Starting phenix.real_space_refine (version: dev) on Wed Dec 14 14:38:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/12_2022/6vfs_21187_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/12_2022/6vfs_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_21187/12_2022/6vfs_21187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/12_2022/6vfs_21187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/12_2022/6vfs_21187_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/12_2022/6vfs_21187_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 25.96, per 1000 atoms: 0.36 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 - 3.50 Amino acid : False - 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: 48.34 Conformation dependent library (CDL) restraints added in 4.6 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... running ksdssp... Secondary structure from input PDB file: 203 helices and 58 sheets defined 47.2% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'E' and resid 67 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 82 through 100 Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.632A pdb=" N ARG E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 173 through 178 removed outlier: 3.812A pdb=" N ARG E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 189 Processing helix chain 'E' and resid 205 through 215 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 254 through 262 Processing helix chain 'E' and resid 283 through 288 removed outlier: 3.540A pdb=" N ILE E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.905A pdb=" N ARG E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 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 332 through 342 Processing helix chain 'E' and resid 351 through 364 Processing helix chain 'E' and resid 367 through 378 removed outlier: 3.554A pdb=" N GLU E 376 " --> pdb=" O SER E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 399 through 403 Processing helix chain 'A' and resid 67 through 76 removed outlier: 4.222A pdb=" N ASP A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.021A pdb=" N ARG A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.522A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.761A pdb=" N ARG A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 367 through 386 removed outlier: 3.500A pdb=" N ARG A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 376 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 380 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A 384 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 386 " --> pdb=" O MET A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 82 through 98 Processing helix chain 'F' and resid 125 through 136 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 169 removed outlier: 3.553A pdb=" N THR F 163 " --> pdb=" O GLN F 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 166 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 178 removed outlier: 4.647A pdb=" N ARG F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 205 through 215 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) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.830A pdb=" N LYS F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 297 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.853A pdb=" N ARG F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'F' and resid 332 through 343 removed outlier: 3.991A pdb=" N GLU F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 367 through 378 removed outlier: 4.405A pdb=" N ARG F 372 " --> pdb=" O ARG F 369 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 374 " --> pdb=" O LEU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 383 No H-bonds generated for 'chain 'F' and resid 380 through 383' Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 399 through 403 Processing helix chain 'C' and resid 67 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 82 through 100 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.526A pdb=" N ARG C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.880A pdb=" N ARG C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 205 through 215 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 252 through 262 removed outlier: 3.952A pdb=" N GLU C 255 " --> pdb=" O ALA C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.624A pdb=" N ILE C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.737A pdb=" N ARG C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 326 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 332 through 342 Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.640A pdb=" N ARG C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 3.513A pdb=" N ARG C 377 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU C 380 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 384 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 386 " --> pdb=" O MET C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 403 removed outlier: 3.587A pdb=" N GLU C 403 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 76 removed outlier: 4.009A pdb=" N ASP B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 removed outlier: 3.900A pdb=" N LEU B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.712A pdb=" N ARG B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.533A pdb=" N ILE B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 166 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 removed outlier: 4.047A pdb=" N ARG B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 205 through 215 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 254 through 262 Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 291 through 297 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.797A pdb=" N ARG B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.653A pdb=" N THR B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.595A pdb=" N GLU B 376 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'D' and resid 67 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 82 through 100 Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.614A pdb=" N ARG D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 173 through 178 removed outlier: 3.863A pdb=" N ARG D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 189 removed outlier: 3.510A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 189' Processing helix chain 'D' and resid 205 through 215 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 254 through 262 Processing helix chain 'D' and resid 282 through 288 removed outlier: 3.747A pdb=" N ILE D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 297 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.606A pdb=" N ARG D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.808A pdb=" N LEU D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 342 Processing helix chain 'D' and resid 351 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 367 through 386 removed outlier: 3.507A pdb=" N LEU D 380 " --> pdb=" O ARG D 377 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 386 " --> pdb=" O MET D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 403 removed outlier: 3.940A pdb=" N GLU D 403 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 31 removed outlier: 3.597A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 58 Processing helix chain 'L' and resid 75 through 87 Processing helix chain 'L' and resid 102 through 109 removed outlier: 3.578A pdb=" N LEU L 107 " --> pdb=" O GLY L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 164 Processing helix chain 'L' and resid 168 through 174 Processing helix chain 'L' and resid 183 through 189 Processing helix chain 'O' and resid 24 through 31 removed outlier: 3.597A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 58 Processing helix chain 'O' and resid 75 through 87 Processing helix chain 'O' and resid 102 through 109 removed outlier: 3.579A pdb=" N LEU O 107 " --> pdb=" O GLY O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 164 Processing helix chain 'O' and resid 168 through 174 Processing helix chain 'O' and resid 183 through 189 Processing helix chain 'P' and resid 24 through 31 removed outlier: 3.597A pdb=" N GLU P 31 " --> pdb=" O ARG P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 58 Processing helix chain 'P' and resid 75 through 87 Processing helix chain 'P' and resid 102 through 109 removed outlier: 3.579A pdb=" N LEU P 107 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 164 Processing helix chain 'P' and resid 168 through 174 Processing helix chain 'P' and resid 183 through 189 Processing helix chain 'Q' and resid 24 through 31 removed outlier: 3.596A pdb=" N GLU Q 31 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 58 Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 102 through 109 removed outlier: 3.580A pdb=" N LEU Q 107 " --> pdb=" O GLY Q 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 164 Processing helix chain 'Q' and resid 168 through 174 Processing helix chain 'Q' and resid 183 through 189 Processing helix chain 'R' and resid 24 through 31 removed outlier: 3.596A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 58 Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 102 through 109 removed outlier: 3.579A pdb=" N LEU R 107 " --> pdb=" O GLY R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 164 Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 183 through 189 Processing helix chain 'S' and resid 24 through 31 removed outlier: 3.597A pdb=" N GLU S 31 " --> pdb=" O ARG S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 58 Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 102 through 109 removed outlier: 3.578A pdb=" N LEU S 107 " --> pdb=" O GLY S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 164 Processing helix chain 'S' and resid 168 through 174 Processing helix chain 'S' and resid 183 through 189 Processing helix chain 'T' and resid 24 through 31 removed outlier: 3.596A pdb=" N GLU T 31 " --> pdb=" O ARG T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 58 Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 102 through 109 removed outlier: 3.580A pdb=" N LEU T 107 " --> pdb=" O GLY T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 164 Processing helix chain 'T' and resid 168 through 174 Processing helix chain 'T' and resid 183 through 189 Processing helix chain 'U' and resid 24 through 31 removed outlier: 3.631A pdb=" N GLU U 31 " --> pdb=" O ARG U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 58 Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 102 through 109 removed outlier: 3.580A pdb=" N LEU U 107 " --> pdb=" O GLY U 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 164 Processing helix chain 'U' and resid 168 through 174 Processing helix chain 'U' and resid 183 through 189 Processing helix chain 'H' and resid 24 through 31 removed outlier: 3.621A pdb=" N GLU H 31 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 58 Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 102 through 109 removed outlier: 3.579A pdb=" N LEU H 107 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 164 Processing helix chain 'H' and resid 168 through 174 Processing helix chain 'H' and resid 183 through 189 Processing helix chain 'I' and resid 24 through 31 removed outlier: 3.621A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 58 Processing helix chain 'I' and resid 75 through 87 Processing helix chain 'I' and resid 102 through 109 removed outlier: 3.579A pdb=" N LEU I 107 " --> pdb=" O GLY I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 164 Processing helix chain 'I' and resid 168 through 174 Processing helix chain 'I' and resid 183 through 189 Processing helix chain 'J' and resid 24 through 31 removed outlier: 3.599A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 58 Processing helix chain 'J' and resid 75 through 87 Processing helix chain 'J' and resid 102 through 109 removed outlier: 3.579A pdb=" N LEU J 107 " --> pdb=" O GLY J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 164 Processing helix chain 'J' and resid 168 through 174 Processing helix chain 'J' and resid 183 through 189 Processing helix chain 'K' and resid 24 through 31 removed outlier: 3.601A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 58 Processing helix chain 'K' and resid 75 through 87 Processing helix chain 'K' and resid 102 through 109 removed outlier: 3.579A pdb=" N LEU K 107 " --> pdb=" O GLY K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 164 Processing helix chain 'K' and resid 168 through 174 Processing helix chain 'K' and resid 183 through 189 Processing helix chain 'M' and resid 24 through 31 removed outlier: 3.597A pdb=" N GLU M 31 " --> pdb=" O ARG M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 75 through 87 Processing helix chain 'M' and resid 102 through 109 removed outlier: 3.577A pdb=" N LEU M 107 " --> pdb=" O GLY M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 164 Processing helix chain 'M' and resid 168 through 174 Processing helix chain 'M' and resid 183 through 189 Processing helix chain 'N' and resid 24 through 31 removed outlier: 3.596A pdb=" N GLU N 31 " --> pdb=" O ARG N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 58 Processing helix chain 'N' and resid 75 through 87 Processing helix chain 'N' and resid 102 through 109 removed outlier: 3.579A pdb=" N LEU N 107 " --> pdb=" O GLY N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 164 Processing helix chain 'N' and resid 168 through 174 Processing helix chain 'N' and resid 183 through 189 Processing sheet with id= A, first strand: chain 'E' and resid 309 through 312 Processing sheet with id= B, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= C, first strand: chain 'E' and resid 346 through 349 Processing sheet with id= D, first strand: chain 'A' and resid 309 through 313 Processing sheet with id= E, first strand: chain 'A' and resid 346 through 349 Processing sheet with id= F, first strand: chain 'F' and resid 309 through 312 Processing sheet with id= G, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= H, first strand: chain 'F' and resid 346 through 349 Processing sheet with id= I, first strand: chain 'C' and resid 309 through 313 removed outlier: 3.686A pdb=" N GLY C 119 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= K, first strand: chain 'C' and resid 346 through 349 Processing sheet with id= L, first strand: chain 'B' and resid 309 through 313 removed outlier: 3.643A pdb=" N GLY B 119 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 219 through 221 Processing sheet with id= N, first strand: chain 'B' and resid 346 through 349 Processing sheet with id= O, first strand: chain 'D' and resid 309 through 312 Processing sheet with id= P, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= Q, first strand: chain 'D' and resid 346 through 349 Processing sheet with id= R, first strand: chain 'L' and resid 10 through 13 Processing sheet with id= S, first strand: chain 'L' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE L 65 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU L 36 " --> pdb=" O PHE L 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR L 67 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN L 194 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 99 through 101 removed outlier: 6.708A pdb=" N ARG L 123 " --> pdb=" O ALA L 100 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 10 through 13 Processing sheet with id= V, first strand: chain 'O' and resid 33 through 37 removed outlier: 6.293A pdb=" N PHE O 65 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU O 36 " --> pdb=" O PHE O 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR O 67 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN O 194 " --> pdb=" O ALA O 118 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 99 through 101 removed outlier: 6.708A pdb=" N ARG O 123 " --> pdb=" O ALA O 100 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 10 through 13 Processing sheet with id= Y, first strand: chain 'P' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE P 65 " --> pdb=" O VAL P 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU P 36 " --> pdb=" O PHE P 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR P 67 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN P 194 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 99 through 101 removed outlier: 6.707A pdb=" N ARG P 123 " --> pdb=" O ALA P 100 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 10 through 13 Processing sheet with id= AB, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE Q 65 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU Q 36 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR Q 67 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN Q 194 " --> pdb=" O ALA Q 118 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 99 through 101 removed outlier: 6.708A pdb=" N ARG Q 123 " --> pdb=" O ALA Q 100 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 10 through 13 Processing sheet with id= AE, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE R 65 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU R 36 " --> pdb=" O PHE R 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR R 67 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN R 194 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 99 through 101 removed outlier: 6.708A pdb=" N ARG R 123 " --> pdb=" O ALA R 100 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'S' and resid 10 through 13 Processing sheet with id= AH, first strand: chain 'S' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE S 65 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU S 36 " --> pdb=" O PHE S 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR S 67 " --> pdb=" O LEU S 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN S 194 " --> pdb=" O ALA S 118 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'S' and resid 99 through 101 removed outlier: 6.707A pdb=" N ARG S 123 " --> pdb=" O ALA S 100 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'T' and resid 10 through 13 Processing sheet with id= AK, first strand: chain 'T' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE T 65 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU T 36 " --> pdb=" O PHE T 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR T 67 " --> pdb=" O LEU T 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN T 194 " --> pdb=" O ALA T 118 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'T' and resid 99 through 101 removed outlier: 6.708A pdb=" N ARG T 123 " --> pdb=" O ALA T 100 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'U' and resid 10 through 13 Processing sheet with id= AN, first strand: chain 'U' and resid 33 through 37 removed outlier: 6.296A pdb=" N PHE U 65 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU U 36 " --> pdb=" O PHE U 65 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR U 67 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN U 194 " --> pdb=" O ALA U 118 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'U' and resid 99 through 101 removed outlier: 6.707A pdb=" N ARG U 123 " --> pdb=" O ALA U 100 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 10 through 13 Processing sheet with id= AQ, first strand: chain 'H' and resid 33 through 37 removed outlier: 6.295A pdb=" N PHE H 65 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU H 36 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR H 67 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN H 194 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 99 through 101 removed outlier: 6.707A pdb=" N ARG H 123 " --> pdb=" O ALA H 100 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 10 through 15 removed outlier: 3.801A pdb=" N GLY I 18 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'I' and resid 33 through 37 removed outlier: 6.295A pdb=" N PHE I 65 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU I 36 " --> pdb=" O PHE I 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR I 67 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN I 194 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 99 through 101 removed outlier: 6.708A pdb=" N ARG I 123 " --> pdb=" O ALA I 100 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 10 through 13 Processing sheet with id= AW, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.292A pdb=" N PHE J 65 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU J 36 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR J 67 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN J 194 " --> pdb=" O ALA J 118 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 99 through 101 removed outlier: 6.707A pdb=" N ARG J 123 " --> pdb=" O ALA J 100 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'K' and resid 10 through 14 Processing sheet with id= AZ, first strand: chain 'K' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE K 65 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU K 36 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR K 67 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN K 194 " --> pdb=" O ALA K 118 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 99 through 101 removed outlier: 6.708A pdb=" N ARG K 123 " --> pdb=" O ALA K 100 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'M' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE M 65 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU M 36 " --> pdb=" O PHE M 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR M 67 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN M 194 " --> pdb=" O ALA M 118 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'M' and resid 99 through 101 removed outlier: 6.707A pdb=" N ARG M 123 " --> pdb=" O ALA M 100 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 10 through 13 Processing sheet with id= BE, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.294A pdb=" N PHE N 65 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU N 36 " --> pdb=" O PHE N 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR N 67 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN N 194 " --> pdb=" O ALA N 118 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'N' and resid 99 through 101 removed outlier: 6.708A pdb=" N ARG N 123 " --> pdb=" O ALA N 100 " (cutoff:3.500A) 1647 hydrogen bonds defined for protein. 4245 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: 28.34 Time building geometry restraints manager: 50.71 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: 98.53 - 106.05: 875 106.05 - 113.57: 89285 113.57 - 121.09: 27216 121.09 - 128.61: 13846 128.61 - 136.14: 96 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: 28008 26.70 - 53.41: 341 53.41 - 80.11: 84 80.11 - 106.82: 4 106.82 - 133.52: 3 Dihedral angle restraints: 28440 sinusoidal: 13813 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 28437 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: 3167 2.18 - 2.79: 152004 2.79 - 3.39: 208958 3.39 - 4.00: 280962 4.00 - 4.60: 437379 Nonbonded interactions: 1082470 Sorted by model distance: nonbonded pdb=" H GLY F 122 " pdb=" O2B ADP F 501 " model vdw 1.581 1.850 nonbonded pdb=" O VAL F 78 " pdb=" HZ1 LYS F 85 " model vdw 1.609 1.850 nonbonded pdb=" OE1 GLN B 225 " pdb=" H GLN B 225 " model vdw 1.681 1.850 nonbonded pdb=" OE1 GLU K 19 " pdb="HH21 ARG M 20 " model vdw 1.691 1.850 nonbonded pdb=" HH TYR F 336 " pdb=" OE1 GLU F 376 " model vdw 1.701 1.850 ... (remaining 1082465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 1.490 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: 0.800 Extract box with map and model: 10.630 Check model and map are aligned: 0.810 Convert atoms to be neutral: 0.470 Process input model: 181.420 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5267 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= 0.236 Angle : 0.710 22.953 48740 Z= 0.466 Chirality : 0.041 0.166 5643 Planarity : 0.003 0.045 6289 Dihedral : 10.717 133.523 13680 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.13 % 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 *********************** 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 : 4.707 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 outliers start: 5 outliers final: 3 residues processed: 1419 average time/residue: 1.1090 time to fit residues: 2410.9804 Evaluate side-chains 795 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 792 time to evaluate : 4.489 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.6986 time to fit residues: 9.5017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 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: 4.9990 chunk 215 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS B 77 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN L 46 ASN O 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 46 ASN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 ASN S 157 ASN T 46 ASN U 46 ASN H 46 ASN I 14 GLN I 69 ASN I 198 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.4877 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= 0.515 Angle : 0.747 8.985 48740 Z= 0.402 Chirality : 0.048 0.267 5643 Planarity : 0.006 0.063 6289 Dihedral : 6.500 132.173 4904 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 2.13 % 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: -0.48 (0.12), residues: 4464 helix: 0.11 (0.10), residues: 2268 sheet: -0.02 (0.19), residues: 633 loop : -0.90 (0.14), residues: 1563 *********************** 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 916 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 834 time to evaluate : 5.663 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 outliers start: 82 outliers final: 60 residues processed: 880 average time/residue: 1.0521 time to fit residues: 1444.5081 Evaluate side-chains 727 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 667 time to evaluate : 4.547 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 3 residues processed: 60 average time/residue: 0.7360 time to fit residues: 84.2208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 342 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 412 optimal weight: 9.9990 chunk 445 optimal weight: 8.9990 chunk 367 optimal weight: 0.9990 chunk 408 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN O 46 ASN U 69 ASN H 46 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 36152 Z= 0.250 Angle : 0.561 6.584 48740 Z= 0.294 Chirality : 0.042 0.146 5643 Planarity : 0.004 0.047 6289 Dihedral : 5.813 120.647 4904 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.99 % 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: -0.01 (0.12), residues: 4464 helix: 0.60 (0.11), residues: 2272 sheet: 0.02 (0.19), residues: 667 loop : -0.79 (0.15), residues: 1525 *********************** 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 756 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 718 time to evaluate : 4.593 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 outliers start: 38 outliers final: 24 residues processed: 738 average time/residue: 1.0186 time to fit residues: 1169.2015 Evaluate side-chains 684 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 660 time to evaluate : 4.533 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 2 residues processed: 24 average time/residue: 0.7118 time to fit residues: 35.6097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 9.9990 chunk 309 optimal weight: 40.0000 chunk 213 optimal weight: 30.0000 chunk 45 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 276 optimal weight: 0.4980 chunk 413 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 391 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 260 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN C 81 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 ASN O 46 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 69 ASN H 46 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 36152 Z= 0.412 Angle : 0.630 7.324 48740 Z= 0.335 Chirality : 0.044 0.149 5643 Planarity : 0.004 0.054 6289 Dihedral : 5.928 120.761 4904 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.97 % 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: -0.36 (0.12), residues: 4464 helix: 0.42 (0.11), residues: 2285 sheet: -0.35 (0.19), residues: 654 loop : -1.04 (0.15), residues: 1525 *********************** 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 770 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 694 time to evaluate : 4.554 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 outliers start: 76 outliers final: 57 residues processed: 728 average time/residue: 1.0002 time to fit residues: 1147.6652 Evaluate side-chains 694 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 637 time to evaluate : 4.575 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 2 residues processed: 57 average time/residue: 0.6753 time to fit residues: 76.6333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 326 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 373 optimal weight: 10.0000 chunk 302 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN B 209 GLN O 46 ASN O 128 GLN P 145 HIS ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 198 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.6260 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= 0.164 Angle : 0.516 6.116 48740 Z= 0.265 Chirality : 0.041 0.148 5643 Planarity : 0.003 0.057 6289 Dihedral : 5.462 118.742 4904 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.55 % 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: 0.86 (0.11), residues: 2290 sheet: -0.15 (0.20), residues: 638 loop : -0.87 (0.15), residues: 1536 *********************** 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 730 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 709 time to evaluate : 4.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 715 average time/residue: 0.9683 time to fit residues: 1094.0725 Evaluate side-chains 663 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 652 time to evaluate : 4.615 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.6399 time to fit residues: 18.6562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 1.9990 chunk 394 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 257 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 438 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 202 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 144 optimal weight: 0.0970 chunk 230 optimal weight: 30.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN L 46 ASN O 46 ASN O 128 GLN T 46 ASN ** H 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5723 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 36152 Z= 0.222 Angle : 0.522 6.275 48740 Z= 0.270 Chirality : 0.041 0.146 5643 Planarity : 0.003 0.033 6289 Dihedral : 5.343 125.875 4904 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 4464 helix: 0.97 (0.11), residues: 2291 sheet: -0.29 (0.20), residues: 646 loop : -0.86 (0.15), residues: 1527 *********************** 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 701 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 666 time to evaluate : 4.675 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 outliers start: 35 outliers final: 24 residues processed: 681 average time/residue: 0.9786 time to fit residues: 1049.7770 Evaluate side-chains 668 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 644 time to evaluate : 4.549 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 3 residues processed: 24 average time/residue: 0.6492 time to fit residues: 34.2208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 249 optimal weight: 20.0000 chunk 320 optimal weight: 8.9990 chunk 247 optimal weight: 20.0000 chunk 368 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 436 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 201 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 160 GLN O 46 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 GLN ** I 127 HIS ** 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 51 GLN ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 ASN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.175 36152 Z= 0.765 Angle : 0.827 11.019 48740 Z= 0.453 Chirality : 0.052 0.243 5643 Planarity : 0.006 0.063 6289 Dihedral : 6.344 132.352 4904 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.12), residues: 4464 helix: -0.21 (0.10), residues: 2271 sheet: -1.10 (0.20), residues: 579 loop : -1.73 (0.14), residues: 1614 *********************** 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 712 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 630 time to evaluate : 4.629 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 outliers start: 82 outliers final: 61 residues processed: 668 average time/residue: 0.9769 time to fit residues: 1028.0189 Evaluate side-chains 661 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 600 time to evaluate : 4.585 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 4 residues processed: 61 average time/residue: 0.6408 time to fit residues: 77.5494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 260 optimal weight: 20.0000 chunk 131 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 81 GLN L 46 ASN O 46 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 GLN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 36152 Z= 0.199 Angle : 0.546 6.568 48740 Z= 0.283 Chirality : 0.041 0.160 5643 Planarity : 0.004 0.061 6289 Dihedral : 5.584 127.022 4904 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.57 % 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: -0.46 (0.12), residues: 4464 helix: 0.58 (0.11), residues: 2259 sheet: -0.88 (0.23), residues: 461 loop : -1.25 (0.14), residues: 1744 *********************** 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 664 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 642 time to evaluate : 4.568 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 outliers start: 22 outliers final: 14 residues processed: 650 average time/residue: 0.9716 time to fit residues: 1014.3951 Evaluate side-chains 622 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 608 time to evaluate : 4.537 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 14 average time/residue: 0.6521 time to fit residues: 22.5871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 381 optimal weight: 0.9990 chunk 406 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 319 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 367 optimal weight: 2.9990 chunk 384 optimal weight: 0.6980 chunk 405 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 36152 Z= 0.213 Angle : 0.536 6.359 48740 Z= 0.276 Chirality : 0.041 0.153 5643 Planarity : 0.003 0.063 6289 Dihedral : 5.393 129.941 4904 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.12), residues: 4464 helix: 0.81 (0.11), residues: 2284 sheet: -0.80 (0.23), residues: 463 loop : -1.13 (0.14), residues: 1717 *********************** 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 649 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 628 time to evaluate : 4.565 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 outliers start: 21 outliers final: 13 residues processed: 633 average time/residue: 0.9727 time to fit residues: 976.3981 Evaluate side-chains 625 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 612 time to evaluate : 4.610 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 13 average time/residue: 0.7339 time to fit residues: 22.3497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 8.9990 chunk 430 optimal weight: 9.9990 chunk 262 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 299 optimal weight: 6.9990 chunk 451 optimal weight: 20.0000 chunk 415 optimal weight: 4.9990 chunk 359 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 220 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** I 127 HIS ** 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 ASN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.113 36152 Z= 0.529 Angle : 0.691 8.443 48740 Z= 0.370 Chirality : 0.046 0.184 5643 Planarity : 0.005 0.057 6289 Dihedral : 5.936 135.902 4904 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.79 % Favored : 93.19 % Rotamer Outliers : 0.44 % 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: -0.90 (0.12), residues: 4464 helix: 0.24 (0.11), residues: 2274 sheet: -1.21 (0.23), residues: 481 loop : -1.46 (0.14), residues: 1709 ********************** 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 621 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 604 time to evaluate : 4.601 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 outliers start: 17 outliers final: 11 residues processed: 608 average time/residue: 0.9502 time to fit residues: 920.6219 Evaluate side-chains 607 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 596 time to evaluate : 4.606 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 11 average time/residue: 0.7057 time to fit residues: 19.7376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 9.9990 chunk 382 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 331 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 359 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 369 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** 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 157 ASN ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.198594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.142694 restraints weight = 168367.331| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.89 r_work: 0.3583 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.7484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 36152 Z= 0.198 Angle : 0.547 7.759 48740 Z= 0.281 Chirality : 0.041 0.155 5643 Planarity : 0.004 0.060 6289 Dihedral : 5.471 134.585 4904 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.39 % 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: -0.36 (0.12), residues: 4464 helix: 0.68 (0.11), residues: 2285 sheet: -0.92 (0.23), residues: 460 loop : -1.24 (0.14), residues: 1719 =============================================================================== Job complete usr+sys time: 19386.92 seconds wall clock time: 334 minutes 35.78 seconds (20075.78 seconds total)