0.251 Chirality : 0.040 0.141 5882 Planarity : 0.003 0.059 6629 Dihedral : 5.468 82.871 5255 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.90 % Allowed : 12.45 % Favored : 86.66 % 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: 1.39 (0.12), residues: 4744 helix: 2.13 (0.11), residues: 2344 sheet: 0.38 (0.20), residues: 558 loop : -0.47 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS n 122 PHE 0.021 0.001 PHE C 235 TYR 0.012 0.001 TYR E 96 ARG 0.003 0.000 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 479 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 443 time to evaluate : 4.757 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 142 MET cc_start: 0.8741 (tpp) cc_final: 0.8511 (mmm) REVERT: B 160 ASN cc_start: 0.9059 (m110) cc_final: 0.8432 (m110) REVERT: C 283 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 331 ASN cc_start: 0.8437 (m-40) cc_final: 0.8166 (m-40) REVERT: D 72 ASN cc_start: 0.8353 (m-40) cc_final: 0.8096 (m110) REVERT: D 191 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7624 (mtm110) REVERT: D 205 GLU cc_start: 0.8239 (tt0) cc_final: 0.7820 (tt0) REVERT: D 235 PHE cc_start: 0.8501 (m-10) cc_final: 0.7896 (m-80) REVERT: D 297 LYS cc_start: 0.9172 (mttt) cc_final: 0.8935 (tptp) REVERT: E 118 ILE cc_start: 0.8831 (mt) cc_final: 0.8532 (mm) REVERT: F 331 ASN cc_start: 0.8459 (p0) cc_final: 0.8203 (t0) REVERT: J 34 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: K 15 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7667 (ptp-170) REVERT: j 36 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: l 129 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7638 (tp40) REVERT: m 60 TYR cc_start: 0.8884 (m-80) cc_final: 0.8673 (m-80) REVERT: n 25 LYS cc_start: 0.9223 (mtpp) cc_final: 0.8979 (mtmt) REVERT: n 60 TYR cc_start: 0.9063 (m-80) cc_final: 0.8846 (m-80) outliers start: 36 outliers final: 19 residues processed: 463 average time/residue: 2.5317 time to fit residues: 1447.6932 Evaluate side-chains 454 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 431 time to evaluate : 4.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain i residue 16 SER Chi-restraints excluded: chain j residue 17 PHE Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain m residue 32 THR Chi-restraints excluded: chain m residue 98 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 1.9990 chunk 450 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 chunk 472 optimal weight: 1.9990 chunk 434 optimal weight: 0.9980 chunk 376 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 290 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN E 94 ASN E 101 ASN E 331 ASN J 41 ASN M 41 ASN h 41 ASN i 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN n 41 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37828 Z= 0.247 Angle : 0.500 6.591 51098 Z= 0.260 Chirality : 0.041 0.154 5882 Planarity : 0.003 0.054 6629 Dihedral : 5.426 75.707 5255 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.82 % Allowed : 12.55 % Favored : 86.63 % 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: 1.38 (0.12), residues: 4744 helix: 2.12 (0.11), residues: 2347 sheet: 0.40 (0.20), residues: 558 loop : -0.49 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS m 122 PHE 0.014 0.001 PHE L 17 TYR 0.019 0.001 TYR A 182 ARG 0.003 0.000 ARG L 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 469 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 436 time to evaluate : 4.743 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 142 MET cc_start: 0.8758 (tpp) cc_final: 0.8526 (mmm) REVERT: B 160 ASN cc_start: 0.9058 (m110) cc_final: 0.8451 (m110) REVERT: C 191 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.7676 (ptm-80) REVERT: C 283 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7414 (tm-30) REVERT: C 331 ASN cc_start: 0.8457 (m-40) cc_final: 0.8185 (m-40) REVERT: D 72 ASN cc_start: 0.8361 (m-40) cc_final: 0.8128 (m110) REVERT: D 191 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7660 (mtm110) REVERT: D 205 GLU cc_start: 0.8247 (tt0) cc_final: 0.7854 (tt0) REVERT: D 235 PHE cc_start: 0.8504 (m-10) cc_final: 0.7903 (m-80) REVERT: D 297 LYS cc_start: 0.9170 (mttt) cc_final: 0.8939 (tptp) REVERT: E 118 ILE cc_start: 0.8820 (mt) cc_final: 0.8516 (mm) REVERT: F 331 ASN cc_start: 0.8493 (p0) cc_final: 0.8248 (t0) REVERT: J 34 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: K 15 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7648 (ptp-170) REVERT: j 36 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: l 129 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7657 (tp40) REVERT: m 60 TYR cc_start: 0.8897 (m-80) cc_final: 0.8686 (m-80) REVERT: n 25 LYS cc_start: 0.9223 (mtpp) cc_final: 0.8979 (mtmt) outliers start: 33 outliers final: 22 residues processed: 455 average time/residue: 2.5107 time to fit residues: 1411.6375 Evaluate side-chains 459 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 433 time to evaluate : 4.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain i residue 16 SER Chi-restraints excluded: chain j residue 17 PHE Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain m residue 32 THR Chi-restraints excluded: chain m residue 98 MET 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: 0.4980 chunk 115 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 chunk 376 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 386 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN E 94 ASN E 101 ASN E 331 ASN J 41 ASN M 41 ASN h 41 ASN ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN n 41 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.145602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.080869 restraints weight = 152548.967| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.94 r_work: 0.2915 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.230 37828 Z= 0.262 Angle : 0.605 59.189 51098 Z= 0.354 Chirality : 0.041 0.222 5882 Planarity : 0.003 0.053 6629 Dihedral : 5.429 75.668 5255 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.87 % Allowed : 12.52 % Favored : 86.61 % Cbeta Deviations : 0.02 % 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: 1.38 (0.12), residues: 4744 helix: 2.12 (0.11), residues: 2347 sheet: 0.41 (0.20), residues: 558 loop : -0.49 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS m 38 PHE 0.014 0.001 PHE L 17 TYR 0.015 0.001 TYR A 182 ARG 0.003 0.000 ARG l 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26081.78 seconds wall clock time: 441 minutes 16.46 seconds (26476.46 seconds total)