Starting phenix.real_space_refine on Sun Feb 18 22:46:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcv_28994/02_2024/8fcv_28994_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcv_28994/02_2024/8fcv_28994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcv_28994/02_2024/8fcv_28994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcv_28994/02_2024/8fcv_28994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcv_28994/02_2024/8fcv_28994_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcv_28994/02_2024/8fcv_28994_updated.pdb" } resolution = 2.95 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= 0.013 sd= 0.890 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: 6 Type Number sf(0) Gaussians P 81 5.49 5 Mg 7 5.21 5 S 75 5.16 5 C 14490 2.51 5 N 4031 2.21 5 O 4432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 25": "OE1" <-> "OE2" Residue "P GLU 72": "OE1" <-> "OE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 326": "OE1" <-> "OE2" Residue "Q GLU 10": "OE1" <-> "OE2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q GLU 210": "OE1" <-> "OE2" Residue "Q PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 95": "OE1" <-> "OE2" Residue "R GLU 272": "OE1" <-> "OE2" Residue "R GLU 321": "OE1" <-> "OE2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S GLU 321": "OE1" <-> "OE2" Residue "T GLU 10": "OE1" <-> "OE2" Residue "T GLU 71": "OE1" <-> "OE2" Residue "T GLU 76": "OE1" <-> "OE2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U GLU 38": "OE1" <-> "OE2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U GLU 71": "OE1" <-> "OE2" Residue "U GLU 76": "OE1" <-> "OE2" Residue "U GLU 95": "OE1" <-> "OE2" Residue "U GLU 108": "OE1" <-> "OE2" Residue "U GLU 144": "OE1" <-> "OE2" Residue "U GLU 172": "OE1" <-> "OE2" Residue "U GLU 333": "OE1" <-> "OE2" Residue "V GLU 71": "OE1" <-> "OE2" Residue "V GLU 157": "OE1" <-> "OE2" Residue "V GLU 210": "OE1" <-> "OE2" Residue "V GLU 333": "OE1" <-> "OE2" Residue "W GLU 24": "OE1" <-> "OE2" Residue "W GLU 35": "OE1" <-> "OE2" Residue "W GLU 95": "OE1" <-> "OE2" Residue "W GLU 118": "OE1" <-> "OE2" Residue "W GLU 321": "OE1" <-> "OE2" Residue "W GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23116 Number of models: 1 Model: "" Number of chains: 17 Chain: "N" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "O" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "P" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2618 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "Q" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2508 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "W" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: 11.84, per 1000 atoms: 0.51 Number of scatterers: 23116 At special positions: 0 Unit cell: (121.21, 161.262, 151.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 81 15.00 Mg 7 11.99 O 4432 8.00 N 4031 7.00 C 14490 6.00 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: 9.93 Conformation dependent library (CDL) restraints added in 4.1 seconds 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 9 sheets defined 54.2% alpha, 5.4% beta 30 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 10.32 Creating SS restraints... Processing helix chain 'P' and resid 37 through 47 Processing helix chain 'P' and resid 52 through 64 removed outlier: 4.670A pdb=" N ALA P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Proline residue: P 62 - end of helix Processing helix chain 'P' and resid 70 through 75 removed outlier: 4.048A pdb=" N SER P 75 " --> pdb=" O SER P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 82 removed outlier: 3.712A pdb=" N LEU P 82 " --> pdb=" O SER P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 92 Processing helix chain 'P' and resid 96 through 108 Processing helix chain 'P' and resid 114 through 117 Processing helix chain 'P' and resid 120 through 122 No H-bonds generated for 'chain 'P' and resid 120 through 122' Processing helix chain 'P' and resid 140 through 148 Processing helix chain 'P' and resid 157 through 160 Processing helix chain 'P' and resid 215 through 234 removed outlier: 4.557A pdb=" N VAL P 219 " --> pdb=" O GLU P 215 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN P 220 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR P 231 " --> pdb=" O LEU P 227 " (cutoff:3.500A) Proline residue: P 232 - end of helix Processing helix chain 'P' and resid 240 through 260 Processing helix chain 'P' and resid 263 through 280 removed outlier: 4.385A pdb=" N GLY P 269 " --> pdb=" O GLY P 266 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY P 270 " --> pdb=" O ASP P 267 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 271 " --> pdb=" O LEU P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 289 through 299 removed outlier: 4.825A pdb=" N ILE P 294 " --> pdb=" O VAL P 290 " (cutoff:3.500A) Proline residue: P 295 - end of helix Processing helix chain 'P' and resid 304 through 309 Processing helix chain 'P' and resid 312 through 322 Processing helix chain 'Q' and resid 9 through 12 removed outlier: 3.716A pdb=" N LEU Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 9 through 12' Processing helix chain 'Q' and resid 16 through 25 Processing helix chain 'Q' and resid 31 through 45 Processing helix chain 'Q' and resid 63 through 82 Proline residue: Q 80 - end of helix Processing helix chain 'Q' and resid 106 through 116 Processing helix chain 'Q' and resid 150 through 163 Processing helix chain 'Q' and resid 173 through 177 Processing helix chain 'Q' and resid 182 through 199 removed outlier: 4.237A pdb=" N GLN Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU Q 189 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET Q 198 " --> pdb=" O SER Q 194 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR Q 199 " --> pdb=" O LEU Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 214 removed outlier: 4.437A pdb=" N THR Q 213 " --> pdb=" O GLU Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 218 through 223 Processing helix chain 'Q' and resid 238 through 253 Processing helix chain 'Q' and resid 265 through 272 removed outlier: 4.661A pdb=" N GLU Q 268 " --> pdb=" O ASP Q 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 278 through 294 Processing helix chain 'Q' and resid 302 through 307 Processing helix chain 'Q' and resid 312 through 330 Processing helix chain 'R' and resid 9 through 12 Processing helix chain 'R' and resid 16 through 25 Processing helix chain 'R' and resid 31 through 45 Processing helix chain 'R' and resid 63 through 84 Proline residue: R 80 - end of helix removed outlier: 3.634A pdb=" N SER R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 117 Processing helix chain 'R' and resid 149 through 163 Processing helix chain 'R' and resid 173 through 177 Processing helix chain 'R' and resid 182 through 199 removed outlier: 3.866A pdb=" N LEU R 185 " --> pdb=" O GLY R 182 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET R 198 " --> pdb=" O LEU R 195 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR R 199 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 219 through 223 Processing helix chain 'R' and resid 238 through 253 Processing helix chain 'R' and resid 265 through 274 removed outlier: 4.644A pdb=" N GLU R 268 " --> pdb=" O ASP R 265 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR R 274 " --> pdb=" O TYR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 295 Processing helix chain 'R' and resid 302 through 307 Processing helix chain 'R' and resid 312 through 328 removed outlier: 3.849A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 342 removed outlier: 3.727A pdb=" N ASN R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 13 removed outlier: 3.661A pdb=" N LEU S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 25 Processing helix chain 'S' and resid 31 through 45 Processing helix chain 'S' and resid 63 through 82 Proline residue: S 80 - end of helix Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 149 through 163 Processing helix chain 'S' and resid 173 through 177 Processing helix chain 'S' and resid 182 through 199 removed outlier: 3.918A pdb=" N LEU S 185 " --> pdb=" O GLY S 182 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET S 198 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 209 through 214 Processing helix chain 'S' and resid 219 through 223 Processing helix chain 'S' and resid 238 through 253 Processing helix chain 'S' and resid 265 through 274 removed outlier: 4.666A pdb=" N GLU S 268 " --> pdb=" O ASP S 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG S 273 " --> pdb=" O PHE S 270 " (cutoff:3.500A) Processing helix chain 'S' and resid 278 through 294 Processing helix chain 'S' and resid 302 through 308 removed outlier: 3.612A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 312 through 328 Processing helix chain 'S' and resid 333 through 343 Processing helix chain 'T' and resid 9 through 12 removed outlier: 3.511A pdb=" N LEU T 12 " --> pdb=" O LEU T 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 9 through 12' Processing helix chain 'T' and resid 16 through 25 Processing helix chain 'T' and resid 31 through 45 Processing helix chain 'T' and resid 63 through 84 Proline residue: T 80 - end of helix removed outlier: 4.017A pdb=" N SER T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 117 Processing helix chain 'T' and resid 149 through 163 Processing helix chain 'T' and resid 173 through 177 Processing helix chain 'T' and resid 182 through 199 removed outlier: 4.004A pdb=" N GLN T 186 " --> pdb=" O GLY T 182 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 214 removed outlier: 3.507A pdb=" N THR T 213 " --> pdb=" O GLU T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 219 through 223 Processing helix chain 'T' and resid 238 through 253 Processing helix chain 'T' and resid 267 through 274 Processing helix chain 'T' and resid 278 through 295 Processing helix chain 'T' and resid 302 through 307 Processing helix chain 'T' and resid 312 through 328 Processing helix chain 'T' and resid 333 through 343 Processing helix chain 'U' and resid 9 through 12 Processing helix chain 'U' and resid 16 through 25 Processing helix chain 'U' and resid 31 through 45 Processing helix chain 'U' and resid 63 through 84 Proline residue: U 80 - end of helix removed outlier: 3.534A pdb=" N SER U 84 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 117 Processing helix chain 'U' and resid 149 through 163 Processing helix chain 'U' and resid 173 through 177 Processing helix chain 'U' and resid 183 through 199 removed outlier: 4.353A pdb=" N MET U 198 " --> pdb=" O LEU U 195 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR U 199 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 214 Processing helix chain 'U' and resid 219 through 223 Processing helix chain 'U' and resid 238 through 253 Processing helix chain 'U' and resid 264 through 274 removed outlier: 4.932A pdb=" N GLU U 268 " --> pdb=" O ASP U 265 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR U 269 " --> pdb=" O HIS U 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR U 274 " --> pdb=" O TYR U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 295 Processing helix chain 'U' and resid 302 through 307 Processing helix chain 'U' and resid 312 through 328 Processing helix chain 'U' and resid 333 through 343 Processing helix chain 'V' and resid 9 through 12 Processing helix chain 'V' and resid 16 through 25 Processing helix chain 'V' and resid 31 through 45 Processing helix chain 'V' and resid 63 through 77 Processing helix chain 'V' and resid 79 through 84 Processing helix chain 'V' and resid 106 through 117 Processing helix chain 'V' and resid 149 through 163 Processing helix chain 'V' and resid 173 through 177 Processing helix chain 'V' and resid 184 through 199 removed outlier: 4.014A pdb=" N LEU V 189 " --> pdb=" O LEU V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 209 through 214 Processing helix chain 'V' and resid 218 through 223 Processing helix chain 'V' and resid 238 through 253 Processing helix chain 'V' and resid 265 through 274 removed outlier: 4.737A pdb=" N GLU V 268 " --> pdb=" O ASP V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 294 Processing helix chain 'V' and resid 302 through 308 removed outlier: 3.606A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 328 removed outlier: 3.846A pdb=" N LYS V 317 " --> pdb=" O ALA V 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE V 319 " --> pdb=" O CYS V 315 " (cutoff:3.500A) Processing helix chain 'V' and resid 333 through 343 Processing helix chain 'W' and resid 9 through 11 No H-bonds generated for 'chain 'W' and resid 9 through 11' Processing helix chain 'W' and resid 16 through 25 Processing helix chain 'W' and resid 31 through 45 Processing helix chain 'W' and resid 63 through 84 removed outlier: 3.648A pdb=" N LEU W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) Proline residue: W 80 - end of helix removed outlier: 4.117A pdb=" N SER W 84 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 117 Processing helix chain 'W' and resid 149 through 163 Processing helix chain 'W' and resid 173 through 176 Processing helix chain 'W' and resid 184 through 199 Processing helix chain 'W' and resid 209 through 214 removed outlier: 3.549A pdb=" N THR W 213 " --> pdb=" O GLU W 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 223 Processing helix chain 'W' and resid 238 through 253 Processing helix chain 'W' and resid 264 through 274 removed outlier: 4.815A pdb=" N GLU W 268 " --> pdb=" O ASP W 265 " (cutoff:3.500A) Processing helix chain 'W' and resid 278 through 294 Processing helix chain 'W' and resid 302 through 307 removed outlier: 3.627A pdb=" N GLN W 306 " --> pdb=" O LEU W 302 " (cutoff:3.500A) Processing helix chain 'W' and resid 312 through 328 Processing helix chain 'W' and resid 333 through 342 Processing sheet with id= A, first strand: chain 'Q' and resid 55 through 57 removed outlier: 7.220A pdb=" N ILE Q 228 " --> pdb=" O TYR Q 56 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.175A pdb=" N VAL Q 167 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE Q 94 " --> pdb=" O VAL Q 167 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE Q 169 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU Q 202 " --> pdb=" O PHE Q 168 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL Q 170 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS Q 204 " --> pdb=" O VAL Q 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'R' and resid 225 through 230 removed outlier: 6.261A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE R 230 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR R 56 " --> pdb=" O PHE R 230 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS R 203 " --> pdb=" O ILE R 53 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL R 55 " --> pdb=" O HIS R 203 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU R 205 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLY R 57 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLY R 207 " --> pdb=" O GLY R 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL R 92 " --> pdb=" O VAL R 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 225 through 230 removed outlier: 6.879A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE S 230 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR S 56 " --> pdb=" O PHE S 230 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS S 203 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL S 55 " --> pdb=" O HIS S 203 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU S 205 " --> pdb=" O VAL S 55 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY S 57 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY S 207 " --> pdb=" O GLY S 57 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 225 through 230 removed outlier: 6.778A pdb=" N PHE T 52 " --> pdb=" O VAL T 226 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS T 203 " --> pdb=" O ILE T 53 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL T 55 " --> pdb=" O HIS T 203 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU T 205 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY T 57 " --> pdb=" O LEU T 205 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'U' and resid 225 through 230 removed outlier: 6.810A pdb=" N PHE U 52 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE U 228 " --> pdb=" O PHE U 52 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE U 54 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE U 230 " --> pdb=" O PHE U 54 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR U 56 " --> pdb=" O PHE U 230 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS U 203 " --> pdb=" O ILE U 53 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL U 55 " --> pdb=" O HIS U 203 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU U 205 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY U 57 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE U 168 " --> pdb=" O CYS U 204 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU U 206 " --> pdb=" O PHE U 168 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL U 170 " --> pdb=" O LEU U 206 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'V' and resid 225 through 230 removed outlier: 6.703A pdb=" N PHE V 52 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE V 228 " --> pdb=" O PHE V 52 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE V 54 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE V 230 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR V 56 " --> pdb=" O PHE V 230 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N HIS V 203 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL V 55 " --> pdb=" O HIS V 203 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU V 205 " --> pdb=" O VAL V 55 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLY V 57 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLY V 207 " --> pdb=" O GLY V 57 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE V 168 " --> pdb=" O CYS V 204 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU V 206 " --> pdb=" O PHE V 168 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL V 170 " --> pdb=" O LEU V 206 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL V 92 " --> pdb=" O PHE V 169 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASP V 171 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE V 94 " --> pdb=" O ASP V 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'W' and resid 225 through 229 removed outlier: 6.685A pdb=" N PHE W 52 " --> pdb=" O VAL W 226 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE W 228 " --> pdb=" O PHE W 52 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE W 54 " --> pdb=" O ILE W 228 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N HIS W 203 " --> pdb=" O ILE W 53 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL W 55 " --> pdb=" O HIS W 203 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU W 205 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL W 92 " --> pdb=" O PHE W 169 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'W' and resid 133 through 135 939 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 6.97 Time building geometry restraints manager: 10.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7184 1.34 - 1.46: 3865 1.46 - 1.58: 12410 1.58 - 1.70: 153 1.70 - 1.82: 104 Bond restraints: 23716 Sorted by residual: bond pdb=" N SER V 59 " pdb=" CA SER V 59 " ideal model delta sigma weight residual 1.463 1.436 0.027 1.30e-02 5.92e+03 4.27e+00 bond pdb=" C GLY U 60 " pdb=" O GLY U 60 " ideal model delta sigma weight residual 1.238 1.221 0.017 1.12e-02 7.97e+03 2.24e+00 bond pdb=" CA ASP V 127 " pdb=" CB ASP V 127 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.61e-02 3.86e+03 1.90e+00 bond pdb=" CG ASP V 187 " pdb=" OD1 ASP V 187 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.70e+00 bond pdb=" CB ASP V 187 " pdb=" CG ASP V 187 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.59e+00 ... (remaining 23711 not shown) Histogram of bond angle deviations from ideal: 94.94 - 103.92: 462 103.92 - 112.90: 13013 112.90 - 121.88: 14149 121.88 - 130.85: 4636 130.85 - 139.83: 131 Bond angle restraints: 32391 Sorted by residual: angle pdb=" N THR U 299 " pdb=" CA THR U 299 " pdb=" C THR U 299 " ideal model delta sigma weight residual 108.74 115.59 -6.85 1.38e+00 5.25e-01 2.46e+01 angle pdb=" N GLU Q 210 " pdb=" CA GLU Q 210 " pdb=" C GLU Q 210 " ideal model delta sigma weight residual 113.21 107.64 5.57 1.15e+00 7.56e-01 2.35e+01 angle pdb=" C VAL S 61 " pdb=" N GLY S 62 " pdb=" CA GLY S 62 " ideal model delta sigma weight residual 122.26 116.35 5.91 1.34e+00 5.57e-01 1.95e+01 angle pdb=" N VAL W 61 " pdb=" CA VAL W 61 " pdb=" C VAL W 61 " ideal model delta sigma weight residual 113.53 109.26 4.27 9.80e-01 1.04e+00 1.90e+01 angle pdb=" N ASP W 294 " pdb=" CA ASP W 294 " pdb=" C ASP W 294 " ideal model delta sigma weight residual 111.28 106.58 4.70 1.09e+00 8.42e-01 1.86e+01 ... (remaining 32386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 11710 17.65 - 35.30: 1731 35.30 - 52.95: 662 52.95 - 70.60: 151 70.60 - 88.25: 24 Dihedral angle restraints: 14278 sinusoidal: 6399 harmonic: 7879 Sorted by residual: dihedral pdb=" CA GLU W 95 " pdb=" C GLU W 95 " pdb=" N ALA W 96 " pdb=" CA ALA W 96 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU P 185 " pdb=" C LEU P 185 " pdb=" N PRO P 186 " pdb=" CA PRO P 186 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP V 187 " pdb=" C ASP V 187 " pdb=" N GLN V 188 " pdb=" CA GLN V 188 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 14275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2684 0.038 - 0.075: 697 0.075 - 0.113: 201 0.113 - 0.150: 45 0.150 - 0.188: 3 Chirality restraints: 3630 Sorted by residual: chirality pdb=" CA ASP W 127 " pdb=" N ASP W 127 " pdb=" C ASP W 127 " pdb=" CB ASP W 127 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA ASP V 127 " pdb=" N ASP V 127 " pdb=" C ASP V 127 " pdb=" CB ASP V 127 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ASP T 127 " pdb=" N ASP T 127 " pdb=" C ASP T 127 " pdb=" CB ASP T 127 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 3627 not shown) Planarity restraints: 3903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE V 126 " 0.012 2.00e-02 2.50e+03 2.12e-02 7.90e+00 pdb=" CG PHE V 126 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE V 126 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE V 126 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE V 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE V 126 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE V 126 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA V 58 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C ALA V 58 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA V 58 " 0.018 2.00e-02 2.50e+03 pdb=" N SER V 59 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 297 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ALA U 297 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA U 297 " 0.014 2.00e-02 2.50e+03 pdb=" N THR U 298 " 0.013 2.00e-02 2.50e+03 ... (remaining 3900 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 254 2.57 - 3.15: 19599 3.15 - 3.73: 39236 3.73 - 4.32: 52171 4.32 - 4.90: 83772 Nonbonded interactions: 195032 Sorted by model distance: nonbonded pdb=" O3A ATP V 600 " pdb="MG MG V 601 " model vdw 1.983 2.170 nonbonded pdb=" O3B ATP T 600 " pdb="MG MG T 601 " model vdw 1.995 2.170 nonbonded pdb=" O3B ATP U 600 " pdb="MG MG U 601 " model vdw 1.999 2.170 nonbonded pdb=" O3B ATP Q 600 " pdb="MG MG Q 601 " model vdw 2.003 2.170 nonbonded pdb=" O3B ATP S 600 " pdb="MG MG S 601 " model vdw 2.006 2.170 ... (remaining 195027 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 'Q' selection = (chain 'R' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'S' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'T' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'U' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'V' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'W' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.080 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 66.700 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.110 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23716 Z= 0.177 Angle : 0.618 8.469 32391 Z= 0.345 Chirality : 0.039 0.188 3630 Planarity : 0.004 0.054 3903 Dihedral : 19.304 88.253 9186 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.11 % Favored : 95.44 % Rotamer: Outliers : 0.73 % Allowed : 25.63 % Favored : 73.64 % 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: 0.45 (0.17), residues: 2677 helix: 1.11 (0.14), residues: 1564 sheet: -0.73 (0.41), residues: 186 loop : -0.79 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 267 HIS 0.010 0.001 HIS W 162 PHE 0.047 0.001 PHE V 126 TYR 0.019 0.001 TYR P 154 ARG 0.010 0.000 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 333 time to evaluate : 2.856 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: P 77 ASN cc_start: 0.8471 (t0) cc_final: 0.8153 (t0) REVERT: P 91 ILE cc_start: 0.5990 (mt) cc_final: 0.5627 (mp) REVERT: P 120 LEU cc_start: 0.8591 (pp) cc_final: 0.8027 (mt) REVERT: P 154 TYR cc_start: 0.8772 (p90) cc_final: 0.8363 (p90) REVERT: P 180 HIS cc_start: 0.8853 (m-70) cc_final: 0.8591 (m-70) REVERT: Q 71 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8412 (mt-10) REVERT: Q 164 HIS cc_start: 0.8400 (t-90) cc_final: 0.8067 (t-90) REVERT: Q 172 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8576 (mm-30) REVERT: Q 321 GLU cc_start: 0.8699 (tt0) cc_final: 0.8272 (tm-30) REVERT: R 138 PHE cc_start: 0.9222 (m-80) cc_final: 0.8489 (m-80) REVERT: R 320 LYS cc_start: 0.8959 (tppt) cc_final: 0.8718 (mtmm) REVERT: R 324 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8128 (tm-30) REVERT: S 9 LEU cc_start: 0.8969 (pt) cc_final: 0.8677 (mm) REVERT: S 121 LEU cc_start: 0.9620 (pt) cc_final: 0.9350 (pp) REVERT: S 124 HIS cc_start: 0.8139 (m90) cc_final: 0.7707 (m90) REVERT: S 128 TYR cc_start: 0.6995 (m-80) cc_final: 0.6656 (m-10) REVERT: S 324 GLU cc_start: 0.8316 (pp20) cc_final: 0.7668 (pp20) REVERT: T 164 HIS cc_start: 0.9037 (t-170) cc_final: 0.8197 (t-90) REVERT: T 189 LEU cc_start: 0.8883 (tp) cc_final: 0.8667 (tp) REVERT: T 210 GLU cc_start: 0.8671 (pt0) cc_final: 0.8124 (tm-30) REVERT: U 25 ASN cc_start: 0.9216 (m-40) cc_final: 0.8578 (m-40) REVERT: U 95 GLU cc_start: 0.7910 (pm20) cc_final: 0.7376 (pm20) REVERT: U 142 ASN cc_start: 0.7027 (m-40) cc_final: 0.6714 (m110) REVERT: U 321 GLU cc_start: 0.9311 (tp30) cc_final: 0.9100 (tp30) REVERT: V 166 ASP cc_start: 0.9050 (t0) cc_final: 0.8842 (m-30) REVERT: W 44 ILE cc_start: 0.9601 (mm) cc_final: 0.9340 (mm) REVERT: W 56 TYR cc_start: 0.6918 (m-10) cc_final: 0.6431 (m-80) REVERT: W 97 ILE cc_start: 0.8472 (pt) cc_final: 0.8222 (tt) REVERT: W 164 HIS cc_start: 0.8358 (t70) cc_final: 0.7850 (p-80) REVERT: W 175 HIS cc_start: 0.8988 (m-70) cc_final: 0.8516 (m-70) REVERT: W 186 GLN cc_start: 0.8279 (tm-30) cc_final: 0.8006 (tm-30) REVERT: W 198 MET cc_start: 0.7822 (mpp) cc_final: 0.7071 (mpp) outliers start: 17 outliers final: 4 residues processed: 346 average time/residue: 1.0511 time to fit residues: 429.9092 Evaluate side-chains 196 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain V residue 301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 248 GLN Q 203 HIS ** R 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN T 242 GLN U 203 HIS V 314 GLN ** W 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 203 HIS W 254 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 23716 Z= 0.498 Angle : 0.716 7.873 32391 Z= 0.371 Chirality : 0.044 0.193 3630 Planarity : 0.005 0.068 3903 Dihedral : 17.147 89.741 3879 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.03 % Favored : 95.67 % Rotamer: Outliers : 5.26 % Allowed : 25.55 % Favored : 69.19 % 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: 0.29 (0.17), residues: 2677 helix: 0.96 (0.13), residues: 1611 sheet: -0.91 (0.40), residues: 186 loop : -0.87 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP V 106 HIS 0.012 0.002 HIS W 254 PHE 0.033 0.002 PHE P 308 TYR 0.025 0.002 TYR T 128 ARG 0.007 0.001 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 181 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 39 SER cc_start: 0.9145 (t) cc_final: 0.8869 (p) REVERT: P 65 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8595 (tp) REVERT: P 119 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8162 (tm) REVERT: P 135 TYR cc_start: 0.8813 (m-80) cc_final: 0.8273 (m-80) REVERT: P 155 GLU cc_start: 0.8897 (mp0) cc_final: 0.8536 (mp0) REVERT: P 180 HIS cc_start: 0.8851 (m-70) cc_final: 0.8505 (m-70) REVERT: P 290 VAL cc_start: 0.8938 (m) cc_final: 0.8679 (p) REVERT: Q 41 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8878 (mmm) REVERT: Q 71 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8427 (mt-10) REVERT: Q 164 HIS cc_start: 0.8657 (t70) cc_final: 0.8369 (t-90) REVERT: Q 172 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8508 (mp0) REVERT: Q 321 GLU cc_start: 0.8931 (tt0) cc_final: 0.8289 (tm-30) REVERT: R 198 MET cc_start: 0.8855 (mtm) cc_final: 0.8309 (mtm) REVERT: R 321 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: R 324 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8404 (tm-30) REVERT: S 9 LEU cc_start: 0.9025 (pt) cc_final: 0.8742 (mm) REVERT: S 121 LEU cc_start: 0.9660 (pt) cc_final: 0.9245 (pp) REVERT: S 124 HIS cc_start: 0.8336 (m90) cc_final: 0.7720 (m90) REVERT: S 324 GLU cc_start: 0.8106 (pp20) cc_final: 0.7844 (tm-30) REVERT: T 210 GLU cc_start: 0.8802 (pt0) cc_final: 0.8058 (tm-30) REVERT: U 59 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8161 (t) REVERT: U 95 GLU cc_start: 0.8239 (pm20) cc_final: 0.7745 (pm20) REVERT: U 130 VAL cc_start: 0.8896 (t) cc_final: 0.8602 (t) REVERT: U 338 ASN cc_start: 0.9242 (m110) cc_final: 0.9020 (m110) REVERT: V 95 GLU cc_start: 0.8379 (pm20) cc_final: 0.7504 (pp20) REVERT: V 166 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8868 (m-30) REVERT: V 234 CYS cc_start: 0.8782 (m) cc_final: 0.8147 (t) REVERT: W 164 HIS cc_start: 0.8379 (t70) cc_final: 0.7981 (p-80) REVERT: W 175 HIS cc_start: 0.9046 (m-70) cc_final: 0.8574 (m-70) REVERT: W 198 MET cc_start: 0.7232 (mpp) cc_final: 0.7007 (mpp) outliers start: 123 outliers final: 43 residues processed: 285 average time/residue: 0.9578 time to fit residues: 328.2892 Evaluate side-chains 201 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 152 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 192 SER Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 277 CYS Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 311 SER Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain S residue 343 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 286 LYS Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 195 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 102 ARG Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 260 THR Chi-restraints excluded: chain W residue 321 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 268 optimal weight: 10.0000 chunk 221 optimal weight: 0.0270 chunk 246 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 GLN ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 252 GLN T 25 ASN T 197 ASN W 188 GLN W 197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23716 Z= 0.166 Angle : 0.573 9.130 32391 Z= 0.288 Chirality : 0.039 0.191 3630 Planarity : 0.004 0.044 3903 Dihedral : 16.781 88.055 3875 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.44 % Favored : 96.26 % Rotamer: Outliers : 3.42 % Allowed : 26.83 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2677 helix: 1.14 (0.13), residues: 1600 sheet: -0.98 (0.39), residues: 189 loop : -0.90 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 146 HIS 0.006 0.001 HIS W 254 PHE 0.018 0.001 PHE U 126 TYR 0.025 0.001 TYR U 103 ARG 0.014 0.000 ARG P 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 192 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 94 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7961 (pmm) REVERT: P 118 THR cc_start: 0.6922 (t) cc_final: 0.6585 (t) REVERT: P 120 LEU cc_start: 0.8605 (pt) cc_final: 0.8107 (mt) REVERT: P 154 TYR cc_start: 0.8589 (p90) cc_final: 0.8337 (p90) REVERT: P 155 GLU cc_start: 0.8824 (mp0) cc_final: 0.8523 (mp0) REVERT: P 166 PHE cc_start: 0.8910 (m-80) cc_final: 0.8679 (m-80) REVERT: P 180 HIS cc_start: 0.8808 (m-70) cc_final: 0.8425 (m-70) REVERT: P 290 VAL cc_start: 0.8890 (m) cc_final: 0.8632 (p) REVERT: Q 71 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8329 (mt-10) REVERT: Q 172 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8432 (mm-30) REVERT: Q 210 GLU cc_start: 0.8698 (mp0) cc_final: 0.8369 (mp0) REVERT: Q 212 LEU cc_start: 0.8478 (pp) cc_final: 0.8140 (mm) REVERT: Q 321 GLU cc_start: 0.8964 (tt0) cc_final: 0.8309 (tm-30) REVERT: R 18 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: R 172 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8809 (mt-10) REVERT: R 220 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8503 (tp-100) REVERT: R 324 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8335 (tm-30) REVERT: S 9 LEU cc_start: 0.8988 (pt) cc_final: 0.8709 (mm) REVERT: S 102 ARG cc_start: 0.8641 (ttm110) cc_final: 0.8176 (ttm110) REVERT: T 210 GLU cc_start: 0.8761 (pt0) cc_final: 0.8030 (tm-30) REVERT: U 164 HIS cc_start: 0.8568 (t-90) cc_final: 0.8328 (t-90) REVERT: U 190 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8809 (m-30) REVERT: U 338 ASN cc_start: 0.9326 (m110) cc_final: 0.9034 (m110) REVERT: V 24 GLU cc_start: 0.9401 (tp30) cc_final: 0.9176 (tp30) REVERT: V 95 GLU cc_start: 0.8345 (pm20) cc_final: 0.7501 (pp20) REVERT: V 234 CYS cc_start: 0.8741 (m) cc_final: 0.8054 (t) REVERT: W 164 HIS cc_start: 0.8388 (t70) cc_final: 0.8186 (t70) REVERT: W 175 HIS cc_start: 0.8955 (m-70) cc_final: 0.8700 (m-70) outliers start: 80 outliers final: 24 residues processed: 259 average time/residue: 1.0185 time to fit residues: 314.1841 Evaluate side-chains 196 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 192 SER Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 343 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 260 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 GLN S 124 HIS ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN U 25 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 23716 Z= 0.368 Angle : 0.612 8.035 32391 Z= 0.313 Chirality : 0.041 0.203 3630 Planarity : 0.004 0.055 3903 Dihedral : 16.647 86.439 3874 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.30 % Favored : 95.44 % Rotamer: Outliers : 4.36 % Allowed : 26.40 % Favored : 69.23 % 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: 0.51 (0.17), residues: 2677 helix: 1.14 (0.13), residues: 1592 sheet: -1.04 (0.39), residues: 186 loop : -0.72 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 146 HIS 0.012 0.001 HIS P 80 PHE 0.027 0.002 PHE U 126 TYR 0.024 0.001 TYR U 103 ARG 0.008 0.001 ARG W 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 170 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 39 SER cc_start: 0.9075 (t) cc_final: 0.8850 (p) REVERT: P 94 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8140 (pmm) REVERT: P 135 TYR cc_start: 0.8554 (m-80) cc_final: 0.8330 (m-80) REVERT: P 155 GLU cc_start: 0.8838 (mp0) cc_final: 0.8583 (mp0) REVERT: P 166 PHE cc_start: 0.9127 (m-80) cc_final: 0.8847 (m-80) REVERT: Q 41 MET cc_start: 0.9179 (mmm) cc_final: 0.8971 (mmm) REVERT: Q 71 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8403 (mt-10) REVERT: Q 100 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8406 (pt0) REVERT: Q 172 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8459 (mp0) REVERT: Q 210 GLU cc_start: 0.8668 (mp0) cc_final: 0.8348 (mp0) REVERT: Q 321 GLU cc_start: 0.8984 (tt0) cc_final: 0.8336 (tm-30) REVERT: R 18 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: R 82 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8440 (pp) REVERT: R 220 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8577 (mm-40) REVERT: R 311 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8194 (p) REVERT: R 324 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8432 (tm-30) REVERT: S 102 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8304 (ttm110) REVERT: T 210 GLU cc_start: 0.8820 (pt0) cc_final: 0.8003 (tm-30) REVERT: U 59 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8561 (t) REVERT: U 146 LYS cc_start: 0.9329 (mppt) cc_final: 0.9076 (mtpt) REVERT: U 164 HIS cc_start: 0.8586 (t-90) cc_final: 0.8212 (t-90) REVERT: U 190 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8856 (m-30) REVERT: U 338 ASN cc_start: 0.9316 (m110) cc_final: 0.8988 (m110) REVERT: V 166 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8917 (m-30) REVERT: V 234 CYS cc_start: 0.8775 (m) cc_final: 0.8093 (t) REVERT: W 164 HIS cc_start: 0.8516 (t70) cc_final: 0.8264 (t70) REVERT: W 188 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8989 (mm110) outliers start: 102 outliers final: 45 residues processed: 259 average time/residue: 1.0086 time to fit residues: 312.1663 Evaluate side-chains 208 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 192 SER Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 311 SER Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain R residue 343 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 195 LEU Chi-restraints excluded: chain V residue 222 SER Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 332 THR Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 260 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 182 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 GLN S 124 HIS ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN U 137 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23716 Z= 0.168 Angle : 0.553 8.787 32391 Z= 0.277 Chirality : 0.039 0.199 3630 Planarity : 0.004 0.044 3903 Dihedral : 16.323 86.501 3873 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.77 % Favored : 95.97 % Rotamer: Outliers : 3.51 % Allowed : 27.51 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2677 helix: 1.24 (0.14), residues: 1597 sheet: -1.08 (0.39), residues: 184 loop : -0.75 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 122 HIS 0.005 0.001 HIS W 254 PHE 0.018 0.001 PHE U 126 TYR 0.026 0.001 TYR U 103 ARG 0.006 0.000 ARG S 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 182 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 39 SER cc_start: 0.9109 (t) cc_final: 0.8851 (p) REVERT: P 94 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8226 (pmm) REVERT: P 120 LEU cc_start: 0.8728 (pt) cc_final: 0.8299 (mt) REVERT: P 135 TYR cc_start: 0.8404 (m-80) cc_final: 0.8172 (m-80) REVERT: P 155 GLU cc_start: 0.8804 (mp0) cc_final: 0.8537 (mp0) REVERT: P 166 PHE cc_start: 0.9072 (m-80) cc_final: 0.8731 (m-80) REVERT: Q 71 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8295 (mt-10) REVERT: Q 100 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: Q 172 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8462 (mp0) REVERT: Q 210 GLU cc_start: 0.8613 (mp0) cc_final: 0.8336 (mp0) REVERT: Q 321 GLU cc_start: 0.8988 (tt0) cc_final: 0.8305 (tm-30) REVERT: R 18 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: R 82 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8325 (pp) REVERT: R 220 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.8717 (tp-100) REVERT: R 324 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8343 (tm-30) REVERT: S 102 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8222 (ttm110) REVERT: T 210 GLU cc_start: 0.8764 (pt0) cc_final: 0.8049 (tm-30) REVERT: U 19 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8266 (mtm180) REVERT: U 59 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8188 (t) REVERT: U 164 HIS cc_start: 0.8638 (t-90) cc_final: 0.8155 (t-90) REVERT: U 190 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8811 (m-30) REVERT: U 338 ASN cc_start: 0.9297 (m110) cc_final: 0.8952 (m110) REVERT: V 95 GLU cc_start: 0.8508 (pm20) cc_final: 0.7587 (pp20) REVERT: V 166 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8925 (m-30) REVERT: V 222 SER cc_start: 0.9487 (OUTLIER) cc_final: 0.8635 (p) REVERT: V 234 CYS cc_start: 0.8773 (m) cc_final: 0.8076 (t) REVERT: W 126 PHE cc_start: 0.8189 (t80) cc_final: 0.7759 (t80) REVERT: W 164 HIS cc_start: 0.8445 (t70) cc_final: 0.8221 (OUTLIER) REVERT: W 178 LYS cc_start: 0.8699 (mttp) cc_final: 0.8451 (mttp) outliers start: 82 outliers final: 33 residues processed: 250 average time/residue: 1.0544 time to fit residues: 314.5063 Evaluate side-chains 206 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 192 SER Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 195 LEU Chi-restraints excluded: chain V residue 222 SER Chi-restraints excluded: chain V residue 345 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 260 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 264 optimal weight: 20.0000 chunk 219 optimal weight: 0.0870 chunk 122 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN ** W 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23716 Z= 0.162 Angle : 0.560 12.903 32391 Z= 0.278 Chirality : 0.039 0.200 3630 Planarity : 0.004 0.043 3903 Dihedral : 16.103 87.075 3873 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.62 % Favored : 96.12 % Rotamer: Outliers : 3.21 % Allowed : 28.07 % Favored : 68.72 % 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: 0.60 (0.17), residues: 2677 helix: 1.26 (0.14), residues: 1597 sheet: -1.07 (0.39), residues: 184 loop : -0.77 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 146 HIS 0.004 0.001 HIS V 30 PHE 0.022 0.001 PHE R 138 TYR 0.026 0.001 TYR U 103 ARG 0.005 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 175 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8744 (tt) REVERT: P 94 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.7876 (pmm) REVERT: P 120 LEU cc_start: 0.8746 (pt) cc_final: 0.8274 (mt) REVERT: P 135 TYR cc_start: 0.8365 (m-80) cc_final: 0.8152 (m-80) REVERT: P 155 GLU cc_start: 0.8817 (mp0) cc_final: 0.8503 (mp0) REVERT: P 166 PHE cc_start: 0.9071 (m-80) cc_final: 0.8720 (m-80) REVERT: Q 41 MET cc_start: 0.9230 (mmm) cc_final: 0.9001 (mmm) REVERT: Q 71 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8252 (mt-10) REVERT: Q 100 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: Q 198 MET cc_start: 0.8974 (mpm) cc_final: 0.8181 (tmm) REVERT: Q 210 GLU cc_start: 0.8591 (mp0) cc_final: 0.8307 (mp0) REVERT: Q 321 GLU cc_start: 0.8994 (tt0) cc_final: 0.8341 (tm-30) REVERT: R 18 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: R 82 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8319 (pp) REVERT: R 220 GLN cc_start: 0.9420 (OUTLIER) cc_final: 0.8933 (tp-100) REVERT: R 324 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8344 (tm-30) REVERT: S 102 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8231 (ttm110) REVERT: T 89 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8101 (m) REVERT: T 210 GLU cc_start: 0.8781 (pt0) cc_final: 0.8051 (tm-30) REVERT: T 293 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8825 (mm) REVERT: U 19 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8344 (mtm180) REVERT: U 95 GLU cc_start: 0.7935 (pm20) cc_final: 0.7163 (pm20) REVERT: U 146 LYS cc_start: 0.9297 (mppt) cc_final: 0.9051 (mtpt) REVERT: U 164 HIS cc_start: 0.8644 (t-90) cc_final: 0.8050 (t-90) REVERT: U 190 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8813 (m-30) REVERT: U 338 ASN cc_start: 0.9292 (m110) cc_final: 0.8940 (m110) REVERT: V 95 GLU cc_start: 0.8546 (pm20) cc_final: 0.7671 (pp20) REVERT: V 166 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8935 (m-30) REVERT: V 198 MET cc_start: 0.8452 (mtm) cc_final: 0.7708 (mtm) REVERT: V 222 SER cc_start: 0.9476 (OUTLIER) cc_final: 0.8612 (p) REVERT: V 234 CYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8047 (t) REVERT: W 126 PHE cc_start: 0.8206 (t80) cc_final: 0.7818 (t80) REVERT: W 164 HIS cc_start: 0.8405 (t70) cc_final: 0.8155 (t70) outliers start: 75 outliers final: 32 residues processed: 239 average time/residue: 1.0032 time to fit residues: 288.9885 Evaluate side-chains 207 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 192 SER Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 ILE Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 222 SER Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 260 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 0.1980 chunk 29 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 192 optimal weight: 0.0770 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 263 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 160 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 HIS U 220 GLN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23716 Z= 0.151 Angle : 0.564 11.453 32391 Z= 0.278 Chirality : 0.038 0.165 3630 Planarity : 0.003 0.043 3903 Dihedral : 15.972 89.026 3873 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.04 % Rotamer: Outliers : 2.61 % Allowed : 28.50 % Favored : 68.89 % 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 (0.17), residues: 2677 helix: 1.32 (0.14), residues: 1581 sheet: -0.96 (0.40), residues: 184 loop : -0.71 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 146 HIS 0.004 0.001 HIS P 80 PHE 0.022 0.001 PHE S 126 TYR 0.027 0.001 TYR U 103 ARG 0.005 0.000 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 181 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8666 (tt) REVERT: P 94 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8226 (pmm) REVERT: P 120 LEU cc_start: 0.8688 (pt) cc_final: 0.8268 (mt) REVERT: P 122 TRP cc_start: 0.7566 (m100) cc_final: 0.7267 (m100) REVERT: P 138 TRP cc_start: 0.8149 (p90) cc_final: 0.7648 (p90) REVERT: P 166 PHE cc_start: 0.9001 (m-80) cc_final: 0.8580 (m-80) REVERT: P 188 MET cc_start: 0.7878 (mmm) cc_final: 0.4378 (pmt) REVERT: Q 71 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8199 (mt-10) REVERT: Q 198 MET cc_start: 0.8968 (mpm) cc_final: 0.8143 (tmm) REVERT: Q 212 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8018 (mm) REVERT: Q 321 GLU cc_start: 0.8983 (tt0) cc_final: 0.8327 (tm-30) REVERT: R 18 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: R 82 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8294 (pp) REVERT: R 216 ASN cc_start: 0.8206 (m-40) cc_final: 0.7928 (m110) REVERT: R 324 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8359 (tm-30) REVERT: S 102 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8244 (ttm110) REVERT: T 89 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8104 (m) REVERT: T 210 GLU cc_start: 0.8768 (pt0) cc_final: 0.8100 (tm-30) REVERT: T 293 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8817 (mm) REVERT: U 19 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8372 (mtm180) REVERT: U 95 GLU cc_start: 0.7969 (pm20) cc_final: 0.7188 (pm20) REVERT: U 164 HIS cc_start: 0.8695 (t-90) cc_final: 0.8100 (t-90) REVERT: U 338 ASN cc_start: 0.9285 (m110) cc_final: 0.8926 (m110) REVERT: V 95 GLU cc_start: 0.8538 (pm20) cc_final: 0.7684 (pp20) REVERT: V 210 GLU cc_start: 0.8895 (pt0) cc_final: 0.8684 (pm20) REVERT: V 222 SER cc_start: 0.9462 (OUTLIER) cc_final: 0.8567 (p) REVERT: V 234 CYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7987 (t) REVERT: W 126 PHE cc_start: 0.8154 (t80) cc_final: 0.7859 (t80) REVERT: W 164 HIS cc_start: 0.8499 (t70) cc_final: 0.8231 (t70) outliers start: 61 outliers final: 31 residues processed: 232 average time/residue: 0.9533 time to fit residues: 267.6196 Evaluate side-chains 201 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 222 SER Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.0870 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 HIS T 25 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN W 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23716 Z= 0.157 Angle : 0.565 11.151 32391 Z= 0.279 Chirality : 0.038 0.204 3630 Planarity : 0.003 0.042 3903 Dihedral : 15.882 88.515 3873 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.51 % Favored : 96.19 % Rotamer: Outliers : 2.65 % Allowed : 28.67 % Favored : 68.68 % 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: 0.73 (0.17), residues: 2677 helix: 1.36 (0.14), residues: 1575 sheet: -0.97 (0.38), residues: 196 loop : -0.64 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 146 HIS 0.004 0.001 HIS S 162 PHE 0.016 0.001 PHE R 138 TYR 0.027 0.001 TYR U 103 ARG 0.008 0.000 ARG W 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 180 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8769 (tt) REVERT: P 81 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9212 (pt) REVERT: P 94 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8029 (pmm) REVERT: P 120 LEU cc_start: 0.8712 (pt) cc_final: 0.8297 (mt) REVERT: P 138 TRP cc_start: 0.8165 (p90) cc_final: 0.7665 (p90) REVERT: P 166 PHE cc_start: 0.8996 (m-80) cc_final: 0.8544 (m-80) REVERT: P 188 MET cc_start: 0.7972 (mmm) cc_final: 0.4724 (pmt) REVERT: Q 71 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8192 (mt-10) REVERT: Q 198 MET cc_start: 0.8952 (mpm) cc_final: 0.8143 (tmm) REVERT: Q 212 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7985 (mm) REVERT: Q 321 GLU cc_start: 0.8974 (tt0) cc_final: 0.8330 (tm-30) REVERT: R 18 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8469 (mp0) REVERT: R 82 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8273 (pp) REVERT: R 216 ASN cc_start: 0.8275 (m-40) cc_final: 0.8031 (m110) REVERT: S 102 ARG cc_start: 0.8721 (ttm110) cc_final: 0.8238 (ttm110) REVERT: S 128 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: T 89 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8107 (m) REVERT: T 210 GLU cc_start: 0.8775 (pt0) cc_final: 0.8112 (tm-30) REVERT: T 293 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8821 (mm) REVERT: U 19 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8347 (mtm180) REVERT: U 95 GLU cc_start: 0.8003 (pm20) cc_final: 0.7331 (pm20) REVERT: U 164 HIS cc_start: 0.8719 (t-90) cc_final: 0.8159 (t-90) REVERT: U 338 ASN cc_start: 0.9284 (m110) cc_final: 0.8928 (m110) REVERT: V 11 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9051 (pp) REVERT: V 95 GLU cc_start: 0.8625 (pm20) cc_final: 0.7706 (pp20) REVERT: V 166 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8920 (m-30) REVERT: V 198 MET cc_start: 0.8472 (mtm) cc_final: 0.7799 (mtm) REVERT: V 222 SER cc_start: 0.9462 (OUTLIER) cc_final: 0.8560 (p) REVERT: V 234 CYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7982 (t) REVERT: W 25 ASN cc_start: 0.9150 (m-40) cc_final: 0.8691 (p0) REVERT: W 164 HIS cc_start: 0.8527 (t70) cc_final: 0.8234 (t70) outliers start: 62 outliers final: 29 residues processed: 234 average time/residue: 0.9539 time to fit residues: 270.9149 Evaluate side-chains 208 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 343 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 222 SER Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 148 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23716 Z= 0.185 Angle : 0.570 10.773 32391 Z= 0.284 Chirality : 0.039 0.177 3630 Planarity : 0.004 0.045 3903 Dihedral : 15.874 86.623 3873 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.70 % Favored : 96.00 % Rotamer: Outliers : 2.31 % Allowed : 29.27 % Favored : 68.42 % 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: 0.77 (0.17), residues: 2677 helix: 1.39 (0.14), residues: 1581 sheet: -0.96 (0.38), residues: 196 loop : -0.66 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 122 HIS 0.006 0.001 HIS P 80 PHE 0.016 0.001 PHE W 126 TYR 0.026 0.001 TYR U 103 ARG 0.005 0.000 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8769 (tt) REVERT: P 94 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8293 (pmm) REVERT: P 120 LEU cc_start: 0.8909 (pt) cc_final: 0.8398 (mt) REVERT: P 166 PHE cc_start: 0.8995 (m-80) cc_final: 0.8558 (m-80) REVERT: Q 71 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8240 (mt-10) REVERT: Q 198 MET cc_start: 0.8958 (mpm) cc_final: 0.8148 (tmm) REVERT: Q 321 GLU cc_start: 0.8975 (tt0) cc_final: 0.8354 (tm-30) REVERT: R 18 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: R 82 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8287 (pp) REVERT: R 216 ASN cc_start: 0.8255 (m-40) cc_final: 0.7980 (m110) REVERT: S 102 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8245 (ttm110) REVERT: S 128 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: S 210 GLU cc_start: 0.8608 (pt0) cc_final: 0.8091 (pp20) REVERT: T 89 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8114 (m) REVERT: T 146 LYS cc_start: 0.8221 (tptt) cc_final: 0.7997 (mmtt) REVERT: T 210 GLU cc_start: 0.8795 (pt0) cc_final: 0.8129 (tm-30) REVERT: T 293 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8809 (mm) REVERT: U 19 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8359 (mtm180) REVERT: U 95 GLU cc_start: 0.8066 (pm20) cc_final: 0.7329 (pm20) REVERT: U 164 HIS cc_start: 0.8726 (t-90) cc_final: 0.8119 (t-90) REVERT: U 338 ASN cc_start: 0.9286 (m110) cc_final: 0.8930 (m110) REVERT: V 11 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9058 (pp) REVERT: V 95 GLU cc_start: 0.8628 (pm20) cc_final: 0.8236 (pm20) REVERT: V 166 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8921 (m-30) REVERT: V 210 GLU cc_start: 0.8835 (pt0) cc_final: 0.8619 (pm20) REVERT: V 222 SER cc_start: 0.9468 (OUTLIER) cc_final: 0.8583 (p) REVERT: V 234 CYS cc_start: 0.8750 (OUTLIER) cc_final: 0.7981 (t) REVERT: W 25 ASN cc_start: 0.9159 (m-40) cc_final: 0.8699 (p0) REVERT: W 41 MET cc_start: 0.8912 (tpt) cc_final: 0.8657 (mmm) REVERT: W 103 TYR cc_start: 0.8815 (m-80) cc_final: 0.8545 (m-10) REVERT: W 164 HIS cc_start: 0.8529 (t70) cc_final: 0.8232 (t70) outliers start: 54 outliers final: 36 residues processed: 222 average time/residue: 1.0251 time to fit residues: 272.5993 Evaluate side-chains 209 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 161 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 98 THR Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 ILE Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 343 LEU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 222 SER Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 271 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 216 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 HIS T 25 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23716 Z= 0.182 Angle : 0.581 11.060 32391 Z= 0.286 Chirality : 0.039 0.151 3630 Planarity : 0.004 0.042 3903 Dihedral : 15.862 84.737 3873 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.81 % Favored : 95.89 % Rotamer: Outliers : 2.31 % Allowed : 29.27 % Favored : 68.42 % 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: 0.74 (0.17), residues: 2677 helix: 1.37 (0.14), residues: 1575 sheet: -0.95 (0.38), residues: 197 loop : -0.65 (0.22), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 146 HIS 0.004 0.001 HIS S 162 PHE 0.014 0.001 PHE U 126 TYR 0.026 0.001 TYR U 103 ARG 0.008 0.000 ARG V 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 163 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8778 (tt) REVERT: P 94 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.7984 (pmm) REVERT: P 100 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9063 (tttp) REVERT: P 120 LEU cc_start: 0.8925 (pt) cc_final: 0.8374 (mt) REVERT: P 166 PHE cc_start: 0.8969 (m-80) cc_final: 0.8491 (m-80) REVERT: P 188 MET cc_start: 0.7753 (mmm) cc_final: 0.4222 (pmt) REVERT: Q 71 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8250 (mt-10) REVERT: Q 164 HIS cc_start: 0.8514 (t-90) cc_final: 0.8098 (t-90) REVERT: Q 172 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8596 (mp0) REVERT: Q 198 MET cc_start: 0.8982 (mpm) cc_final: 0.8147 (tmm) REVERT: Q 321 GLU cc_start: 0.8952 (tt0) cc_final: 0.8360 (tm-30) REVERT: R 18 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: R 82 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8285 (pp) REVERT: R 216 ASN cc_start: 0.8243 (m-40) cc_final: 0.7966 (m110) REVERT: R 318 MET cc_start: 0.7864 (mtt) cc_final: 0.7660 (mtt) REVERT: S 102 ARG cc_start: 0.8724 (ttm110) cc_final: 0.8248 (ttm110) REVERT: S 128 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: T 89 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8118 (m) REVERT: T 146 LYS cc_start: 0.8217 (tptt) cc_final: 0.7991 (mmtt) REVERT: T 210 GLU cc_start: 0.8795 (pt0) cc_final: 0.8126 (tm-30) REVERT: T 293 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8819 (mm) REVERT: U 19 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8447 (mtm180) REVERT: U 59 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8293 (t) REVERT: U 95 GLU cc_start: 0.8059 (pm20) cc_final: 0.7356 (pm20) REVERT: U 146 LYS cc_start: 0.9439 (ptmm) cc_final: 0.9062 (mppt) REVERT: U 164 HIS cc_start: 0.8734 (t-90) cc_final: 0.8141 (t-90) REVERT: U 338 ASN cc_start: 0.9285 (m110) cc_final: 0.8927 (m110) REVERT: V 11 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9061 (pp) REVERT: V 166 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8924 (m-30) REVERT: V 210 GLU cc_start: 0.8839 (pt0) cc_final: 0.8624 (pm20) REVERT: V 222 SER cc_start: 0.9472 (OUTLIER) cc_final: 0.8589 (p) REVERT: V 234 CYS cc_start: 0.8750 (OUTLIER) cc_final: 0.7980 (t) REVERT: W 25 ASN cc_start: 0.9160 (m-40) cc_final: 0.8700 (p0) REVERT: W 41 MET cc_start: 0.8895 (tpt) cc_final: 0.8650 (mmm) REVERT: W 103 TYR cc_start: 0.8800 (m-80) cc_final: 0.8588 (m-80) REVERT: W 164 HIS cc_start: 0.8616 (t70) cc_final: 0.8286 (t70) outliers start: 54 outliers final: 34 residues processed: 210 average time/residue: 1.0021 time to fit residues: 252.9119 Evaluate side-chains 208 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 100 LYS Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 192 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 ILE Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 343 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 222 SER Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.6980 chunk 230 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 216 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 chunk 222 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN T 242 GLN V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.057696 restraints weight = 74542.608| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.26 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23716 Z= 0.291 Angle : 0.618 10.701 32391 Z= 0.309 Chirality : 0.040 0.152 3630 Planarity : 0.004 0.048 3903 Dihedral : 15.998 81.432 3873 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.00 % Favored : 95.74 % Rotamer: Outliers : 2.44 % Allowed : 29.40 % Favored : 68.16 % 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: 0.70 (0.17), residues: 2677 helix: 1.33 (0.14), residues: 1575 sheet: -1.02 (0.39), residues: 196 loop : -0.63 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 146 HIS 0.010 0.001 HIS W 162 PHE 0.027 0.002 PHE W 126 TYR 0.024 0.001 TYR U 103 ARG 0.008 0.000 ARG V 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5996.27 seconds wall clock time: 109 minutes 27.38 seconds (6567.38 seconds total)