Starting phenix.real_space_refine on Sun Sep 29 07:44:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/09_2024/6vfx_21194_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/09_2024/6vfx_21194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/09_2024/6vfx_21194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/09_2024/6vfx_21194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/09_2024/6vfx_21194_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/09_2024/6vfx_21194_trim.cif" } resolution = 2.9 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= 0.120 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 17 5.49 5 Mg 5 5.21 5 S 154 5.16 5 C 23050 2.51 5 N 6213 2.21 5 O 7013 1.98 5 H 36896 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 73348 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 5207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5207 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain breaks: 3 Chain: "B" Number of atoms: 5283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5283 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 14, 'TRANS': 322} Chain breaks: 2 Chain: "E" Number of atoms: 5357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5357 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 2 Chain: "F" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 5038 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 3 Chain: "D" Number of atoms: 5314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5314 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain breaks: 2 Chain: "A" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5311 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 2 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 34 Classifications: {'peptide': 7} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "P" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "Q" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "R" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "S" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "T" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "U" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "H" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2968 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2982 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "K" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3007 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain: "M" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2910 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Chain breaks: 1 Chain: "N" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.82, per 1000 atoms: 0.38 Number of scatterers: 73348 At special positions: 0 Unit cell: (132.5, 146.28, 183.38, 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 154 16.00 P 17 15.00 Mg 5 11.99 O 7013 8.00 N 6213 7.00 C 23050 6.00 H 36896 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: 15.18 Conformation dependent library (CDL) restraints added in 4.8 seconds 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8620 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 60 sheets defined 52.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.751A pdb=" N ASP C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 100 Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 159 through 168 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.692A pdb=" N ILE C 189 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER C 190 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 216 removed outlier: 4.331A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.720A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 287 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 300 through 306 removed outlier: 3.659A pdb=" N ARG C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.793A pdb=" N ASN C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C 326 " --> pdb=" O ILE C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 343 removed outlier: 4.159A pdb=" N GLU C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.544A pdb=" N ALA C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 365 No H-bonds generated for 'chain 'C' and resid 364 through 365' Processing helix chain 'C' and resid 366 through 367 No H-bonds generated for 'chain 'C' and resid 366 through 367' Processing helix chain 'C' and resid 368 through 386 removed outlier: 4.154A pdb=" N ARG C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N THR C 382 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 removed outlier: 3.766A pdb=" N ILE C 402 " --> pdb=" O GLY C 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.807A pdb=" N ASP B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.065A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.694A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 216 removed outlier: 4.476A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.600A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 287 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 317 through 327 removed outlier: 3.675A pdb=" N ILE B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.697A pdb=" N GLU B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 365 No H-bonds generated for 'chain 'B' and resid 364 through 365' Processing helix chain 'B' and resid 366 through 367 No H-bonds generated for 'chain 'B' and resid 366 through 367' Processing helix chain 'B' and resid 368 through 379 removed outlier: 4.156A pdb=" N ARG B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 Processing helix chain 'B' and resid 398 through 404 removed outlier: 3.803A pdb=" N ILE B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 76 removed outlier: 3.832A pdb=" N ASP E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 100 Processing helix chain 'E' and resid 124 through 134 removed outlier: 3.589A pdb=" N ARG E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.214A pdb=" N ILE E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 185 through 190 removed outlier: 3.744A pdb=" N ILE E 189 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 4.289A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.511A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 290 through 298 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 317 through 327 Processing helix chain 'E' and resid 331 through 342 Processing helix chain 'E' and resid 350 through 364 Processing helix chain 'E' and resid 370 through 384 removed outlier: 5.408A pdb=" N ASP E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR E 382 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 404 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.522A pdb=" N VAL F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 99 Processing helix chain 'F' and resid 124 through 136 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 159 through 168 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 185 through 190 removed outlier: 3.996A pdb=" N ILE F 189 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 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: 3.546A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 288 removed outlier: 3.565A pdb=" N ILE F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 284 through 288' Processing helix chain 'F' and resid 290 through 298 Processing helix chain 'F' and resid 300 through 306 removed outlier: 3.516A pdb=" N ARG F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.511A pdb=" N LEU F 325 " --> pdb=" O LEU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 342 Processing helix chain 'F' and resid 350 through 363 Processing helix chain 'F' and resid 364 through 365 No H-bonds generated for 'chain 'F' and resid 364 through 365' Processing helix chain 'F' and resid 366 through 369 Processing helix chain 'F' and resid 370 through 384 removed outlier: 4.267A pdb=" N ASP F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N THR F 382 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 404 removed outlier: 3.761A pdb=" N ILE F 402 " --> pdb=" O GLY F 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 75 Processing helix chain 'D' and resid 81 through 100 Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 158 through 169 removed outlier: 4.170A pdb=" N ILE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.656A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER D 190 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 216 removed outlier: 4.404A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.711A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 287 Processing helix chain 'D' and resid 290 through 298 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.892A pdb=" N LEU D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR D 326 " --> pdb=" O ILE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 343 removed outlier: 3.961A pdb=" N GLU D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 364 removed outlier: 3.543A pdb=" N GLU D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 368 through 379 removed outlier: 4.106A pdb=" N ARG D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 386 Processing helix chain 'D' and resid 398 through 404 removed outlier: 3.586A pdb=" N ILE D 402 " --> pdb=" O GLY D 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 81 through 101 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.616A pdb=" N ASP A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.082A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.992A pdb=" N SER A 190 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 removed outlier: 3.610A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 331 through 342 Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 368 through 379 removed outlier: 4.226A pdb=" N ARG A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 398 through 404 removed outlier: 3.594A pdb=" N ILE A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 31 removed outlier: 3.580A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 59 Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 102 through 110 Processing helix chain 'L' and resid 138 through 165 Processing helix chain 'L' and resid 167 through 175 Processing helix chain 'L' and resid 182 through 190 Processing helix chain 'O' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 59 Processing helix chain 'O' and resid 74 through 88 Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 138 through 165 Processing helix chain 'O' and resid 167 through 175 Processing helix chain 'O' and resid 182 through 190 Processing helix chain 'P' and resid 24 through 31 removed outlier: 3.580A pdb=" N GLU P 31 " --> pdb=" O ARG P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 59 Processing helix chain 'P' and resid 74 through 88 Processing helix chain 'P' and resid 102 through 110 Processing helix chain 'P' and resid 138 through 165 Processing helix chain 'P' and resid 167 through 175 Processing helix chain 'P' and resid 182 through 190 Processing helix chain 'Q' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU Q 31 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 59 Processing helix chain 'Q' and resid 74 through 88 Processing helix chain 'Q' and resid 102 through 110 Processing helix chain 'Q' and resid 138 through 165 Processing helix chain 'Q' and resid 167 through 175 Processing helix chain 'Q' and resid 182 through 190 Processing helix chain 'R' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 59 Processing helix chain 'R' and resid 74 through 88 Processing helix chain 'R' and resid 102 through 110 Processing helix chain 'R' and resid 138 through 165 Processing helix chain 'R' and resid 167 through 175 Processing helix chain 'R' and resid 182 through 190 Processing helix chain 'S' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU S 31 " --> pdb=" O ARG S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 59 Processing helix chain 'S' and resid 74 through 88 Processing helix chain 'S' and resid 102 through 110 Processing helix chain 'S' and resid 138 through 165 Processing helix chain 'S' and resid 167 through 175 Processing helix chain 'S' and resid 182 through 190 Processing helix chain 'T' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU T 31 " --> pdb=" O ARG T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 59 Processing helix chain 'T' and resid 74 through 88 Processing helix chain 'T' and resid 102 through 110 Processing helix chain 'T' and resid 138 through 165 Processing helix chain 'T' and resid 167 through 175 Processing helix chain 'T' and resid 182 through 190 Processing helix chain 'U' and resid 24 through 30 Processing helix chain 'U' and resid 41 through 59 Processing helix chain 'U' and resid 74 through 88 Processing helix chain 'U' and resid 102 through 110 Processing helix chain 'U' and resid 138 through 165 Processing helix chain 'U' and resid 167 through 175 Processing helix chain 'U' and resid 182 through 190 Processing helix chain 'H' and resid 24 through 31 removed outlier: 3.595A pdb=" N GLU H 31 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 59 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 102 through 110 Processing helix chain 'H' and resid 138 through 165 Processing helix chain 'H' and resid 167 through 175 Processing helix chain 'H' and resid 182 through 190 Processing helix chain 'I' and resid 24 through 31 removed outlier: 3.591A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 59 Processing helix chain 'I' and resid 74 through 88 Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 138 through 165 Processing helix chain 'I' and resid 167 through 175 Processing helix chain 'I' and resid 182 through 190 Processing helix chain 'J' and resid 24 through 31 removed outlier: 3.613A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 59 Processing helix chain 'J' and resid 74 through 88 Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 138 through 165 Processing helix chain 'J' and resid 167 through 175 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'K' and resid 24 through 31 removed outlier: 3.581A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 59 Processing helix chain 'K' and resid 74 through 88 Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 138 through 165 Processing helix chain 'K' and resid 167 through 175 Processing helix chain 'K' and resid 182 through 190 Processing helix chain 'M' and resid 24 through 31 removed outlier: 3.581A pdb=" N GLU M 31 " --> pdb=" O ARG M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 59 Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 138 through 165 Processing helix chain 'M' and resid 167 through 175 Processing helix chain 'M' and resid 182 through 190 Processing helix chain 'N' and resid 24 through 30 Processing helix chain 'N' and resid 41 through 59 Processing helix chain 'N' and resid 74 through 88 Processing helix chain 'N' and resid 102 through 110 Processing helix chain 'N' and resid 138 through 165 Processing helix chain 'N' and resid 167 through 175 Processing helix chain 'N' and resid 182 through 190 Processing sheet with id=AA1, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.447A pdb=" N VAL C 181 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY C 248 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 183 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 219 through 222 Processing sheet with id=AA3, first strand: chain 'C' and resid 346 through 349 removed outlier: 6.230A pdb=" N GLU C 346 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL C 397 " --> pdb=" O GLU C 346 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU C 348 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.485A pdb=" N VAL B 181 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLY B 248 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 183 " --> pdb=" O GLY B 248 " (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 346 through 349 removed outlier: 6.369A pdb=" N GLU B 346 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL B 397 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU B 348 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 140 through 144 removed outlier: 6.545A pdb=" N VAL E 181 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY E 248 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE E 183 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 219 through 222 Processing sheet with id=AA9, first strand: chain 'E' and resid 346 through 349 removed outlier: 6.046A pdb=" N GLU E 346 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL E 397 " --> pdb=" O GLU E 346 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU E 348 " --> pdb=" O VAL E 397 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.424A pdb=" N VAL F 141 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASP F 184 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA F 143 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL F 181 " --> pdb=" O ILE F 246 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY F 248 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE F 183 " --> pdb=" O GLY F 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 219 through 222 Processing sheet with id=AB3, first strand: chain 'F' and resid 346 through 349 removed outlier: 6.354A pdb=" N GLU F 346 " --> pdb=" O VAL F 395 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL F 397 " --> pdb=" O GLU F 346 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU F 348 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS F 394 " --> pdb=" O VAL F 411 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 411 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 144 removed outlier: 6.512A pdb=" N VAL D 181 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY D 248 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE D 183 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 219 through 222 Processing sheet with id=AB6, first strand: chain 'D' and resid 346 through 349 removed outlier: 6.296A pdb=" N GLU D 346 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL D 397 " --> pdb=" O GLU D 346 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU D 348 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 140 through 144 Processing sheet with id=AB8, first strand: chain 'A' and resid 219 through 222 Processing sheet with id=AB9, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.109A pdb=" N GLU A 346 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 397 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 348 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC2, first strand: chain 'L' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER L 70 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN L 99 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG L 123 " --> pdb=" O CYS L 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY L 98 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N MET L 125 " --> pdb=" O GLY L 98 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA L 100 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER L 70 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN L 99 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE L 117 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR L 94 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 10 through 13 Processing sheet with id=AC5, first strand: chain 'O' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER O 70 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN O 99 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG O 123 " --> pdb=" O CYS O 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY O 98 " --> pdb=" O ARG O 123 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N MET O 125 " --> pdb=" O GLY O 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA O 100 " --> pdb=" O MET O 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER O 70 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN O 99 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE O 117 " --> pdb=" O VAL O 92 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR O 94 " --> pdb=" O PHE O 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 10 through 13 Processing sheet with id=AC8, first strand: chain 'P' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER P 70 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN P 99 " --> pdb=" O SER P 70 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG P 123 " --> pdb=" O CYS P 96 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY P 98 " --> pdb=" O ARG P 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N MET P 125 " --> pdb=" O GLY P 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA P 100 " --> pdb=" O MET P 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER P 70 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN P 99 " --> pdb=" O SER P 70 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE P 117 " --> pdb=" O VAL P 92 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR P 94 " --> pdb=" O PHE P 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 10 through 13 Processing sheet with id=AD2, first strand: chain 'Q' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER Q 70 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN Q 99 " --> pdb=" O SER Q 70 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG Q 123 " --> pdb=" O CYS Q 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY Q 98 " --> pdb=" O ARG Q 123 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N MET Q 125 " --> pdb=" O GLY Q 98 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA Q 100 " --> pdb=" O MET Q 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER Q 70 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN Q 99 " --> pdb=" O SER Q 70 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE Q 117 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR Q 94 " --> pdb=" O PHE Q 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'R' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER R 70 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN R 99 " --> pdb=" O SER R 70 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG R 123 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY R 98 " --> pdb=" O ARG R 123 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N MET R 125 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA R 100 " --> pdb=" O MET R 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER R 70 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN R 99 " --> pdb=" O SER R 70 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE R 117 " --> pdb=" O VAL R 92 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR R 94 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 10 through 13 Processing sheet with id=AD8, first strand: chain 'S' and resid 33 through 37 removed outlier: 5.095A pdb=" N SER S 70 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN S 99 " --> pdb=" O SER S 70 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG S 123 " --> pdb=" O CYS S 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY S 98 " --> pdb=" O ARG S 123 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N MET S 125 " --> pdb=" O GLY S 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA S 100 " --> pdb=" O MET S 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 33 through 37 removed outlier: 5.095A pdb=" N SER S 70 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN S 99 " --> pdb=" O SER S 70 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE S 117 " --> pdb=" O VAL S 92 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR S 94 " --> pdb=" O PHE S 117 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 10 through 13 Processing sheet with id=AE2, first strand: chain 'T' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER T 70 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN T 99 " --> pdb=" O SER T 70 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG T 123 " --> pdb=" O CYS T 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY T 98 " --> pdb=" O ARG T 123 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N MET T 125 " --> pdb=" O GLY T 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA T 100 " --> pdb=" O MET T 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER T 70 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN T 99 " --> pdb=" O SER T 70 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE T 117 " --> pdb=" O VAL T 92 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR T 94 " --> pdb=" O PHE T 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 10 through 13 Processing sheet with id=AE5, first strand: chain 'U' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER U 70 " --> pdb=" O LEU U 97 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN U 99 " --> pdb=" O SER U 70 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG U 123 " --> pdb=" O CYS U 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY U 98 " --> pdb=" O ARG U 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N MET U 125 " --> pdb=" O GLY U 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA U 100 " --> pdb=" O MET U 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER U 70 " --> pdb=" O LEU U 97 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN U 99 " --> pdb=" O SER U 70 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE U 117 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR U 94 " --> pdb=" O PHE U 117 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE8, first strand: chain 'H' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER H 70 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN H 99 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG H 123 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY H 98 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N MET H 125 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA H 100 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER H 70 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN H 99 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE H 117 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR H 94 " --> pdb=" O PHE H 117 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 14 Processing sheet with id=AF2, first strand: chain 'I' and resid 33 through 37 removed outlier: 5.098A pdb=" N SER I 70 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN I 99 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG I 123 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY I 98 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N MET I 125 " --> pdb=" O GLY I 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA I 100 " --> pdb=" O MET I 125 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 33 through 37 removed outlier: 5.098A pdb=" N SER I 70 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN I 99 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE I 117 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR I 94 " --> pdb=" O PHE I 117 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AF5, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER J 70 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN J 99 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG J 123 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY J 98 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N MET J 125 " --> pdb=" O GLY J 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA J 100 " --> pdb=" O MET J 125 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER J 70 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN J 99 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE J 117 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR J 94 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 10 through 15 removed outlier: 3.609A pdb=" N GLY K 18 " --> pdb=" O SER K 15 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER K 70 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN K 99 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG K 123 " --> pdb=" O CYS K 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY K 98 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N MET K 125 " --> pdb=" O GLY K 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA K 100 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 33 through 37 removed outlier: 5.097A pdb=" N SER K 70 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN K 99 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE K 117 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR K 94 " --> pdb=" O PHE K 117 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AG2, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER M 70 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN M 99 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG M 123 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY M 98 " --> pdb=" O ARG M 123 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N MET M 125 " --> pdb=" O GLY M 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA M 100 " --> pdb=" O MET M 125 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER M 70 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN M 99 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE M 117 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR M 94 " --> pdb=" O PHE M 117 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AG5, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER N 70 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN N 99 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG N 123 " --> pdb=" O CYS N 96 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY N 98 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N MET N 125 " --> pdb=" O GLY N 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA N 100 " --> pdb=" O MET N 125 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.096A pdb=" N SER N 70 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN N 99 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE N 117 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR N 94 " --> pdb=" O PHE N 117 " (cutoff:3.500A) 2026 hydrogen bonds defined for protein. 5850 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: 36.59 Time building geometry restraints manager: 18.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 36850 1.03 - 1.23: 48 1.23 - 1.42: 14638 1.42 - 1.62: 22053 1.62 - 1.81: 262 Bond restraints: 73851 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.04e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.98e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.88e+01 ... (remaining 73846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 133958 3.60 - 7.20: 133 7.20 - 10.79: 16 10.79 - 14.39: 0 14.39 - 17.99: 10 Bond angle restraints: 134117 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.88 17.99 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 122.07 17.80 1.00e+00 1.00e+00 3.17e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 122.10 17.77 1.00e+00 1.00e+00 3.16e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 122.16 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 122.35 17.52 1.00e+00 1.00e+00 3.07e+02 ... (remaining 134112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 31981 16.64 - 33.27: 1448 33.27 - 49.91: 585 49.91 - 66.54: 266 66.54 - 83.18: 30 Dihedral angle restraints: 34310 sinusoidal: 19358 harmonic: 14952 Sorted by residual: dihedral pdb=" CA ASN A 195 " pdb=" C ASN A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta harmonic sigma weight residual 180.00 126.05 53.95 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA ILE A 198 " pdb=" C ILE A 198 " pdb=" N THR A 199 " pdb=" CA THR A 199 " ideal model delta harmonic sigma weight residual 180.00 147.20 32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA ASP A 194 " pdb=" C ASP A 194 " pdb=" N ASN A 195 " pdb=" CA ASN A 195 " ideal model delta harmonic sigma weight residual -180.00 -149.73 -30.27 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 34307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4014 0.033 - 0.066: 1047 0.066 - 0.098: 437 0.098 - 0.131: 242 0.131 - 0.164: 7 Chirality restraints: 5747 Sorted by residual: chirality pdb=" C1' ATP A 501 " pdb=" C2' ATP A 501 " pdb=" N9 ATP A 501 " pdb=" O4' ATP A 501 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" C1' ATP C 501 " pdb=" C2' ATP C 501 " pdb=" N9 ATP C 501 " pdb=" O4' ATP C 501 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" C1' ATP B 501 " pdb=" C2' ATP B 501 " pdb=" N9 ATP B 501 " pdb=" O4' ATP B 501 " both_signs ideal model delta sigma weight residual False 2.41 2.56 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 5744 not shown) Planarity restraints: 10906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 195 " 0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 196 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 59 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO K 60 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO K 60 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO K 60 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 138 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 139 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.019 5.00e-02 4.00e+02 ... (remaining 10903 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 1606 2.10 - 2.72: 131629 2.72 - 3.35: 220764 3.35 - 3.97: 289382 3.97 - 4.60: 456097 Nonbonded interactions: 1099478 Sorted by model distance: nonbonded pdb=" H SER A 197 " pdb=" O UNK G 9 " model vdw 1.472 2.450 nonbonded pdb=" O ALA F 143 " pdb=" H ASP F 184 " model vdw 1.507 2.450 nonbonded pdb=" H PHE C 269 " pdb=" OH TYR I 67 " model vdw 1.567 2.450 nonbonded pdb=" O SER B 197 " pdb=" HZ2 LYS A 192 " model vdw 1.572 2.450 nonbonded pdb=" HZ3 LYS B 393 " pdb=" O PHE B 412 " model vdw 1.580 2.450 ... (remaining 1099473 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 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 225 or \ resid 234 through 274 or (resid 283 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 \ or name HG22 or name HG23)) or resid 284 through 412)) selection = (chain 'B' and (resid 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 274 or \ (resid 283 and (name N or name CA or name C or name O or name CB or name OG1 or \ name CG2 or name HA or name HB or name HG1 or name HG21 or name HG22 or name HG2 \ 3)) or resid 284 through 412)) selection = (chain 'C' and (resid 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 225 or \ resid 234 through 274 or (resid 283 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 \ or name HG22 or name HG23)) or resid 284 through 412)) selection = (chain 'D' and (resid 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 225 or \ resid 234 through 274 or (resid 283 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 \ or name HG22 or name HG23)) or resid 284 through 412)) selection = (chain 'E' and (resid 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 225 or \ (resid 234 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or \ name HG3)) or resid 235 through 274 or (resid 283 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name H \ G1 or name HG21 or name HG22 or name HG23)) or resid 284 through 412)) selection = (chain 'F' and (resid 63 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 225 or resid 234 \ through 412)) } ncs_group { reference = (chain 'H' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'I' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'J' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'K' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'L' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = chain 'M' selection = (chain 'N' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'O' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'P' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'Q' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'R' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'S' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'T' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'U' and (resid 6 through 12 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 21 through 198)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.000 Extract box with map and model: 2.190 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 136.510 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 36955 Z= 0.198 Angle : 0.598 17.989 49835 Z= 0.410 Chirality : 0.040 0.164 5747 Planarity : 0.003 0.091 6450 Dihedral : 10.939 83.175 14135 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 0.10 % Allowed : 0.46 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -1.34 (0.11), residues: 4588 helix: -0.73 (0.09), residues: 2327 sheet: -0.14 (0.20), residues: 610 loop : -1.17 (0.13), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 101 PHE 0.017 0.002 PHE N 65 TYR 0.007 0.001 TYR F 96 ARG 0.004 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 1395 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1391 time to evaluate : 4.379 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7874 (tp40) REVERT: F 216 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7178 (mt-10) REVERT: F 375 VAL cc_start: 0.7446 (t) cc_final: 0.7195 (p) REVERT: D 213 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8350 (tptm) REVERT: A 236 ILE cc_start: 0.7263 (mt) cc_final: 0.7060 (mt) REVERT: P 103 MET cc_start: 0.5007 (mmm) cc_final: 0.4621 (mpp) REVERT: M 144 ILE cc_start: 0.5934 (mt) cc_final: 0.5453 (mt) REVERT: N 127 HIS cc_start: 0.5950 (p90) cc_final: 0.5586 (p90) outliers start: 4 outliers final: 5 residues processed: 1393 average time/residue: 2.7819 time to fit residues: 4677.4034 Evaluate side-chains 726 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 721 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain K residue 165 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 363 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 421 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN B 242 ASN E 73 ASN E 101 HIS D 185 GLN D 260 GLN A 279 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 GLN T 179 ASN U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 179 ASN H 46 ASN H 51 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN K 46 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 36955 Z= 0.473 Angle : 0.684 11.034 49835 Z= 0.367 Chirality : 0.047 0.176 5747 Planarity : 0.006 0.089 6450 Dihedral : 8.162 84.804 5181 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.87 % Allowed : 16.81 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.44 (0.12), residues: 4588 helix: 0.39 (0.10), residues: 2375 sheet: -0.29 (0.20), residues: 620 loop : -1.21 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS P 127 PHE 0.026 0.002 PHE L 180 TYR 0.017 0.002 TYR T 67 ARG 0.011 0.001 ARG D 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 910 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 758 time to evaluate : 4.485 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 407 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: F 175 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7751 (mmtt) REVERT: F 373 SER cc_start: 0.7263 (m) cc_final: 0.6945 (p) REVERT: F 375 VAL cc_start: 0.7562 (t) cc_final: 0.7263 (p) REVERT: D 260 GLN cc_start: 0.7909 (tt0) cc_final: 0.7285 (tm130) REVERT: D 342 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8568 (tpp) REVERT: A 153 TYR cc_start: 0.8279 (m-80) cc_final: 0.7985 (m-80) REVERT: A 156 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: A 165 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7595 (tt) REVERT: A 236 ILE cc_start: 0.7182 (mt) cc_final: 0.6964 (mt) REVERT: A 293 ASP cc_start: 0.8330 (m-30) cc_final: 0.8102 (m-30) REVERT: A 342 MET cc_start: 0.8205 (mtp) cc_final: 0.7909 (mtp) REVERT: L 41 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.5715 (p) REVERT: O 143 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.4908 (tm-30) REVERT: P 141 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6238 (t0) REVERT: Q 81 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.4901 (mp) REVERT: Q 181 MET cc_start: 0.4493 (mtm) cc_final: 0.4285 (mpp) REVERT: S 30 LYS cc_start: 0.5820 (OUTLIER) cc_final: 0.5205 (tppt) REVERT: H 14 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7944 (mm110) REVERT: H 127 HIS cc_start: 0.5299 (OUTLIER) cc_final: 0.4654 (p-80) REVERT: M 7 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7132 (mp) REVERT: M 68 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8011 (tp) outliers start: 152 outliers final: 51 residues processed: 854 average time/residue: 2.6642 time to fit residues: 2770.2408 Evaluate side-chains 667 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 604 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 141 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 145 HIS Chi-restraints excluded: chain T residue 195 ILE Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 173 ARG Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 103 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 422 optimal weight: 9.9990 chunk 456 optimal weight: 9.9990 chunk 375 optimal weight: 2.9990 chunk 418 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 338 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN E 83 GLN F 77 HIS F 323 ASN D 160 GLN A 209 GLN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 198 ASN Q 128 GLN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN H 138 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 121 ASN I 179 ASN K 46 ASN M 46 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 36955 Z= 0.473 Angle : 0.650 9.984 49835 Z= 0.345 Chirality : 0.045 0.167 5747 Planarity : 0.005 0.091 6450 Dihedral : 7.909 85.803 5173 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.23 % Allowed : 19.07 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.25 (0.12), residues: 4588 helix: 0.69 (0.10), residues: 2382 sheet: -0.47 (0.20), residues: 609 loop : -1.26 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS I 127 PHE 0.019 0.002 PHE C 349 TYR 0.017 0.002 TYR F 96 ARG 0.013 0.001 ARG S 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 829 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 663 time to evaluate : 4.450 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7210 (mp-120) REVERT: F 165 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8988 (tp) REVERT: F 175 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7862 (mmtt) REVERT: F 373 SER cc_start: 0.7182 (m) cc_final: 0.6936 (p) REVERT: F 375 VAL cc_start: 0.7633 (t) cc_final: 0.7374 (p) REVERT: F 406 ARG cc_start: 0.6964 (tpp80) cc_final: 0.6547 (ttp-110) REVERT: D 260 GLN cc_start: 0.7871 (tt0) cc_final: 0.7362 (tm-30) REVERT: D 342 MET cc_start: 0.8985 (tpp) cc_final: 0.8736 (tpp) REVERT: A 156 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6860 (mt-10) REVERT: A 165 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7752 (tt) REVERT: A 213 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7653 (tppp) REVERT: A 293 ASP cc_start: 0.8313 (m-30) cc_final: 0.8032 (m-30) REVERT: O 123 ARG cc_start: 0.5662 (mmm-85) cc_final: 0.5334 (mmm160) REVERT: O 143 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5041 (tm-30) REVERT: S 30 LYS cc_start: 0.5910 (OUTLIER) cc_final: 0.5136 (tppt) REVERT: T 79 MET cc_start: 0.3970 (tpp) cc_final: 0.3757 (tpp) REVERT: H 127 HIS cc_start: 0.5209 (OUTLIER) cc_final: 0.4681 (p-80) REVERT: M 62 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: M 68 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8092 (tp) outliers start: 166 outliers final: 71 residues processed: 776 average time/residue: 2.7060 time to fit residues: 2546.4997 Evaluate side-chains 662 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 581 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 176 ASP Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 145 HIS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 150 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 219 optimal weight: 30.0000 chunk 46 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 423 optimal weight: 8.9990 chunk 448 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 401 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN F 323 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 GLN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN H 46 ASN H 51 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN H 138 GLN H 198 ASN I 46 ASN I 121 ASN K 46 ASN ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 36955 Z= 0.491 Angle : 0.656 10.642 49835 Z= 0.347 Chirality : 0.046 0.150 5747 Planarity : 0.005 0.090 6450 Dihedral : 7.957 83.831 5173 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.41 % Allowed : 19.99 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.07 % 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: -0.37 (0.12), residues: 4588 helix: 0.68 (0.10), residues: 2387 sheet: -0.62 (0.20), residues: 629 loop : -1.45 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS E 101 PHE 0.020 0.002 PHE C 349 TYR 0.018 0.002 TYR F 96 ARG 0.011 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 805 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 632 time to evaluate : 4.854 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: symmetry clash REVERT: C 98 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7918 (mtm-85) REVERT: B 406 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7326 (ttm-80) REVERT: E 174 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7052 (tm-30) REVERT: E 364 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7380 (mtt-85) REVERT: F 175 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7772 (mmtt) REVERT: F 344 ASN cc_start: 0.5564 (p0) cc_final: 0.4963 (t0) REVERT: F 373 SER cc_start: 0.7179 (m) cc_final: 0.6922 (p) REVERT: F 375 VAL cc_start: 0.7625 (t) cc_final: 0.7372 (p) REVERT: F 382 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.6904 (p) REVERT: F 406 ARG cc_start: 0.7122 (tpp80) cc_final: 0.6689 (ttp-110) REVERT: F 410 LEU cc_start: 0.7363 (mt) cc_final: 0.7142 (mm) REVERT: D 260 GLN cc_start: 0.7900 (tt0) cc_final: 0.7387 (tm-30) REVERT: A 156 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: A 165 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7700 (tt) REVERT: A 293 ASP cc_start: 0.8278 (m-30) cc_final: 0.8001 (m-30) REVERT: O 143 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5033 (tm-30) REVERT: S 30 LYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5159 (tppt) REVERT: S 41 THR cc_start: 0.6669 (OUTLIER) cc_final: 0.6438 (p) REVERT: T 195 ILE cc_start: 0.5924 (OUTLIER) cc_final: 0.5700 (tp) REVERT: U 14 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7045 (mm-40) REVERT: H 127 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.4700 (p-80) REVERT: M 7 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6998 (mp) REVERT: M 62 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8242 (mttp) REVERT: M 68 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8162 (tp) REVERT: N 194 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6534 (mp10) outliers start: 173 outliers final: 81 residues processed: 758 average time/residue: 2.7008 time to fit residues: 2488.7868 Evaluate side-chains 672 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 576 time to evaluate : 4.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 160 MET Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 153 LYS Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 145 HIS Chi-restraints excluded: chain T residue 195 ILE Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 128 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 141 ASP Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 194 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 333 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 382 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 402 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN L 46 ASN O 14 GLN Q 86 ASN Q 128 GLN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN U 46 ASN H 14 GLN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 128 GLN H 198 ASN I 46 ASN I 121 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 ASN ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 36955 Z= 0.406 Angle : 0.612 9.771 49835 Z= 0.322 Chirality : 0.044 0.146 5747 Planarity : 0.005 0.090 6450 Dihedral : 7.842 82.940 5173 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.95 % Allowed : 20.63 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.23 (0.12), residues: 4588 helix: 0.88 (0.11), residues: 2382 sheet: -0.69 (0.20), residues: 623 loop : -1.46 (0.14), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS E 101 PHE 0.021 0.002 PHE O 180 TYR 0.017 0.002 TYR E 153 ARG 0.011 0.001 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 768 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 613 time to evaluate : 4.492 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7900 (mtm-85) REVERT: B 314 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: E 174 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7050 (tm-30) REVERT: E 364 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7377 (mtt-85) REVERT: F 175 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7794 (mmtt) REVERT: F 344 ASN cc_start: 0.5681 (p0) cc_final: 0.5032 (t0) REVERT: F 375 VAL cc_start: 0.7581 (t) cc_final: 0.7353 (p) REVERT: F 377 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7338 (ttp80) REVERT: F 382 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.7009 (p) REVERT: F 406 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6717 (ttp-110) REVERT: F 410 LEU cc_start: 0.7536 (mt) cc_final: 0.7291 (mm) REVERT: D 260 GLN cc_start: 0.7870 (tt0) cc_final: 0.7389 (tm-30) REVERT: D 343 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: A 156 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: A 165 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7513 (tt) REVERT: A 191 ARG cc_start: 0.6883 (ttm110) cc_final: 0.6676 (ttm-80) REVERT: O 143 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5144 (tm-30) REVERT: Q 81 ILE cc_start: 0.5431 (OUTLIER) cc_final: 0.5063 (mp) REVERT: Q 171 LEU cc_start: 0.6142 (mm) cc_final: 0.5907 (mm) REVERT: H 127 HIS cc_start: 0.5288 (OUTLIER) cc_final: 0.4630 (p-80) REVERT: I 125 MET cc_start: 0.7862 (tmt) cc_final: 0.7450 (tmt) REVERT: M 62 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8213 (mttp) REVERT: N 194 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6531 (mp10) outliers start: 155 outliers final: 78 residues processed: 724 average time/residue: 2.7647 time to fit residues: 2433.8078 Evaluate side-chains 651 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 561 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 153 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 194 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 1.9990 chunk 403 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 263 optimal weight: 30.0000 chunk 110 optimal weight: 0.4980 chunk 448 optimal weight: 9.9990 chunk 372 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 37 optimal weight: 0.0170 chunk 148 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN L 46 ASN Q 128 GLN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 GLN U 14 GLN U 46 ASN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN H 198 ASN I 46 ASN I 51 GLN I 121 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36955 Z= 0.168 Angle : 0.535 7.250 49835 Z= 0.277 Chirality : 0.041 0.143 5747 Planarity : 0.004 0.087 6450 Dihedral : 7.453 85.040 5173 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.52 % Allowed : 21.93 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: 0.38 (0.12), residues: 4588 helix: 1.43 (0.11), residues: 2387 sheet: -0.60 (0.20), residues: 612 loop : -1.18 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 127 PHE 0.018 0.001 PHE N 180 TYR 0.012 0.001 TYR R 82 ARG 0.012 0.000 ARG P 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 756 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 657 time to evaluate : 4.419 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 174 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7046 (tm-30) REVERT: E 256 LYS cc_start: 0.8245 (mtpt) cc_final: 0.8019 (mtmm) REVERT: F 144 ASP cc_start: 0.7808 (t0) cc_final: 0.7099 (t0) REVERT: F 158 VAL cc_start: 0.7814 (p) cc_final: 0.7455 (t) REVERT: F 175 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7791 (mmtt) REVERT: F 344 ASN cc_start: 0.5696 (p0) cc_final: 0.5133 (t0) REVERT: F 375 VAL cc_start: 0.7535 (t) cc_final: 0.7317 (p) REVERT: F 406 ARG cc_start: 0.6928 (tpp80) cc_final: 0.6488 (ttp-110) REVERT: D 260 GLN cc_start: 0.7761 (tt0) cc_final: 0.7230 (tm130) REVERT: A 165 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7599 (tt) REVERT: A 213 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7513 (tppp) REVERT: L 48 VAL cc_start: 0.6531 (OUTLIER) cc_final: 0.6066 (t) REVERT: H 127 HIS cc_start: 0.5049 (OUTLIER) cc_final: 0.4400 (p-80) REVERT: J 42 ASP cc_start: 0.6679 (p0) cc_final: 0.6403 (p0) REVERT: J 160 MET cc_start: 0.6392 (mmm) cc_final: 0.6100 (mmm) REVERT: N 194 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6507 (mp10) outliers start: 99 outliers final: 38 residues processed: 726 average time/residue: 2.8575 time to fit residues: 2560.4272 Evaluate side-chains 637 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 594 time to evaluate : 4.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 194 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 377 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 447 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN F 323 ASN L 46 ASN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 GLN T 128 GLN U 14 GLN U 46 ASN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 121 ASN ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 36955 Z= 0.511 Angle : 0.648 11.228 49835 Z= 0.342 Chirality : 0.046 0.149 5747 Planarity : 0.005 0.089 6450 Dihedral : 7.848 81.509 5173 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.21 % Favored : 94.77 % Rotamer: Outliers : 3.39 % Allowed : 22.31 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.12 (0.12), residues: 4588 helix: 1.02 (0.11), residues: 2384 sheet: -0.69 (0.20), residues: 644 loop : -1.47 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS E 101 PHE 0.022 0.002 PHE L 106 TYR 0.020 0.002 TYR F 96 ARG 0.013 0.001 ARG I 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 728 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 595 time to evaluate : 4.471 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: C 98 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7870 (mtm-85) REVERT: B 314 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: E 174 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7108 (tm-30) REVERT: E 256 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8032 (mtmm) REVERT: E 364 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7420 (mtt-85) REVERT: F 175 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7816 (mmtt) REVERT: F 344 ASN cc_start: 0.5765 (p0) cc_final: 0.5154 (t0) REVERT: F 375 VAL cc_start: 0.7698 (t) cc_final: 0.7447 (p) REVERT: F 376 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6741 (tp30) REVERT: F 377 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7382 (ttp80) REVERT: F 406 ARG cc_start: 0.7079 (tpp80) cc_final: 0.6652 (ttp-110) REVERT: F 410 LEU cc_start: 0.7710 (mt) cc_final: 0.7415 (mm) REVERT: D 260 GLN cc_start: 0.7885 (tt0) cc_final: 0.7367 (tm-30) REVERT: A 156 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: A 165 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 191 ARG cc_start: 0.6860 (ttm110) cc_final: 0.6657 (ttm-80) REVERT: A 264 LYS cc_start: 0.6980 (pmtt) cc_final: 0.6709 (pmtt) REVERT: O 143 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5249 (tm-30) REVERT: R 123 ARG cc_start: 0.4943 (OUTLIER) cc_final: 0.4727 (mpp80) REVERT: U 14 GLN cc_start: 0.7512 (mm-40) cc_final: 0.6926 (mm110) REVERT: H 112 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5763 (mp0) REVERT: H 127 HIS cc_start: 0.5380 (OUTLIER) cc_final: 0.4673 (p-80) REVERT: K 64 ILE cc_start: 0.7626 (mt) cc_final: 0.7409 (mt) REVERT: N 194 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6511 (mp10) outliers start: 133 outliers final: 64 residues processed: 672 average time/residue: 2.7620 time to fit residues: 2260.0272 Evaluate side-chains 637 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 562 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 125 MET Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 194 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 30.0000 chunk 178 optimal weight: 0.1980 chunk 267 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 284 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 351 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN B 260 GLN L 46 ASN ** S 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN I 46 ASN I 121 ASN ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36955 Z= 0.210 Angle : 0.561 7.343 49835 Z= 0.290 Chirality : 0.041 0.143 5747 Planarity : 0.004 0.088 6450 Dihedral : 7.553 85.188 5173 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.81 % Allowed : 24.01 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: 0.35 (0.12), residues: 4588 helix: 1.43 (0.11), residues: 2381 sheet: -0.62 (0.20), residues: 613 loop : -1.23 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS T 127 PHE 0.017 0.001 PHE N 180 TYR 0.011 0.001 TYR F 96 ARG 0.011 0.001 ARG N 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 675 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 604 time to evaluate : 4.562 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: E 174 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7109 (tm-30) REVERT: E 256 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7988 (mtmm) REVERT: F 158 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7434 (t) REVERT: F 175 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7855 (mmtt) REVERT: F 344 ASN cc_start: 0.5754 (p0) cc_final: 0.5249 (t0) REVERT: F 375 VAL cc_start: 0.7594 (t) cc_final: 0.7358 (p) REVERT: F 382 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.7013 (p) REVERT: F 406 ARG cc_start: 0.6883 (tpp80) cc_final: 0.6476 (ttp-110) REVERT: D 259 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8197 (ttm-80) REVERT: D 260 GLN cc_start: 0.7797 (tt0) cc_final: 0.7255 (tm130) REVERT: D 343 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6452 (mp0) REVERT: A 156 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: A 165 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7632 (tt) REVERT: A 191 ARG cc_start: 0.6892 (ttm110) cc_final: 0.6655 (ttm-80) REVERT: A 264 LYS cc_start: 0.6854 (pmtt) cc_final: 0.6609 (pmtt) REVERT: L 48 VAL cc_start: 0.6823 (OUTLIER) cc_final: 0.6391 (t) REVERT: U 173 ARG cc_start: 0.6178 (mtm110) cc_final: 0.5818 (mtm110) REVERT: H 127 HIS cc_start: 0.5155 (OUTLIER) cc_final: 0.4492 (p-80) REVERT: K 64 ILE cc_start: 0.7551 (mt) cc_final: 0.7186 (mt) REVERT: N 194 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.6455 (mp10) outliers start: 71 outliers final: 36 residues processed: 648 average time/residue: 2.8453 time to fit residues: 2250.1677 Evaluate side-chains 610 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 566 time to evaluate : 4.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain Q residue 153 LYS Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 125 MET Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain N residue 194 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 10.0000 chunk 428 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 416 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 376 optimal weight: 0.8980 chunk 394 optimal weight: 0.6980 chunk 415 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 ASN ** S 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 GLN U 14 GLN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 121 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36955 Z= 0.216 Angle : 0.555 7.884 49835 Z= 0.287 Chirality : 0.041 0.141 5747 Planarity : 0.004 0.088 6450 Dihedral : 7.450 86.248 5173 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.73 % Allowed : 24.32 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: 0.55 (0.13), residues: 4588 helix: 1.62 (0.11), residues: 2380 sheet: -0.51 (0.20), residues: 625 loop : -1.19 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS M 127 PHE 0.019 0.001 PHE T 180 TYR 0.013 0.001 TYR F 96 ARG 0.010 0.000 ARG N 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 673 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 605 time to evaluate : 4.515 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: B 160 GLN cc_start: 0.8189 (tp40) cc_final: 0.7981 (tp-100) REVERT: E 174 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7143 (tm-30) REVERT: E 256 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7995 (mtmm) REVERT: F 158 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7401 (t) REVERT: F 175 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7866 (mmtt) REVERT: F 182 TYR cc_start: 0.8178 (t80) cc_final: 0.7782 (t80) REVERT: F 185 GLN cc_start: 0.8663 (mt0) cc_final: 0.8446 (mt0) REVERT: F 344 ASN cc_start: 0.5734 (p0) cc_final: 0.5264 (t0) REVERT: F 375 VAL cc_start: 0.7548 (t) cc_final: 0.7302 (p) REVERT: F 377 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7384 (ttp80) REVERT: F 382 THR cc_start: 0.7226 (OUTLIER) cc_final: 0.6560 (p) REVERT: F 406 ARG cc_start: 0.6923 (tpp80) cc_final: 0.6522 (ttp-110) REVERT: D 260 GLN cc_start: 0.7742 (tt0) cc_final: 0.7205 (tm130) REVERT: D 274 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7264 (p90) REVERT: A 156 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6626 (mt-10) REVERT: A 165 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7683 (tt) REVERT: A 264 LYS cc_start: 0.6865 (pmtt) cc_final: 0.6607 (pmtt) REVERT: L 48 VAL cc_start: 0.7020 (OUTLIER) cc_final: 0.6626 (t) REVERT: R 123 ARG cc_start: 0.4938 (OUTLIER) cc_final: 0.4675 (mpp80) REVERT: S 181 MET cc_start: 0.5860 (mtm) cc_final: 0.5656 (mtm) REVERT: U 173 ARG cc_start: 0.6146 (mtm110) cc_final: 0.5825 (mtm110) REVERT: K 64 ILE cc_start: 0.7581 (mt) cc_final: 0.7273 (mt) outliers start: 68 outliers final: 37 residues processed: 644 average time/residue: 2.6671 time to fit residues: 2092.7122 Evaluate side-chains 612 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 568 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 20.0000 chunk 440 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 306 optimal weight: 1.9990 chunk 462 optimal weight: 20.0000 chunk 425 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS B 260 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 HIS L 46 ASN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN U 14 GLN U 46 ASN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 HIS I 46 ASN I 51 GLN I 121 ASN J 51 GLN K 14 GLN ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.103 36955 Z= 0.701 Angle : 0.753 12.317 49835 Z= 0.399 Chirality : 0.051 0.188 5747 Planarity : 0.006 0.090 6450 Dihedral : 8.071 81.909 5173 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.96 % Allowed : 24.47 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.07 % 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: -0.55 (0.12), residues: 4588 helix: 0.64 (0.10), residues: 2384 sheet: -0.67 (0.20), residues: 642 loop : -1.73 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS E 101 PHE 0.026 0.003 PHE L 106 TYR 0.025 0.002 TYR F 96 ARG 0.014 0.001 ARG O 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 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. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 638 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 561 time to evaluate : 4.522 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: E 174 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7192 (tm-30) REVERT: E 256 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8079 (mtmm) REVERT: F 158 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7612 (t) REVERT: F 175 LYS cc_start: 0.8288 (mmtt) cc_final: 0.7862 (mmtt) REVERT: F 344 ASN cc_start: 0.5813 (p0) cc_final: 0.5254 (t0) REVERT: F 375 VAL cc_start: 0.7708 (t) cc_final: 0.7430 (p) REVERT: F 406 ARG cc_start: 0.7249 (tpp80) cc_final: 0.6792 (ttp-110) REVERT: D 260 GLN cc_start: 0.7920 (tt0) cc_final: 0.7355 (tm-30) REVERT: A 156 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: A 165 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7672 (tt) REVERT: R 123 ARG cc_start: 0.5004 (OUTLIER) cc_final: 0.4697 (mpp80) REVERT: H 127 HIS cc_start: 0.5456 (OUTLIER) cc_final: 0.4801 (p-80) outliers start: 77 outliers final: 44 residues processed: 612 average time/residue: 2.7911 time to fit residues: 2090.9662 Evaluate side-chains 585 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 536 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 125 MET Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 6.9990 chunk 392 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 339 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 368 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 378 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 HIS L 46 ASN R 157 ASN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN I 46 ASN I 121 ASN ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.196789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141754 restraints weight = 137575.731| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.28 r_work: 0.3423 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36955 Z= 0.191 Angle : 0.572 6.857 49835 Z= 0.296 Chirality : 0.041 0.145 5747 Planarity : 0.004 0.098 6450 Dihedral : 7.526 84.044 5173 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.50 % Allowed : 25.21 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: 0.24 (0.12), residues: 4588 helix: 1.37 (0.11), residues: 2382 sheet: -0.53 (0.21), residues: 590 loop : -1.38 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS T 127 PHE 0.019 0.001 PHE L 106 TYR 0.011 0.001 TYR A 96 ARG 0.014 0.001 ARG F 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34038.20 seconds wall clock time: 583 minutes 34.27 seconds (35014.27 seconds total)