Starting phenix.real_space_refine on Sat Sep 28 22:29:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/09_2024/6vfs_21187_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/09_2024/6vfs_21187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/09_2024/6vfs_21187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/09_2024/6vfs_21187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/09_2024/6vfs_21187_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/09_2024/6vfs_21187_trim.cif" } resolution = 3.3 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= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 154 5.16 5 C 22581 2.51 5 N 6068 2.21 5 O 6848 1.98 5 H 36156 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 71827 Number of models: 1 Model: "" Number of chains: 27 Chain: "E" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5250 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 3 Chain: "A" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4660 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 6 Chain: "F" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4760 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 3 Chain: "C" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5180 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 3 Chain: "B" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5005 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 4 Chain: "D" Number of atoms: 5138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5138 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 13, 'TRANS': 312} Chain breaks: 4 Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 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: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2974 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: "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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} 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: "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} Time building chain proxies: 26.47, per 1000 atoms: 0.37 Number of scatterers: 71827 At special positions: 0 Unit cell: (136.74, 146.28, 180.2, 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 16 15.00 Mg 4 11.99 O 6848 8.00 N 6068 7.00 C 22581 6.00 H 36156 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: 14.53 Conformation dependent library (CDL) restraints added in 4.9 seconds 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8444 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 60 sheets defined 52.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'E' and resid 66 through 76 removed outlier: 3.765A 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: 3.632A 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 169 removed outlier: 4.270A pdb=" N ILE E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 185 through 190 removed outlier: 3.778A pdb=" N SER E 190 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 4.351A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.914A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 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 removed outlier: 3.758A pdb=" N LEU E 325 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 326 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 342 Processing helix chain 'E' and resid 350 through 364 Processing helix chain 'E' and resid 365 through 368 removed outlier: 7.724A pdb=" N ALA E 368 " --> pdb=" O LYS E 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 368' Processing helix chain 'E' and resid 369 through 386 removed outlier: 3.864A pdb=" N SER E 373 " --> pdb=" O ARG E 369 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR E 382 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 404 removed outlier: 3.789A pdb=" N ILE E 402 " --> pdb=" O GLY E 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 124 through 136 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 157 through 158 No H-bonds generated for 'chain 'A' and resid 157 through 158' Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.538A pdb=" N CYS A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.522A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 319 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 384 removed outlier: 4.415A pdb=" N ARG A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N THR A 382 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 3.514A pdb=" N ILE A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 Processing helix chain 'F' and resid 81 through 100 removed outlier: 3.545A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.642A pdb=" N LYS F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 removed outlier: 4.201A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 204 through 216 removed outlier: 4.343A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 243 No H-bonds generated for 'chain 'F' and resid 241 through 243' Processing helix chain 'F' and resid 251 through 258 removed outlier: 3.807A pdb=" N GLU F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 298 Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 317 through 327 Processing helix chain 'F' and resid 331 through 342 Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 366 through 369 removed outlier: 3.821A pdb=" N ARG F 369 " --> pdb=" O THR F 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 366 through 369' Processing helix chain 'F' and resid 370 through 384 removed outlier: 4.653A pdb=" N ASP F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR F 382 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 389 Processing helix chain 'F' and resid 398 through 404 Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.755A pdb=" N ASP C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.526A pdb=" N ARG C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) 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 158 through 169 removed outlier: 4.244A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.784A pdb=" N SER C 190 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 216 removed outlier: 4.154A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 281 through 287 removed outlier: 3.812A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.524A pdb=" N LEU C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 326 " --> pdb=" O ILE C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 342 Processing helix chain 'C' and resid 350 through 363 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: 4.068A pdb=" N ARG C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASP C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N THR C 382 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 removed outlier: 3.846A pdb=" N ILE C 402 " --> pdb=" O GLY C 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 81 through 101 removed outlier: 3.900A pdb=" N LEU B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 removed outlier: 3.712A pdb=" N ARG B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) 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: 4.135A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.741A 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 Processing helix chain 'B' and resid 204 through 216 removed outlier: 4.413A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 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: 3.653A pdb=" N THR B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 365 through 368 removed outlier: 7.729A pdb=" N ALA B 368 " --> pdb=" O LYS B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 369 through 386 removed outlier: 3.598A pdb=" N SER B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASP B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR B 382 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 404 removed outlier: 3.890A pdb=" N ILE B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.782A pdb=" N ASP D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.614A pdb=" N ARG D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) 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 159 through 169 removed outlier: 3.840A 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: 3.510A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 190 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 216 removed outlier: 4.379A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 243 No H-bonds generated for 'chain 'D' and resid 241 through 243' Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 282 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: 3.808A pdb=" N LEU D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 326 " --> pdb=" O ILE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 342 Processing helix chain 'D' and resid 350 through 364 removed outlier: 3.600A 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 386 removed outlier: 4.091A pdb=" N ARG D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N THR D 382 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'L' and resid 24 through 30 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 183 through 190 Processing helix chain 'O' and resid 24 through 30 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 183 through 190 Processing helix chain 'P' and resid 24 through 30 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 183 through 190 Processing helix chain 'Q' and resid 24 through 30 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 183 through 190 Processing helix chain 'R' and resid 24 through 30 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 183 through 190 Processing helix chain 'S' and resid 24 through 30 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 183 through 190 Processing helix chain 'T' and resid 24 through 30 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 183 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 183 through 190 Processing helix chain 'H' and resid 24 through 30 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 183 through 190 Processing helix chain 'I' and resid 24 through 30 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 183 through 190 Processing helix chain 'J' and resid 24 through 30 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 183 through 190 Processing helix chain 'K' and resid 24 through 30 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 183 through 190 Processing helix chain 'M' and resid 24 through 30 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 183 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 183 through 190 Processing sheet with id=AA1, first strand: chain 'E' and resid 140 through 144 Processing sheet with id=AA2, first strand: chain 'E' and resid 219 through 222 Processing sheet with id=AA3, first strand: chain 'E' and resid 346 through 349 removed outlier: 6.223A pdb=" N GLU E 346 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL E 397 " --> pdb=" O GLU E 346 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU E 348 " --> pdb=" O VAL E 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 144 removed outlier: 6.632A pdb=" N VAL A 141 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP A 184 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA A 143 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 181 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY A 248 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 183 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.259A pdb=" N GLU A 346 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 397 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU A 348 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.338A pdb=" N VAL F 141 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP F 184 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA F 143 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL F 181 " --> pdb=" O ILE F 246 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLY F 248 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE F 183 " --> pdb=" O GLY F 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 219 through 222 Processing sheet with id=AA9, first strand: chain 'F' and resid 346 through 349 removed outlier: 6.400A pdb=" N GLU F 346 " --> pdb=" O VAL F 395 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL F 397 " --> pdb=" O GLU F 346 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU F 348 " --> pdb=" O VAL F 397 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 140 through 144 Processing sheet with id=AB2, first strand: chain 'C' and resid 219 through 222 Processing sheet with id=AB3, first strand: chain 'C' and resid 346 through 349 removed outlier: 6.369A pdb=" N GLU C 346 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL C 397 " --> pdb=" O GLU C 346 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU C 348 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.276A pdb=" N VAL B 181 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY B 248 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 183 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB6, first strand: chain 'B' and resid 346 through 349 removed outlier: 6.396A pdb=" N GLU B 346 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 397 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU B 348 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 140 through 144 removed outlier: 6.275A pdb=" N VAL D 181 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY D 248 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE D 183 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 219 through 222 Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 349 removed outlier: 6.422A pdb=" N GLU D 346 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL D 397 " --> pdb=" O GLU D 346 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU D 348 " --> pdb=" O VAL D 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: 5.030A pdb=" N SER L 70 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN L 99 " --> pdb=" O SER L 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 33 through 37 removed outlier: 5.030A pdb=" N SER L 70 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN L 99 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE L 117 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 6.184A 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: 5.029A pdb=" N SER O 70 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN O 99 " --> pdb=" O SER O 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER O 70 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN O 99 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE O 117 " --> pdb=" O VAL O 92 " (cutoff:3.500A) removed outlier: 6.185A 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: 5.029A pdb=" N SER P 70 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN P 99 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER P 70 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN P 99 " --> pdb=" O SER P 70 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE P 117 " --> pdb=" O VAL P 92 " (cutoff:3.500A) removed outlier: 6.186A 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: 5.029A pdb=" N SER Q 70 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN Q 99 " --> pdb=" O SER Q 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER Q 70 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN Q 99 " --> pdb=" O SER Q 70 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE Q 117 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 6.185A 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: 5.029A pdb=" N SER R 70 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN R 99 " --> pdb=" O SER R 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER R 70 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN R 99 " --> pdb=" O SER R 70 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE R 117 " --> pdb=" O VAL R 92 " (cutoff:3.500A) removed outlier: 6.185A 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: 5.029A pdb=" N SER S 70 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN S 99 " --> pdb=" O SER S 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER S 70 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN S 99 " --> pdb=" O SER S 70 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE S 117 " --> pdb=" O VAL S 92 " (cutoff:3.500A) removed outlier: 6.184A 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: 5.029A pdb=" N SER T 70 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN T 99 " --> pdb=" O SER T 70 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER T 70 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN T 99 " --> pdb=" O SER T 70 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE T 117 " --> pdb=" O VAL T 92 " (cutoff:3.500A) removed outlier: 6.185A 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: 5.031A pdb=" N SER U 70 " --> pdb=" O LEU U 97 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN U 99 " --> pdb=" O SER U 70 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 33 through 37 removed outlier: 5.031A pdb=" N SER U 70 " --> pdb=" O LEU U 97 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN U 99 " --> pdb=" O SER U 70 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE U 117 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 6.200A 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: 5.030A pdb=" N SER H 70 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN H 99 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 33 through 37 removed outlier: 5.030A pdb=" N SER H 70 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN H 99 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE H 117 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.204A 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: 5.029A pdb=" N SER I 70 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN I 99 " --> pdb=" O SER I 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER I 70 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN I 99 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE I 117 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.187A 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: 5.029A pdb=" N SER J 70 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN J 99 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER J 70 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN J 99 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE J 117 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 6.197A 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: 3.887A 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: 5.029A pdb=" N SER K 70 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN K 99 " --> pdb=" O SER K 70 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER K 70 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN K 99 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE K 117 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 6.214A 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: 5.028A pdb=" N SER M 70 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN M 99 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.028A pdb=" N SER M 70 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN M 99 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE M 117 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 6.186A 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: 5.029A pdb=" N SER N 70 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN N 99 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.029A pdb=" N SER N 70 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN N 99 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE N 117 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR N 94 " --> pdb=" O PHE N 117 " (cutoff:3.500A) 2056 hydrogen bonds defined for protein. 5889 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: 27.57 Time building geometry restraints manager: 17.71 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: 36110 1.03 - 1.23: 51 1.23 - 1.42: 14293 1.42 - 1.62: 21592 1.62 - 1.81: 262 Bond restraints: 72308 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.73e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.20e+01 ... (remaining 72303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 131225 4.59 - 9.18: 81 9.18 - 13.77: 4 13.77 - 18.36: 2 18.36 - 22.95: 6 Bond angle restraints: 131318 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 116.92 22.95 1.00e+00 1.00e+00 5.27e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 117.82 22.05 1.00e+00 1.00e+00 4.86e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 120.12 19.75 1.00e+00 1.00e+00 3.90e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 117.31 19.52 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.08 18.79 1.00e+00 1.00e+00 3.53e+02 ... (remaining 131313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.70: 32410 26.70 - 53.41: 915 53.41 - 80.11: 219 80.11 - 106.82: 6 106.82 - 133.52: 3 Dihedral angle restraints: 33553 sinusoidal: 18926 harmonic: 14627 Sorted by residual: dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 73.52 -133.52 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 73.19 -133.20 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 -168.87 108.87 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 33550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3820 0.033 - 0.067: 1187 0.067 - 0.100: 393 0.100 - 0.133: 227 0.133 - 0.166: 16 Chirality restraints: 5643 Sorted by residual: chirality pdb=" CA VAL B 138 " pdb=" N VAL B 138 " pdb=" C VAL B 138 " pdb=" CB VAL B 138 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 79 " pdb=" N ILE B 79 " pdb=" C ILE B 79 " pdb=" CB ILE B 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 5640 not shown) Planarity restraints: 10636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 222 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO D 223 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 223 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 224 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 224 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 224 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 386 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 387 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.020 5.00e-02 4.00e+02 ... (remaining 10633 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2944 2.18 - 2.79: 151811 2.79 - 3.39: 208783 3.39 - 4.00: 280580 4.00 - 4.60: 436938 Nonbonded interactions: 1081056 Sorted by model distance: nonbonded pdb=" H GLY F 122 " pdb=" O2B ADP F 501 " model vdw 1.581 2.450 nonbonded pdb=" O VAL F 78 " pdb=" HZ1 LYS F 85 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLN B 225 " pdb=" H GLN B 225 " model vdw 1.681 2.450 nonbonded pdb=" OE1 GLU K 19 " pdb="HH21 ARG M 20 " model vdw 1.691 2.450 nonbonded pdb=" HH TYR F 336 " pdb=" OE1 GLU F 376 " model vdw 1.701 2.450 ... (remaining 1081051 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 101 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 113 through 125 o \ r (resid 126 and (name N or name CA or name C or name O or name CB or name OG1 o \ r name CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG2 \ 3)) or resid 127 through 258 or (resid 288 and (name N or name CA or name C or n \ ame O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or name \ HD12 or name HD13)) or resid 289 through 412)) selection = (chain 'B' and (resid 63 through 148 or (resid 157 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 158 through 190 or (resid 205 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name OE1 or name OE2 or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 22 \ 3 or (resid 237 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name \ HD22)) or resid 238 through 258 or (resid 288 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB o \ r name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or \ name HD12 or name HD13)) or resid 289 through 412)) selection = (chain 'C' and (resid 63 through 101 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 113 through 125 o \ r (resid 126 and (name N or name CA or name C or name O or name CB or name OG1 o \ r name CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG2 \ 3)) or resid 127 through 148 or (resid 157 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 or na \ me HB3)) or resid 158 through 190 or (resid 205 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 223 or (re \ sid 237 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) \ or resid 238 through 258 or (resid 288 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or name H \ G12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD1 \ 2 or name HD13)) or resid 289 through 412)) selection = (chain 'D' and (resid 63 through 101 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 113 through 125 o \ r (resid 126 and (name N or name CA or name C or name O or name CB or name OG1 o \ r name CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG2 \ 3)) or resid 127 through 148 or (resid 157 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 or na \ me HB3)) or resid 158 through 190 or (resid 205 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 223 or (re \ sid 237 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) \ or resid 238 through 258 or (resid 288 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or name H \ G12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD1 \ 2 or name HD13)) or resid 289 through 412)) selection = (chain 'E' and (resid 63 through 101 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 113 through 148 o \ r (resid 157 and (name N or name CA or name C or name O or name CB or name CG or \ name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 158 through \ 190 or (resid 205 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name \ HG2 or name HG3)) or resid 206 through 223 or (resid 237 and (name N or name CA \ or name C or name O or name CB or name CG or name OD1 or name ND2 or name HA or \ name HB2 or name HB3 or name HD21 or name HD22)) or resid 238 through 258 or (r \ esid 288 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 or name HG21 \ or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) or resid 289 \ through 412)) selection = (chain 'F' and (resid 63 through 101 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 113 through 125 o \ r (resid 126 and (name N or name CA or name C or name O or name CB or name OG1 o \ r name CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG2 \ 3)) or resid 127 through 148 or (resid 157 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 or na \ me HB3)) or resid 158 through 190 or (resid 205 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 223 or (re \ sid 237 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) \ or resid 238 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 198)) selection = (chain 'M' and (resid 6 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 58 through 198)) 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA or name HB2 or name HB3)) or resid 58 th \ rough 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.930 Extract box with map and model: 1.940 Check model and map are aligned: 0.400 Set scattering table: 0.490 Process input model: 122.300 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 36152 Z= 0.238 Angle : 0.710 22.953 48740 Z= 0.466 Chirality : 0.041 0.166 5643 Planarity : 0.003 0.045 6289 Dihedral : 11.049 133.523 13804 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.11), residues: 4464 helix: -0.40 (0.09), residues: 2289 sheet: 0.87 (0.18), residues: 667 loop : -0.64 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 95 PHE 0.019 0.002 PHE T 65 TYR 0.015 0.001 TYR F 96 ARG 0.007 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 1424 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1419 time to evaluate : 4.186 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 144 ASP cc_start: 0.8018 (t0) cc_final: 0.7700 (t0) REVERT: A 239 ASP cc_start: 0.6568 (t0) cc_final: 0.5949 (m-30) REVERT: F 203 SER cc_start: 0.7861 (p) cc_final: 0.7498 (m) REVERT: F 342 MET cc_start: 0.5698 (mmm) cc_final: 0.5310 (mmt) REVERT: C 107 ASN cc_start: 0.7727 (m-40) cc_final: 0.7452 (t0) REVERT: B 153 TYR cc_start: 0.8506 (m-80) cc_final: 0.8297 (m-80) REVERT: O 103 MET cc_start: 0.0170 (mmm) cc_final: -0.0516 (mmm) REVERT: P 85 MET cc_start: 0.1985 (mtp) cc_final: 0.1194 (tmm) REVERT: J 125 MET cc_start: 0.6545 (tmm) cc_final: 0.6185 (ttp) REVERT: K 27 ARG cc_start: 0.7076 (tpt90) cc_final: 0.6655 (tpt90) outliers start: 5 outliers final: 3 residues processed: 1419 average time/residue: 1.1745 time to fit residues: 2531.7061 Evaluate side-chains 797 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 794 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain K residue 19 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 3.9990 chunk 343 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 355 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 411 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 GLN C 101 HIS D 160 GLN L 46 ASN O 138 GLN ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 138 GLN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 ASN S 157 ASN U 46 ASN H 46 ASN I 14 GLN I 69 ASN J 46 ASN J 69 ASN J 157 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 ASN M 46 ASN N 69 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 36152 Z= 0.435 Angle : 0.691 8.319 48740 Z= 0.373 Chirality : 0.046 0.314 5643 Planarity : 0.005 0.080 6289 Dihedral : 7.752 120.843 5035 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.82 % Allowed : 10.03 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 4464 helix: 0.64 (0.10), residues: 2343 sheet: 0.12 (0.19), residues: 617 loop : -0.72 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS F 95 PHE 0.022 0.002 PHE N 54 TYR 0.027 0.002 TYR D 93 ARG 0.012 0.001 ARG F 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 918 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 848 time to evaluate : 4.288 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 144 ASP cc_start: 0.8303 (t0) cc_final: 0.7912 (t0) REVERT: E 284 LYS cc_start: 0.8489 (tttt) cc_final: 0.8077 (pttm) REVERT: F 322 ILE cc_start: 0.8432 (mt) cc_final: 0.8144 (mt) REVERT: C 107 ASN cc_start: 0.7804 (m-40) cc_final: 0.7387 (t0) REVERT: B 153 TYR cc_start: 0.8514 (m-80) cc_final: 0.8134 (m-80) REVERT: B 184 ASP cc_start: 0.8515 (t0) cc_final: 0.8282 (t0) REVERT: B 393 LYS cc_start: 0.6875 (mtmm) cc_final: 0.6438 (tttm) REVERT: L 65 PHE cc_start: 0.2654 (OUTLIER) cc_final: 0.0797 (t80) REVERT: P 85 MET cc_start: 0.2229 (mtp) cc_final: 0.1259 (tmm) REVERT: S 125 MET cc_start: 0.3101 (tmm) cc_final: 0.2177 (ttt) outliers start: 70 outliers final: 48 residues processed: 885 average time/residue: 1.1141 time to fit residues: 1535.4357 Evaluate side-chains 743 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 694 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 162 LYS Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain U residue 158 ARG Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 342 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 412 optimal weight: 4.9990 chunk 445 optimal weight: 20.0000 chunk 367 optimal weight: 4.9990 chunk 408 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 330 optimal weight: 20.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS B 209 GLN D 107 ASN L 46 ASN O 46 ASN ** S 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN I 69 ASN J 69 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 36152 Z= 0.357 Angle : 0.616 7.036 48740 Z= 0.329 Chirality : 0.043 0.162 5643 Planarity : 0.004 0.039 6289 Dihedral : 7.466 113.512 5035 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.16 % Allowed : 11.98 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 4464 helix: 1.02 (0.11), residues: 2344 sheet: -0.23 (0.19), residues: 625 loop : -0.92 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 95 PHE 0.028 0.002 PHE M 66 TYR 0.014 0.002 TYR F 182 ARG 0.010 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 796 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 713 time to evaluate : 4.247 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 201 ASP cc_start: 0.8292 (t0) cc_final: 0.8085 (t0) REVERT: E 284 LYS cc_start: 0.8556 (tttt) cc_final: 0.8113 (pttm) REVERT: C 107 ASN cc_start: 0.8003 (m-40) cc_final: 0.7353 (t0) REVERT: C 376 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 153 TYR cc_start: 0.8511 (m-80) cc_final: 0.8138 (m-80) REVERT: B 393 LYS cc_start: 0.7039 (mtmm) cc_final: 0.6643 (tttm) REVERT: L 22 PHE cc_start: 0.4484 (m-80) cc_final: 0.4116 (m-10) REVERT: R 177 ARG cc_start: 0.4805 (mmt90) cc_final: 0.4567 (mtt90) REVERT: U 85 MET cc_start: 0.4407 (mtp) cc_final: 0.3956 (mtp) outliers start: 83 outliers final: 64 residues processed: 757 average time/residue: 1.0778 time to fit residues: 1276.6337 Evaluate side-chains 701 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 637 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 10.0000 chunk 309 optimal weight: 40.0000 chunk 213 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 413 optimal weight: 0.9980 chunk 437 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 391 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 HIS A 77 HIS F 73 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN O 46 ASN ** O 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 ASN ** S 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN I 69 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 ASN ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 36152 Z= 0.512 Angle : 0.691 8.270 48740 Z= 0.373 Chirality : 0.046 0.172 5643 Planarity : 0.005 0.048 6289 Dihedral : 7.731 118.154 5035 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.70 % Allowed : 12.91 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 4464 helix: 0.78 (0.10), residues: 2337 sheet: -0.47 (0.19), residues: 675 loop : -1.44 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.002 HIS C 274 PHE 0.020 0.002 PHE M 66 TYR 0.021 0.002 TYR F 93 ARG 0.009 0.001 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 785 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 681 time to evaluate : 4.303 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: symmetry clash REVERT: E 76 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: E 144 ASP cc_start: 0.8322 (t0) cc_final: 0.8121 (t0) REVERT: E 160 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: E 284 LYS cc_start: 0.8646 (tttt) cc_final: 0.8405 (tttp) REVERT: A 73 ASN cc_start: 0.7521 (m110) cc_final: 0.7320 (m110) REVERT: C 107 ASN cc_start: 0.8109 (m-40) cc_final: 0.7239 (t0) REVERT: C 376 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7531 (mm-30) REVERT: B 153 TYR cc_start: 0.8508 (m-80) cc_final: 0.8131 (m-80) REVERT: B 393 LYS cc_start: 0.7268 (mtmm) cc_final: 0.6895 (tmtt) REVERT: D 160 GLN cc_start: 0.7885 (tt0) cc_final: 0.7630 (tt0) REVERT: L 22 PHE cc_start: 0.4607 (m-80) cc_final: 0.4290 (m-10) REVERT: R 147 ARG cc_start: 0.4996 (mmm160) cc_final: 0.4711 (tpt90) REVERT: S 85 MET cc_start: 0.5124 (ttm) cc_final: 0.4881 (ttm) REVERT: U 85 MET cc_start: 0.5097 (mtp) cc_final: 0.4717 (mtp) REVERT: J 31 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7824 (mm-30) REVERT: K 198 ASN cc_start: 0.4527 (OUTLIER) cc_final: 0.3311 (t0) outliers start: 104 outliers final: 89 residues processed: 737 average time/residue: 1.0673 time to fit residues: 1240.8616 Evaluate side-chains 717 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 625 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 81 ILE Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 46 ASN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Chi-restraints excluded: chain N residue 184 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 0.8980 chunk 248 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 326 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 373 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 ASN P 145 HIS ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 36152 Z= 0.160 Angle : 0.529 6.579 48740 Z= 0.274 Chirality : 0.041 0.190 5643 Planarity : 0.003 0.039 6289 Dihedral : 7.209 114.071 5035 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.71 % Allowed : 14.03 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.12), residues: 4464 helix: 1.41 (0.11), residues: 2342 sheet: -0.36 (0.19), residues: 678 loop : -1.21 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS R 127 PHE 0.015 0.001 PHE K 54 TYR 0.014 0.001 TYR F 96 ARG 0.005 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 731 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 665 time to evaluate : 4.401 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: E 144 ASP cc_start: 0.8147 (t0) cc_final: 0.7918 (t0) REVERT: E 160 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: E 201 ASP cc_start: 0.8394 (t0) cc_final: 0.8105 (t0) REVERT: E 284 LYS cc_start: 0.8359 (tttt) cc_final: 0.7896 (pttp) REVERT: A 208 GLN cc_start: 0.7250 (tm-30) cc_final: 0.7021 (tm-30) REVERT: F 255 GLU cc_start: 0.5847 (tm-30) cc_final: 0.5489 (tm-30) REVERT: C 107 ASN cc_start: 0.7987 (m-40) cc_final: 0.7261 (t0) REVERT: B 153 TYR cc_start: 0.8417 (m-80) cc_final: 0.7901 (m-80) REVERT: B 393 LYS cc_start: 0.6633 (mtmm) cc_final: 0.6427 (tttm) REVERT: D 160 GLN cc_start: 0.7855 (tt0) cc_final: 0.7592 (tt0) REVERT: D 259 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7433 (ttm170) REVERT: L 22 PHE cc_start: 0.4484 (m-80) cc_final: 0.4274 (m-10) REVERT: U 85 MET cc_start: 0.4513 (mtp) cc_final: 0.4164 (mtp) REVERT: J 103 MET cc_start: 0.6228 (mmt) cc_final: 0.5772 (mmt) REVERT: M 56 GLU cc_start: 0.6511 (tt0) cc_final: 0.6221 (tt0) outliers start: 66 outliers final: 47 residues processed: 696 average time/residue: 1.1073 time to fit residues: 1220.6508 Evaluate side-chains 661 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 613 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 46 ASN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 85 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 0.8980 chunk 394 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 438 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 202 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN C 274 HIS D 107 ASN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 GLN ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 36152 Z= 0.341 Angle : 0.586 6.915 48740 Z= 0.310 Chirality : 0.043 0.163 5643 Planarity : 0.004 0.057 6289 Dihedral : 7.383 121.625 5035 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.90 % Allowed : 14.29 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 4464 helix: 1.31 (0.11), residues: 2343 sheet: -0.65 (0.21), residues: 571 loop : -1.34 (0.14), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS L 127 PHE 0.018 0.001 PHE N 54 TYR 0.015 0.002 TYR F 96 ARG 0.010 0.001 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 699 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 626 time to evaluate : 4.305 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: symmetry clash revert: symmetry clash REVERT: E 160 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: E 284 LYS cc_start: 0.8520 (tttt) cc_final: 0.8304 (tttp) REVERT: A 177 GLN cc_start: 0.8117 (pp30) cc_final: 0.7315 (pp30) REVERT: A 208 GLN cc_start: 0.7240 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 260 GLN cc_start: 0.7531 (pm20) cc_final: 0.6699 (pp30) REVERT: C 107 ASN cc_start: 0.8025 (m-40) cc_final: 0.7180 (t0) REVERT: B 153 TYR cc_start: 0.8490 (m-80) cc_final: 0.8051 (m-80) REVERT: B 393 LYS cc_start: 0.7162 (mtmm) cc_final: 0.6918 (tmtt) REVERT: D 160 GLN cc_start: 0.7927 (tt0) cc_final: 0.7647 (tt0) REVERT: D 259 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7513 (ttm170) REVERT: L 22 PHE cc_start: 0.4461 (m-80) cc_final: 0.4174 (m-10) REVERT: O 160 MET cc_start: 0.2724 (mmm) cc_final: 0.1577 (mmm) REVERT: U 85 MET cc_start: 0.5063 (mtp) cc_final: 0.4782 (mtp) REVERT: J 103 MET cc_start: 0.6188 (mmt) cc_final: 0.5888 (mmt) REVERT: M 32 ARG cc_start: 0.4863 (mtp85) cc_final: 0.4066 (mtp85) REVERT: N 46 ASN cc_start: 0.6124 (m110) cc_final: 0.5886 (m-40) outliers start: 73 outliers final: 65 residues processed: 665 average time/residue: 0.9805 time to fit residues: 1026.4864 Evaluate side-chains 666 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 600 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 46 ASN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 320 optimal weight: 8.9990 chunk 247 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 436 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN D 107 ASN ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 ASN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 138 GLN ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 GLN ** 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: 0.5974 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.178 36152 Z= 0.779 Angle : 0.840 10.935 48740 Z= 0.462 Chirality : 0.053 0.309 5643 Planarity : 0.006 0.063 6289 Dihedral : 8.078 120.901 5035 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.99 % Allowed : 14.24 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 4464 helix: 0.18 (0.10), residues: 2341 sheet: -1.44 (0.20), residues: 574 loop : -1.90 (0.14), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS F 95 PHE 0.033 0.003 PHE N 54 TYR 0.035 0.003 TYR F 93 ARG 0.013 0.001 ARG U 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 722 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 607 time to evaluate : 4.360 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: E 76 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: E 160 GLN cc_start: 0.8915 (tp40) cc_final: 0.8431 (mp10) REVERT: E 284 LYS cc_start: 0.8685 (tttt) cc_final: 0.8128 (pttm) REVERT: A 177 GLN cc_start: 0.8195 (pp30) cc_final: 0.7742 (pp30) REVERT: A 208 GLN cc_start: 0.7353 (tm-30) cc_final: 0.7064 (tm-30) REVERT: C 107 ASN cc_start: 0.8115 (m-40) cc_final: 0.7115 (t0) REVERT: B 153 TYR cc_start: 0.8566 (m-80) cc_final: 0.8186 (m-80) REVERT: B 393 LYS cc_start: 0.7475 (mtmm) cc_final: 0.7044 (tmtt) REVERT: B 407 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8054 (pm20) REVERT: D 160 GLN cc_start: 0.7969 (tt0) cc_final: 0.7634 (tt0) REVERT: L 22 PHE cc_start: 0.4564 (m-80) cc_final: 0.4317 (m-10) REVERT: P 79 MET cc_start: 0.4802 (tpp) cc_final: 0.4465 (tpp) REVERT: R 41 THR cc_start: 0.5300 (OUTLIER) cc_final: 0.4919 (p) REVERT: R 97 LEU cc_start: 0.5071 (OUTLIER) cc_final: 0.4360 (mt) REVERT: U 85 MET cc_start: 0.5336 (mtp) cc_final: 0.5079 (mtp) REVERT: J 103 MET cc_start: 0.6445 (mmt) cc_final: 0.6038 (mmt) REVERT: K 27 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7807 (tpt170) REVERT: K 198 ASN cc_start: 0.4914 (OUTLIER) cc_final: 0.3899 (t0) REVERT: M 32 ARG cc_start: 0.5120 (mtp85) cc_final: 0.4585 (mtp85) outliers start: 115 outliers final: 95 residues processed: 671 average time/residue: 0.9994 time to fit residues: 1067.0493 Evaluate side-chains 662 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 563 time to evaluate : 4.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 260 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 277 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 40 optimal weight: 0.0270 chunk 343 optimal weight: 10.0000 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 ASN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 GLN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.7174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36152 Z= 0.167 Angle : 0.558 6.456 48740 Z= 0.290 Chirality : 0.042 0.163 5643 Planarity : 0.004 0.058 6289 Dihedral : 7.293 114.302 5032 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.56 % Allowed : 15.93 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4464 helix: 1.09 (0.11), residues: 2353 sheet: -1.33 (0.22), residues: 468 loop : -1.40 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS F 95 PHE 0.023 0.001 PHE M 117 TYR 0.016 0.001 TYR F 96 ARG 0.010 0.001 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 691 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 631 time to evaluate : 4.292 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: E 160 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: E 284 LYS cc_start: 0.8483 (tttt) cc_final: 0.8056 (pttm) REVERT: A 177 GLN cc_start: 0.8023 (pp30) cc_final: 0.7661 (pp30) REVERT: A 208 GLN cc_start: 0.7404 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 107 ASN cc_start: 0.8001 (m-40) cc_final: 0.7082 (t0) REVERT: B 153 TYR cc_start: 0.8472 (m-80) cc_final: 0.7937 (m-80) REVERT: D 160 GLN cc_start: 0.7942 (tt0) cc_final: 0.7672 (tt0) REVERT: D 259 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7370 (ttm170) REVERT: O 160 MET cc_start: 0.2905 (mmm) cc_final: 0.1702 (mmm) REVERT: P 79 MET cc_start: 0.4339 (tpp) cc_final: 0.4069 (tpp) REVERT: R 97 LEU cc_start: 0.4640 (OUTLIER) cc_final: 0.4295 (mt) REVERT: U 85 MET cc_start: 0.5150 (mtp) cc_final: 0.4944 (mtp) REVERT: J 103 MET cc_start: 0.6156 (mmt) cc_final: 0.5876 (mmt) REVERT: K 79 MET cc_start: 0.5208 (mmp) cc_final: 0.4975 (mmp) REVERT: K 198 ASN cc_start: 0.4101 (OUTLIER) cc_final: 0.2915 (t0) REVERT: M 32 ARG cc_start: 0.4900 (mtp85) cc_final: 0.4094 (mtp85) outliers start: 60 outliers final: 53 residues processed: 666 average time/residue: 0.9783 time to fit residues: 1043.4115 Evaluate side-chains 653 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 597 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 85 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 6.9990 chunk 418 optimal weight: 7.9990 chunk 381 optimal weight: 2.9990 chunk 406 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 319 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 384 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 ASN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 ASN N 14 GLN N 46 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.7284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36152 Z= 0.241 Angle : 0.561 7.498 48740 Z= 0.294 Chirality : 0.042 0.151 5643 Planarity : 0.004 0.048 6289 Dihedral : 7.241 121.581 5032 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.64 % Allowed : 16.11 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4464 helix: 1.29 (0.11), residues: 2347 sheet: -1.36 (0.22), residues: 469 loop : -1.36 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS I 145 PHE 0.031 0.001 PHE M 66 TYR 0.015 0.001 TYR F 96 ARG 0.014 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 668 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 605 time to evaluate : 4.500 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: E 160 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: E 284 LYS cc_start: 0.8485 (tttt) cc_final: 0.8047 (pttm) REVERT: A 177 GLN cc_start: 0.8144 (pp30) cc_final: 0.7780 (pp30) REVERT: C 107 ASN cc_start: 0.7985 (m-40) cc_final: 0.7065 (t0) REVERT: B 69 GLU cc_start: 0.7057 (tp30) cc_final: 0.6616 (tp30) REVERT: B 153 TYR cc_start: 0.8485 (m-80) cc_final: 0.7913 (m-80) REVERT: D 160 GLN cc_start: 0.8002 (tt0) cc_final: 0.7715 (tt0) REVERT: D 191 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7520 (mtm110) REVERT: O 103 MET cc_start: -0.0077 (mmm) cc_final: -0.0292 (mmm) REVERT: O 160 MET cc_start: 0.3054 (mmm) cc_final: 0.1764 (mmm) REVERT: P 79 MET cc_start: 0.4246 (tpp) cc_final: 0.3948 (tpp) REVERT: R 97 LEU cc_start: 0.4818 (OUTLIER) cc_final: 0.4461 (mt) REVERT: U 85 MET cc_start: 0.5168 (mtp) cc_final: 0.4957 (mtp) REVERT: J 103 MET cc_start: 0.6221 (mmt) cc_final: 0.5965 (mmt) REVERT: K 198 ASN cc_start: 0.4539 (OUTLIER) cc_final: 0.3412 (t0) REVERT: M 32 ARG cc_start: 0.5042 (mtp85) cc_final: 0.3952 (mtp85) outliers start: 63 outliers final: 57 residues processed: 640 average time/residue: 0.9544 time to fit residues: 974.1358 Evaluate side-chains 657 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 596 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 9.9990 chunk 430 optimal weight: 9.9990 chunk 262 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 299 optimal weight: 1.9990 chunk 451 optimal weight: 20.0000 chunk 415 optimal weight: 8.9990 chunk 359 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS N 14 GLN ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 36152 Z= 0.381 Angle : 0.664 59.181 48740 Z= 0.372 Chirality : 0.044 0.658 5643 Planarity : 0.004 0.046 6289 Dihedral : 7.247 121.666 5032 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.77 % Allowed : 16.19 % Favored : 82.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.12), residues: 4464 helix: 1.27 (0.11), residues: 2353 sheet: -1.35 (0.22), residues: 469 loop : -1.37 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS I 145 PHE 0.028 0.002 PHE U 180 TYR 0.022 0.002 TYR K 25 ARG 0.009 0.001 ARG B 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 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 SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 662 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 594 time to evaluate : 4.334 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: E 160 GLN cc_start: 0.8595 (tp40) cc_final: 0.8182 (mp10) REVERT: E 284 LYS cc_start: 0.8487 (tttt) cc_final: 0.8049 (pttm) REVERT: A 177 GLN cc_start: 0.8131 (pp30) cc_final: 0.7785 (pp30) REVERT: C 107 ASN cc_start: 0.7953 (m-40) cc_final: 0.7036 (t0) REVERT: B 69 GLU cc_start: 0.7083 (tp30) cc_final: 0.6639 (tp30) REVERT: B 153 TYR cc_start: 0.8494 (m-80) cc_final: 0.7928 (m-80) REVERT: D 160 GLN cc_start: 0.8018 (tt0) cc_final: 0.7731 (tt0) REVERT: D 191 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7534 (mtm110) REVERT: O 103 MET cc_start: -0.0041 (mmm) cc_final: -0.0272 (mmm) REVERT: O 160 MET cc_start: 0.3073 (mmm) cc_final: 0.1789 (mmm) REVERT: P 79 MET cc_start: 0.4230 (tpp) cc_final: 0.3963 (tpp) REVERT: R 97 LEU cc_start: 0.4702 (OUTLIER) cc_final: 0.4409 (mt) REVERT: J 103 MET cc_start: 0.6234 (mmt) cc_final: 0.5988 (mmt) REVERT: K 198 ASN cc_start: 0.4610 (OUTLIER) cc_final: 0.3491 (t0) REVERT: M 32 ARG cc_start: 0.5075 (mtp85) cc_final: 0.4013 (mtp85) outliers start: 68 outliers final: 63 residues processed: 633 average time/residue: 0.9948 time to fit residues: 1010.0111 Evaluate side-chains 658 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 592 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 125 MET Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 20.0000 chunk 382 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 331 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 359 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 369 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 GLN ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.196876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134437 restraints weight = 168929.991| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.99 r_work: 0.3509 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 36152 Z= 0.381 Angle : 0.664 59.181 48740 Z= 0.372 Chirality : 0.044 0.658 5643 Planarity : 0.004 0.046 6289 Dihedral : 7.247 121.666 5032 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.71 % Allowed : 16.19 % Favored : 82.10 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.12), residues: 4464 helix: 1.27 (0.11), residues: 2353 sheet: -1.35 (0.22), residues: 469 loop : -1.37 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS I 145 PHE 0.028 0.002 PHE U 180 TYR 0.022 0.002 TYR K 25 ARG 0.009 0.001 ARG B 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20985.11 seconds wall clock time: 356 minutes 44.66 seconds (21404.66 seconds total)