Starting phenix.real_space_refine on Wed Apr 10 15:41:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/04_2024/6vfs_21187_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/04_2024/6vfs_21187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/04_2024/6vfs_21187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/04_2024/6vfs_21187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/04_2024/6vfs_21187_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfs_21187/04_2024/6vfs_21187_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 154 5.16 5 C 22581 2.51 5 N 6068 2.21 5 O 6848 1.98 5 H 36156 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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-5288/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: 23.59, per 1000 atoms: 0.33 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: 49.31 Conformation dependent library (CDL) restraints added in 5.7 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: 8.98 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: 28.08 Time building geometry restraints manager: 52.03 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: 32410 26.70 - 53.41: 915 53.41 - 80.11: 219 80.11 - 106.82: 6 106.82 - 133.52: 3 Dihedral angle restraints: 33553 sinusoidal: 18926 harmonic: 14627 Sorted by residual: dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 73.52 -133.52 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 73.19 -133.20 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 -168.87 108.87 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 33550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3820 0.033 - 0.067: 1187 0.067 - 0.100: 393 0.100 - 0.133: 227 0.133 - 0.166: 16 Chirality restraints: 5643 Sorted by residual: chirality pdb=" CA VAL B 138 " pdb=" N VAL B 138 " pdb=" C VAL B 138 " pdb=" CB VAL B 138 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 79 " pdb=" N ILE B 79 " pdb=" C ILE B 79 " pdb=" CB ILE B 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 5640 not shown) Planarity restraints: 10636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 222 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO D 223 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 223 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 224 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 224 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 224 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 386 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 387 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.020 5.00e-02 4.00e+02 ... (remaining 10633 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.840 Extract box with map and model: 9.150 Check model and map are aligned: 0.820 Set scattering table: 0.510 Process input model: 188.490 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 36152 Z= 0.236 Angle : 0.710 22.953 48740 Z= 0.466 Chirality : 0.041 0.166 5643 Planarity : 0.003 0.045 6289 Dihedral : 11.049 133.523 13804 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.11), residues: 4464 helix: -0.40 (0.09), residues: 2289 sheet: 0.87 (0.18), residues: 667 loop : -0.64 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 95 PHE 0.019 0.002 PHE T 65 TYR 0.015 0.001 TYR F 96 ARG 0.007 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 1424 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1419 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 144 ASP cc_start: 0.8018 (t0) cc_final: 0.7700 (t0) REVERT: A 239 ASP cc_start: 0.6568 (t0) cc_final: 0.5949 (m-30) REVERT: F 203 SER cc_start: 0.7861 (p) cc_final: 0.7498 (m) REVERT: F 342 MET cc_start: 0.5698 (mmm) cc_final: 0.5310 (mmt) REVERT: C 107 ASN cc_start: 0.7727 (m-40) cc_final: 0.7452 (t0) REVERT: B 153 TYR cc_start: 0.8506 (m-80) cc_final: 0.8297 (m-80) REVERT: O 103 MET cc_start: 0.0170 (mmm) cc_final: -0.0516 (mmm) REVERT: P 85 MET cc_start: 0.1985 (mtp) cc_final: 0.1194 (tmm) REVERT: J 125 MET cc_start: 0.6545 (tmm) cc_final: 0.6185 (ttp) REVERT: K 27 ARG cc_start: 0.7076 (tpt90) cc_final: 0.6655 (tpt90) outliers start: 5 outliers final: 3 residues processed: 1419 average time/residue: 1.1649 time to fit residues: 2511.3553 Evaluate side-chains 797 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 794 time to evaluate : 4.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain K residue 19 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 3.9990 chunk 343 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 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: 0.6980 chunk 411 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 GLN C 101 HIS ** 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 69 ASN J 46 ASN J 69 ASN J 157 ASN K 46 ASN M 46 ASN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36152 Z= 0.359 Angle : 0.652 6.731 48740 Z= 0.349 Chirality : 0.044 0.198 5643 Planarity : 0.005 0.056 6289 Dihedral : 7.613 128.432 5035 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.92 % Allowed : 9.90 % Favored : 88.18 % 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: -0.04 (0.12), residues: 4464 helix: 0.39 (0.10), residues: 2281 sheet: 0.34 (0.19), residues: 624 loop : -0.63 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 95 PHE 0.018 0.002 PHE N 54 TYR 0.024 0.002 TYR D 93 ARG 0.010 0.001 ARG E 98 *********************** 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 920 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 846 time to evaluate : 4.407 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: E 284 LYS cc_start: 0.8398 (tttt) cc_final: 0.7985 (pttm) REVERT: F 79 ILE cc_start: 0.7650 (mm) cc_final: 0.7036 (tp) REVERT: F 203 SER cc_start: 0.8348 (p) cc_final: 0.8025 (m) REVERT: C 107 ASN cc_start: 0.7774 (m-40) cc_final: 0.7367 (t0) REVERT: B 153 TYR cc_start: 0.8489 (m-80) cc_final: 0.8014 (m-80) REVERT: B 393 LYS cc_start: 0.7153 (mtmm) cc_final: 0.6734 (tttm) REVERT: L 65 PHE cc_start: 0.2360 (OUTLIER) cc_final: 0.0585 (t80) REVERT: P 85 MET cc_start: 0.2164 (mtp) cc_final: 0.1309 (tmm) REVERT: S 125 MET cc_start: 0.3338 (tmm) cc_final: 0.2438 (ttt) outliers start: 74 outliers final: 55 residues processed: 888 average time/residue: 1.1024 time to fit residues: 1523.9190 Evaluate side-chains 753 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 697 time to evaluate : 4.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 176 ASP Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 162 LYS Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 158 ARG Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 30.0000 chunk 127 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 412 optimal weight: 7.9990 chunk 445 optimal weight: 20.0000 chunk 367 optimal weight: 3.9990 chunk 408 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 330 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN F 177 GLN C 274 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 160 GLN L 46 ASN O 46 ASN U 69 ASN H 46 ASN J 69 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 36152 Z= 0.374 Angle : 0.609 6.804 48740 Z= 0.326 Chirality : 0.043 0.148 5643 Planarity : 0.004 0.062 6289 Dihedral : 7.541 121.030 5035 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.34 % Allowed : 12.39 % Favored : 85.27 % 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: 0.59 (0.11), residues: 2270 sheet: -0.03 (0.19), residues: 658 loop : -0.73 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS F 95 PHE 0.019 0.002 PHE D 269 TYR 0.016 0.002 TYR E 96 ARG 0.008 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 799 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 709 time to evaluate : 4.327 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: E 144 ASP cc_start: 0.8311 (t0) cc_final: 0.8030 (t0) REVERT: E 201 ASP cc_start: 0.8344 (t0) cc_final: 0.8034 (t0) REVERT: E 284 LYS cc_start: 0.8552 (tttt) cc_final: 0.8124 (pttm) REVERT: F 203 SER cc_start: 0.8475 (p) cc_final: 0.8200 (m) REVERT: C 107 ASN cc_start: 0.8015 (m-40) cc_final: 0.7324 (t0) REVERT: B 100 ARG cc_start: 0.6510 (tpp80) cc_final: 0.6167 (ttp80) REVERT: B 153 TYR cc_start: 0.8493 (m-80) cc_final: 0.8196 (m-80) REVERT: B 184 ASP cc_start: 0.8589 (t0) cc_final: 0.8288 (t0) REVERT: B 393 LYS cc_start: 0.7523 (mtmm) cc_final: 0.7170 (tttm) REVERT: B 403 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: D 160 GLN cc_start: 0.8232 (tt0) cc_final: 0.7983 (tt0) REVERT: R 147 ARG cc_start: 0.5302 (mmm160) cc_final: 0.5035 (tpt170) outliers start: 90 outliers final: 71 residues processed: 756 average time/residue: 1.0532 time to fit residues: 1246.0094 Evaluate side-chains 724 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 652 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 9.9990 chunk 309 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 196 optimal weight: 30.0000 chunk 276 optimal weight: 8.9990 chunk 413 optimal weight: 20.0000 chunk 437 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 391 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 114 ASN A 177 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN C 81 GLN C 274 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** J 198 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 36152 Z= 0.555 Angle : 0.703 8.470 48740 Z= 0.381 Chirality : 0.046 0.168 5643 Planarity : 0.005 0.062 6289 Dihedral : 7.834 121.809 5035 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.22 % Allowed : 13.12 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4464 helix: 0.21 (0.11), residues: 2247 sheet: -0.62 (0.19), residues: 665 loop : -1.17 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS F 95 PHE 0.021 0.002 PHE B 349 TYR 0.022 0.002 TYR F 93 ARG 0.009 0.001 ARG F 98 *********************** 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 802 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 678 time to evaluate : 4.337 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: E 76 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: E 284 LYS cc_start: 0.8657 (tttt) cc_final: 0.8136 (pttp) REVERT: A 208 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6883 (tm-30) REVERT: A 247 CYS cc_start: 0.8139 (m) cc_final: 0.7699 (p) REVERT: F 203 SER cc_start: 0.8482 (p) cc_final: 0.8241 (m) REVERT: F 362 MET cc_start: 0.8365 (tpp) cc_final: 0.8058 (tpp) REVERT: C 107 ASN cc_start: 0.8130 (m-40) cc_final: 0.7232 (t0) REVERT: B 100 ARG cc_start: 0.6675 (tpp80) cc_final: 0.6227 (ttp80) REVERT: B 153 TYR cc_start: 0.8506 (m-80) cc_final: 0.8115 (m-80) REVERT: B 257 VAL cc_start: 0.9337 (t) cc_final: 0.9113 (t) REVERT: B 393 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7345 (tttm) REVERT: K 198 ASN cc_start: 0.4993 (OUTLIER) cc_final: 0.3687 (t0) outliers start: 124 outliers final: 96 residues processed: 746 average time/residue: 1.0259 time to fit residues: 1216.3857 Evaluate side-chains 733 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 635 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 46 ASN Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Chi-restraints excluded: chain N residue 184 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 326 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 373 optimal weight: 6.9990 chunk 302 optimal weight: 8.9990 chunk 0 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 393 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** B 209 GLN D 107 ASN O 46 ASN P 145 HIS ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 69 ASN ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 145 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 36152 Z= 0.161 Angle : 0.520 6.244 48740 Z= 0.269 Chirality : 0.041 0.154 5643 Planarity : 0.004 0.052 6289 Dihedral : 7.137 116.677 5032 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.87 % Allowed : 14.71 % Favored : 83.42 % 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: 0.02 (0.12), residues: 4464 helix: 0.81 (0.11), residues: 2265 sheet: -0.33 (0.20), residues: 631 loop : -0.90 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 95 PHE 0.022 0.001 PHE M 117 TYR 0.014 0.001 TYR F 96 ARG 0.005 0.000 ARG I 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 766 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 694 time to evaluate : 4.390 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: E 284 LYS cc_start: 0.8483 (tttt) cc_final: 0.8034 (pttp) REVERT: F 203 SER cc_start: 0.8483 (p) cc_final: 0.8183 (m) REVERT: F 362 MET cc_start: 0.8192 (tpp) cc_final: 0.7973 (tpp) REVERT: C 107 ASN cc_start: 0.8011 (m-40) cc_final: 0.7187 (t0) REVERT: B 100 ARG cc_start: 0.6429 (tpp80) cc_final: 0.6032 (ttp80) REVERT: B 153 TYR cc_start: 0.8442 (m-80) cc_final: 0.7916 (m-80) REVERT: B 184 ASP cc_start: 0.8464 (t0) cc_final: 0.8122 (t0) REVERT: B 393 LYS cc_start: 0.7493 (mtmm) cc_final: 0.7215 (tttm) REVERT: S 191 LEU cc_start: 0.4677 (OUTLIER) cc_final: 0.4339 (mp) REVERT: U 141 ASP cc_start: 0.3477 (m-30) cc_final: 0.3246 (m-30) REVERT: M 32 ARG cc_start: 0.5023 (mtp85) cc_final: 0.3909 (mtp85) outliers start: 72 outliers final: 55 residues processed: 730 average time/residue: 1.0060 time to fit residues: 1147.7225 Evaluate side-chains 694 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 638 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain P residue 81 ILE Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 2.9990 chunk 394 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 438 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 chunk 202 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** D 130 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** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 145 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36152 Z= 0.255 Angle : 0.535 6.134 48740 Z= 0.280 Chirality : 0.041 0.147 5643 Planarity : 0.004 0.046 6289 Dihedral : 7.177 123.320 5032 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.18 % Allowed : 14.89 % Favored : 82.93 % 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: 0.04 (0.12), residues: 4464 helix: 0.88 (0.11), residues: 2262 sheet: -0.48 (0.20), residues: 631 loop : -0.90 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 95 PHE 0.017 0.001 PHE M 117 TYR 0.014 0.001 TYR F 96 ARG 0.007 0.000 ARG I 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 748 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 664 time to evaluate : 4.389 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: E 284 LYS cc_start: 0.8495 (tttt) cc_final: 0.8031 (pttp) REVERT: F 362 MET cc_start: 0.8278 (tpp) cc_final: 0.8007 (tpp) REVERT: C 107 ASN cc_start: 0.8002 (m-40) cc_final: 0.7184 (t0) REVERT: B 100 ARG cc_start: 0.6540 (tpp80) cc_final: 0.6062 (ttp80) REVERT: B 153 TYR cc_start: 0.8439 (m-80) cc_final: 0.7913 (m-80) REVERT: B 184 ASP cc_start: 0.8482 (t0) cc_final: 0.8161 (t0) REVERT: B 255 GLU cc_start: 0.8044 (pt0) cc_final: 0.7820 (pt0) REVERT: B 393 LYS cc_start: 0.7494 (mtmm) cc_final: 0.7226 (tttm) REVERT: B 403 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: M 32 ARG cc_start: 0.5068 (mtp85) cc_final: 0.4147 (mtp85) REVERT: N 55 LEU cc_start: 0.6618 (mt) cc_final: 0.6397 (mt) REVERT: N 95 LEU cc_start: 0.5665 (tp) cc_final: 0.5328 (tp) outliers start: 84 outliers final: 68 residues processed: 713 average time/residue: 1.0161 time to fit residues: 1135.0744 Evaluate side-chains 709 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 640 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 180 PHE Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 320 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 436 optimal weight: 0.8980 chunk 273 optimal weight: 30.0000 chunk 266 optimal weight: 20.0000 chunk 201 optimal weight: 30.0000 overall best weight: 7.3790 ------------------------------------------------------------------------------- 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 160 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 160 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** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.141 36152 Z= 0.686 Angle : 0.783 10.468 48740 Z= 0.427 Chirality : 0.050 0.271 5643 Planarity : 0.006 0.060 6289 Dihedral : 7.908 128.736 5032 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.77 % Favored : 93.21 % Rotamer: Outliers : 3.27 % Allowed : 14.73 % Favored : 82.00 % 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: -1.23 (0.12), residues: 4464 helix: -0.09 (0.11), residues: 2257 sheet: -1.38 (0.22), residues: 474 loop : -1.50 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS I 145 PHE 0.025 0.002 PHE N 65 TYR 0.028 0.003 TYR F 93 ARG 0.009 0.001 ARG I 147 *********************** 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 751 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 625 time to evaluate : 4.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: E 284 LYS cc_start: 0.8699 (tttt) cc_final: 0.7972 (pttp) REVERT: A 73 ASN cc_start: 0.7627 (m110) cc_final: 0.7352 (m110) REVERT: C 81 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7516 (mp-120) REVERT: C 107 ASN cc_start: 0.8071 (m-40) cc_final: 0.7110 (t0) REVERT: C 314 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 100 ARG cc_start: 0.6549 (tpp80) cc_final: 0.6042 (ttp80) REVERT: B 153 TYR cc_start: 0.8556 (m-80) cc_final: 0.8165 (m-80) REVERT: B 393 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7406 (tttm) REVERT: B 403 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: B 407 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7729 (mt-10) REVERT: R 41 THR cc_start: 0.5598 (OUTLIER) cc_final: 0.5253 (p) REVERT: K 27 ARG cc_start: 0.8229 (tpt90) cc_final: 0.7684 (tpt170) REVERT: K 198 ASN cc_start: 0.4903 (OUTLIER) cc_final: 0.3935 (t0) outliers start: 126 outliers final: 104 residues processed: 698 average time/residue: 1.0001 time to fit residues: 1087.5633 Evaluate side-chains 708 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 598 time to evaluate : 4.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain O residue 180 PHE Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Chi-restraints excluded: chain N residue 188 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 277 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN 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** H 46 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 36152 Z= 0.314 Angle : 0.582 6.470 48740 Z= 0.307 Chirality : 0.042 0.165 5643 Planarity : 0.004 0.062 6289 Dihedral : 7.490 129.329 5032 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.55 % Allowed : 15.46 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.12), residues: 4464 helix: 0.34 (0.11), residues: 2256 sheet: -1.20 (0.23), residues: 462 loop : -1.35 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS F 95 PHE 0.024 0.002 PHE O 66 TYR 0.014 0.002 TYR L 82 ARG 0.010 0.000 ARG I 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 728 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 630 time to evaluate : 5.024 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: E 284 LYS cc_start: 0.8622 (tttt) cc_final: 0.8124 (pttp) REVERT: E 314 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: A 73 ASN cc_start: 0.7606 (m110) cc_final: 0.7328 (m110) REVERT: F 362 MET cc_start: 0.8262 (tpp) cc_final: 0.8000 (tpp) REVERT: C 107 ASN cc_start: 0.8037 (m-40) cc_final: 0.7116 (t0) REVERT: B 100 ARG cc_start: 0.6499 (tpp80) cc_final: 0.6064 (ttp80) REVERT: B 153 TYR cc_start: 0.8508 (m-80) cc_final: 0.8027 (m-80) REVERT: B 212 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8499 (mm) REVERT: B 393 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7369 (tttm) REVERT: B 403 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: J 130 LEU cc_start: 0.5820 (mt) cc_final: 0.5444 (pp) REVERT: K 198 ASN cc_start: 0.4434 (OUTLIER) cc_final: 0.3392 (t0) REVERT: M 32 ARG cc_start: 0.5272 (mtp85) cc_final: 0.4223 (mtp85) outliers start: 98 outliers final: 84 residues processed: 682 average time/residue: 0.9997 time to fit residues: 1087.8943 Evaluate side-chains 695 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 607 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain O residue 180 PHE Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 4.9990 chunk 418 optimal weight: 6.9990 chunk 381 optimal weight: 9.9990 chunk 406 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 319 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 367 optimal weight: 1.9990 chunk 384 optimal weight: 5.9990 chunk 405 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 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** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN ** 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: 0.5841 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 36152 Z= 0.228 Angle : 0.543 6.395 48740 Z= 0.283 Chirality : 0.041 0.158 5643 Planarity : 0.004 0.054 6289 Dihedral : 7.196 129.190 5032 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.03 % Allowed : 16.19 % Favored : 81.79 % 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: -0.38 (0.12), residues: 4464 helix: 0.70 (0.11), residues: 2250 sheet: -1.11 (0.23), residues: 466 loop : -1.18 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS I 145 PHE 0.025 0.001 PHE P 180 TYR 0.014 0.001 TYR A 336 ARG 0.008 0.000 ARG I 147 *********************** 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 704 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 626 time to evaluate : 4.404 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: E 284 LYS cc_start: 0.8577 (tttt) cc_final: 0.8119 (pttm) REVERT: F 255 GLU cc_start: 0.6246 (tm-30) cc_final: 0.5916 (tm-30) REVERT: F 362 MET cc_start: 0.8209 (tpp) cc_final: 0.7993 (tpp) REVERT: C 81 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7270 (mp-120) REVERT: C 107 ASN cc_start: 0.7961 (m-40) cc_final: 0.7070 (t0) REVERT: B 100 ARG cc_start: 0.6358 (tpp80) cc_final: 0.5819 (ttp80) REVERT: B 153 TYR cc_start: 0.8505 (m-80) cc_final: 0.7922 (m-80) REVERT: B 212 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8493 (mm) REVERT: B 393 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7361 (tttm) REVERT: B 403 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: Q 79 MET cc_start: 0.1904 (mmm) cc_final: 0.1459 (mmm) REVERT: S 40 VAL cc_start: 0.6303 (t) cc_final: 0.6013 (t) REVERT: J 130 LEU cc_start: 0.5725 (mt) cc_final: 0.5490 (pp) REVERT: M 32 ARG cc_start: 0.5261 (mtp85) cc_final: 0.4239 (mtp85) REVERT: N 95 LEU cc_start: 0.5468 (tp) cc_final: 0.5248 (tp) outliers start: 78 outliers final: 70 residues processed: 671 average time/residue: 0.9522 time to fit residues: 1014.0841 Evaluate side-chains 685 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 612 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 180 PHE Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 8.9990 chunk 430 optimal weight: 9.9990 chunk 262 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 299 optimal weight: 20.0000 chunk 451 optimal weight: 20.0000 chunk 415 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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** ** F 95 HIS ** 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** R 138 GLN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 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 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5985 moved from start: 0.7602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.149 36152 Z= 0.664 Angle : 0.777 9.685 48740 Z= 0.422 Chirality : 0.050 0.274 5643 Planarity : 0.006 0.060 6289 Dihedral : 8.013 136.962 5032 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.06 % Favored : 91.89 % Rotamer: Outliers : 2.52 % Allowed : 16.00 % Favored : 81.48 % 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: -1.37 (0.12), residues: 4464 helix: -0.13 (0.11), residues: 2255 sheet: -1.61 (0.22), residues: 467 loop : -1.62 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS I 145 PHE 0.027 0.002 PHE N 65 TYR 0.028 0.003 TYR F 93 ARG 0.009 0.001 ARG F 98 ********************** 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 698 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 601 time to evaluate : 4.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 284 LYS cc_start: 0.8715 (tttt) cc_final: 0.8014 (pttp) REVERT: E 314 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: C 81 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7442 (mp-120) REVERT: B 100 ARG cc_start: 0.6550 (tpp80) cc_final: 0.5932 (ttp80) REVERT: B 153 TYR cc_start: 0.8559 (m-80) cc_final: 0.8208 (m-80) REVERT: B 212 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8663 (mm) REVERT: B 393 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7500 (tttm) REVERT: B 403 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: B 407 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7721 (mt-10) REVERT: U 23 ASP cc_start: 0.6108 (OUTLIER) cc_final: 0.5862 (p0) REVERT: K 27 ARG cc_start: 0.8212 (tpt90) cc_final: 0.7834 (tpt170) REVERT: K 198 ASN cc_start: 0.5191 (OUTLIER) cc_final: 0.4083 (t0) outliers start: 97 outliers final: 82 residues processed: 651 average time/residue: 0.9638 time to fit residues: 995.6643 Evaluate side-chains 672 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 584 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 180 PHE Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 22 PHE Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 85 MET Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 145 HIS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 46 ASN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 173 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 9.9990 chunk 382 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 331 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 359 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 369 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 107 ASN F 160 GLN L 46 ASN O 46 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** 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** M 163 HIS ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.198777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.144875 restraints weight = 168400.831| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.65 r_work: 0.3603 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.003 0.054 36152 Z= 0.167 Angle : 0.546 7.969 48740 Z= 0.281 Chirality : 0.041 0.156 5643 Planarity : 0.004 0.051 6289 Dihedral : 7.201 133.233 5032 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.77 % Allowed : 16.84 % Favored : 81.40 % 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: 0.61 (0.11), residues: 2259 sheet: -1.11 (0.23), residues: 452 loop : -1.25 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS I 145 PHE 0.021 0.001 PHE U 117 TYR 0.025 0.001 TYR P 82 ARG 0.007 0.000 ARG I 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20668.65 seconds wall clock time: 355 minutes 28.94 seconds (21328.94 seconds total)