Starting phenix.real_space_refine on Sat Jul 4 19:45:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fcv_28994/07_2026/8fcv_28994.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcv_28994/07_2026/8fcv_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/cci-nas-00/data/ceres_data/8fcv_28994/07_2026/8fcv_28994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcv_28994/07_2026/8fcv_28994.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fcv_28994/07_2026/8fcv_28994.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fcv_28994/07_2026/8fcv_28994.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fcv_28994/07_2026/8fcv_28994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcv_28994/07_2026/8fcv_28994.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 5.33, per 1000 atoms: 0.23 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 131 helices and 16 sheets defined 62.6% alpha, 6.0% beta 30 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'P' and resid 36 through 48 Processing helix chain 'P' and resid 51 through 65 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 69 through 74 Processing helix chain 'P' and resid 75 through 77 No H-bonds generated for 'chain 'P' and resid 75 through 77' Processing helix chain 'P' and resid 78 through 83 Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 95 through 110 Processing helix chain 'P' and resid 113 through 118 removed outlier: 3.604A pdb=" N THR P 118 " --> pdb=" O ARG P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 123 Processing helix chain 'P' and resid 139 through 149 Processing helix chain 'P' and resid 156 through 161 Processing helix chain 'P' and resid 214 through 235 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 removed outlier: 4.452A pdb=" N GLY P 235 " --> pdb=" O THR P 231 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 261 Processing helix chain 'P' and resid 263 through 281 removed outlier: 3.830A pdb=" N ASP P 267 " --> pdb=" O LYS P 263 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLY P 270 " --> pdb=" O GLY P 266 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE P 271 " --> pdb=" O ASP P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 300 Processing helix chain 'P' and resid 303 through 310 Processing helix chain 'P' and resid 311 through 323 Processing helix chain 'Q' and resid 8 through 13 removed outlier: 3.716A pdb=" N LEU Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 25 Processing helix chain 'Q' and resid 30 through 46 Processing helix chain 'Q' and resid 62 through 83 Proline residue: Q 80 - end of helix removed outlier: 4.384A pdb=" N GLU Q 83 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 117 removed outlier: 3.787A pdb=" N TYR Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 164 Processing helix chain 'Q' and resid 172 through 178 removed outlier: 3.534A pdb=" N LYS Q 178 " --> pdb=" O HIS Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 198 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) Processing helix chain 'Q' and resid 208 through 212 Processing helix chain 'Q' and resid 217 through 224 removed outlier: 3.904A pdb=" N LEU Q 221 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG Q 224 " --> pdb=" O GLN Q 220 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 254 Processing helix chain 'Q' and resid 266 through 273 removed outlier: 3.575A pdb=" N ARG Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 295 Processing helix chain 'Q' and resid 301 through 308 removed outlier: 3.867A pdb=" N ARG Q 308 " --> pdb=" O ASP Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 330 Processing helix chain 'R' and resid 8 through 13 removed outlier: 3.595A pdb=" N LEU R 11 " --> pdb=" O PRO R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 26 removed outlier: 3.505A pdb=" N ARG R 19 " --> pdb=" O PRO R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 46 removed outlier: 3.561A pdb=" N GLU R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 85 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 105 through 118 Processing helix chain 'R' and resid 148 through 164 Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.510A pdb=" N LYS R 178 " --> pdb=" O HIS R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 200 removed outlier: 3.528A pdb=" N ASP R 187 " --> pdb=" O TYR R 183 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET R 198 " --> pdb=" O SER R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 218 through 224 Processing helix chain 'R' and resid 237 through 254 removed outlier: 3.533A pdb=" N VAL R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 275 Processing helix chain 'R' and resid 277 through 296 Processing helix chain 'R' and resid 301 through 308 removed outlier: 3.507A pdb=" N LEU R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG R 308 " --> pdb=" O ASP R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 329 removed outlier: 3.849A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 343 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 8 through 14 removed outlier: 3.661A pdb=" N LEU S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 26 removed outlier: 3.502A pdb=" N ARG S 19 " --> pdb=" O PRO S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.610A pdb=" N GLU S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 Proline residue: S 80 - end of helix Processing helix chain 'S' and resid 105 through 118 Processing helix chain 'S' and resid 148 through 164 Processing helix chain 'S' and resid 172 through 178 removed outlier: 3.568A pdb=" N LYS S 178 " --> pdb=" O HIS S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 200 removed outlier: 3.832A pdb=" N ASP S 187 " --> pdb=" O TYR S 183 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET S 198 " --> pdb=" O SER S 194 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR S 199 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 215 Processing helix chain 'S' and resid 218 through 224 removed outlier: 3.734A pdb=" N ARG S 224 " --> pdb=" O GLN S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 254 Processing helix chain 'S' and resid 266 through 275 Processing helix chain 'S' and resid 277 through 295 removed outlier: 3.540A pdb=" N LEU S 281 " --> pdb=" O CYS S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 309 removed outlier: 3.612A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 329 Processing helix chain 'S' and resid 332 through 343 removed outlier: 3.658A pdb=" N VAL S 336 " --> pdb=" O THR S 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 13 removed outlier: 3.511A pdb=" N LEU T 12 " --> pdb=" O LEU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 26 removed outlier: 3.736A pdb=" N ARG T 19 " --> pdb=" O PRO T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 46 Processing helix chain 'T' and resid 62 through 85 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 105 through 118 removed outlier: 4.097A pdb=" N TYR T 109 " --> pdb=" O ASN T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 148 through 164 Processing helix chain 'T' and resid 172 through 178 removed outlier: 3.511A pdb=" N LYS T 178 " --> pdb=" O HIS T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 200 removed outlier: 3.519A pdb=" N LEU T 185 " --> pdb=" O SER T 181 " (cutoff:3.500A) 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 208 through 215 removed outlier: 3.507A pdb=" N THR T 213 " --> pdb=" O GLU T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 218 through 224 Processing helix chain 'T' and resid 237 through 254 Processing helix chain 'T' and resid 266 through 275 Processing helix chain 'T' and resid 277 through 296 Processing helix chain 'T' and resid 301 through 308 removed outlier: 3.550A pdb=" N ARG T 308 " --> pdb=" O ASP T 304 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 329 Processing helix chain 'T' and resid 332 through 343 removed outlier: 3.632A pdb=" N VAL T 336 " --> pdb=" O THR T 332 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 13 removed outlier: 3.574A pdb=" N LEU U 11 " --> pdb=" O PRO U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 26 removed outlier: 3.582A pdb=" N ARG U 19 " --> pdb=" O PRO U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 46 removed outlier: 3.590A pdb=" N GLU U 46 " --> pdb=" O ARG U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 85 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 105 through 118 Processing helix chain 'U' and resid 148 through 164 Processing helix chain 'U' and resid 172 through 178 Processing helix chain 'U' and resid 183 through 200 removed outlier: 3.726A pdb=" N ASP U 187 " --> pdb=" O TYR U 183 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET U 198 " --> pdb=" O SER U 194 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR U 199 " --> pdb=" O LEU U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 215 Processing helix chain 'U' and resid 218 through 224 Processing helix chain 'U' and resid 237 through 254 Processing helix chain 'U' and resid 263 through 265 No H-bonds generated for 'chain 'U' and resid 263 through 265' Processing helix chain 'U' and resid 266 through 275 removed outlier: 3.551A pdb=" N PHE U 270 " --> pdb=" O HIS U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 277 through 296 Processing helix chain 'U' and resid 301 through 308 removed outlier: 3.716A pdb=" N ARG U 308 " --> pdb=" O ASP U 304 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 329 Processing helix chain 'U' and resid 332 through 344 removed outlier: 3.751A pdb=" N VAL U 336 " --> pdb=" O THR U 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 13 removed outlier: 3.545A pdb=" N LEU V 11 " --> pdb=" O PRO V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 26 Processing helix chain 'V' and resid 30 through 46 removed outlier: 4.118A pdb=" N GLU V 46 " --> pdb=" O ARG V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 78 Processing helix chain 'V' and resid 78 through 85 Processing helix chain 'V' and resid 105 through 118 Processing helix chain 'V' and resid 148 through 164 Processing helix chain 'V' and resid 173 through 178 removed outlier: 3.754A pdb=" N LYS V 178 " --> pdb=" O HIS V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 200 removed outlier: 4.014A pdb=" N LEU V 189 " --> pdb=" O LEU V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 215 Processing helix chain 'V' and resid 217 through 224 removed outlier: 4.010A pdb=" N LEU V 221 " --> pdb=" O LEU V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 237 through 254 Processing helix chain 'V' and resid 266 through 275 Processing helix chain 'V' and resid 277 through 295 removed outlier: 3.623A pdb=" N ARG V 295 " --> pdb=" O ASP V 291 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 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 311 through 329 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 332 through 344 Processing helix chain 'W' and resid 8 through 12 removed outlier: 3.635A pdb=" N LEU W 11 " --> pdb=" O PRO W 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU W 12 " --> pdb=" O LEU W 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 8 through 12' Processing helix chain 'W' and resid 15 through 26 Processing helix chain 'W' and resid 30 through 46 removed outlier: 3.647A pdb=" N GLU W 46 " --> pdb=" O ARG W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 83 removed outlier: 3.648A pdb=" N LEU W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) Proline residue: W 80 - end of helix Processing helix chain 'W' and resid 105 through 118 Processing helix chain 'W' and resid 148 through 164 Processing helix chain 'W' and resid 172 through 177 removed outlier: 3.783A pdb=" N HIS W 175 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY W 177 " --> pdb=" O GLN W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 200 Processing helix chain 'W' and resid 208 through 215 removed outlier: 3.549A pdb=" N THR W 213 " --> pdb=" O GLU W 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 224 removed outlier: 3.606A pdb=" N ARG W 224 " --> pdb=" O GLN W 220 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 254 Processing helix chain 'W' and resid 263 through 265 No H-bonds generated for 'chain 'W' and resid 263 through 265' Processing helix chain 'W' and resid 266 through 275 Processing helix chain 'W' and resid 277 through 295 Processing helix chain 'W' and resid 301 through 308 removed outlier: 3.927A pdb=" N LEU W 305 " --> pdb=" O THR W 301 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN W 306 " --> pdb=" O LEU W 302 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 329 Processing helix chain 'W' and resid 332 through 343 Processing sheet with id=AA1, first strand: chain 'P' and resid 7 through 8 removed outlier: 3.544A pdb=" N TRP P 8 " --> pdb=" O THR Q 27 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR Q 27 " --> pdb=" O TRP P 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'P' and resid 166 through 167 removed outlier: 3.611A pdb=" N GLN P 172 " --> pdb=" O CYS P 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 55 through 57 Processing sheet with id=AA4, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.646A pdb=" N VAL Q 92 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP Q 171 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE Q 94 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE Q 168 " --> pdb=" O CYS Q 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'R' and resid 91 through 95 removed outlier: 3.572A pdb=" N VAL R 92 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE R 168 " --> pdb=" O CYS R 204 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU R 206 " --> pdb=" O PHE R 168 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL R 170 " --> pdb=" O LEU R 206 " (cutoff:3.500A) 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) Processing sheet with id=AA6, first strand: chain 'R' and resid 133 through 134 removed outlier: 3.790A pdb=" N SER R 134 " --> pdb=" O ASN R 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 91 through 95 removed outlier: 6.661A pdb=" N VAL S 92 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP S 171 " --> pdb=" O VAL S 92 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE S 94 " --> pdb=" O ASP S 171 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE S 53 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLY S 207 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL S 55 " --> pdb=" O GLY S 207 " (cutoff:3.500A) 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) Processing sheet with id=AA8, first strand: chain 'S' and resid 133 through 134 removed outlier: 3.550A pdb=" N SER S 134 " --> pdb=" O ASN S 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 91 through 95 Processing sheet with id=AB1, first strand: chain 'T' and resid 133 through 134 Processing sheet with id=AB2, first strand: chain 'U' and resid 91 through 95 removed outlier: 6.951A pdb=" N VAL U 92 " --> pdb=" O PHE U 169 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP U 171 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE U 94 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE U 53 " --> pdb=" O LEU U 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 133 through 134 Processing sheet with id=AB4, first strand: chain 'V' and resid 92 through 95 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) removed outlier: 6.198A pdb=" N ILE V 53 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY V 207 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL V 55 " --> pdb=" O GLY V 207 " (cutoff:3.500A) 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) Processing sheet with id=AB5, first strand: chain 'V' and resid 133 through 134 removed outlier: 3.836A pdb=" N SER V 134 " --> pdb=" O ASN V 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'W' and resid 92 through 94 removed outlier: 7.142A pdb=" N VAL W 92 " --> pdb=" O PHE W 169 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE W 53 " --> pdb=" O LEU W 205 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY W 207 " --> pdb=" O ILE W 53 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL W 55 " --> pdb=" O GLY W 207 " (cutoff:3.500A) 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) Processing sheet with id=AB7, first strand: chain 'W' and resid 133 through 135 1137 hydrogen bonds defined for protein. 3180 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: 4.30 Time building geometry restraints manager: 2.65 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=" C3' DC N 10 " pdb=" O3' DC N 10 " ideal model delta sigma weight residual 1.435 1.404 0.031 1.30e-02 5.92e+03 5.81e+00 bond pdb=" C3' DA N 3 " pdb=" C2' DA N 3 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.01e+00 bond pdb=" C1' DC O 68 " pdb=" N1 DC O 68 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.77e+00 bond pdb=" C1' DC O 76 " pdb=" N1 DC O 76 " ideal model delta sigma weight residual 1.468 1.497 -0.029 1.40e-02 5.10e+03 4.35e+00 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 ... (remaining 23711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 31485 1.69 - 3.39: 765 3.39 - 5.08: 95 5.08 - 6.77: 32 6.77 - 8.47: 14 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: 11651 17.65 - 35.30: 1656 35.30 - 52.95: 595 52.95 - 70.60: 142 70.60 - 88.25: 17 Dihedral angle restraints: 14061 sinusoidal: 6182 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 14058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2618 0.038 - 0.075: 740 0.075 - 0.113: 221 0.113 - 0.150: 48 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: 250 2.57 - 3.15: 19414 3.15 - 3.73: 39118 3.73 - 4.32: 51761 4.32 - 4.90: 83697 Nonbonded interactions: 194240 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 194235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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: 1.120 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.740 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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= 0.213 Angle : 0.637 8.469 32391 Z= 0.390 Chirality : 0.040 0.188 3630 Planarity : 0.004 0.054 3903 Dihedral : 18.721 88.253 8969 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.000 ARG V 131 TYR 0.019 0.001 TYR P 154 PHE 0.047 0.001 PHE V 126 TRP 0.017 0.001 TRP S 267 HIS 0.010 0.001 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.21 (23716) covalent geometry : angle 0.63723 / 0.39 (32391) hydrogen bonds : bond 0.17137 / 19.21 ( 1212) hydrogen bonds : angle 5.89098 / 6.59 ( 3330) *********************** 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 to be fit. rotamer outliers: 17 poor density : 333 time to evaluate : 0.947 Fit side-chains 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: 0.5623 (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: 0.8678 (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: 0.6658 (m-10) REVERT: S 324 GLU cc_start: 0.8316 (pp20) cc_final: 0.7864 (tm-30) 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: 0.7290 (mpp) outliers start: 17 outliers final: 4 residues processed: 346 average time/residue: 0.5168 time to fit residues: 211.6219 Evaluate side-chains 196 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 248 GLN ** Q 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 266 HIS T 25 ASN T 197 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 338 ASN V 314 GLN W 203 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.090286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062374 restraints weight = 73874.156| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.41 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23716 Z= 0.154 Angle : 0.647 11.040 32391 Z= 0.333 Chirality : 0.042 0.211 3630 Planarity : 0.005 0.044 3903 Dihedral : 15.667 72.610 3662 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.62 % Favored : 96.08 % Rotamer: Outliers : 3.72 % Allowed : 25.42 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2677 helix: 1.26 (0.13), residues: 1605 sheet: -0.81 (0.40), residues: 191 loop : -0.90 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 133 TYR 0.023 0.001 TYR U 103 PHE 0.037 0.002 PHE P 308 TRP 0.012 0.001 TRP P 146 HIS 0.015 0.001 HIS W 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (23716) covalent geometry : angle 0.64739 / 0.33 (32391) hydrogen bonds : bond 0.05051 / 5.47 ( 1212) hydrogen bonds : angle 4.64722 / 5.50 ( 3330) *********************** 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 294 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 207 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 119 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8243 (tm) REVERT: P 135 TYR cc_start: 0.8559 (m-80) cc_final: 0.7942 (m-80) REVERT: P 154 TYR cc_start: 0.8774 (p90) cc_final: 0.8456 (p90) REVERT: P 155 GLU cc_start: 0.8837 (mp0) cc_final: 0.8564 (mp0) REVERT: P 161 PHE cc_start: 0.9147 (m-80) cc_final: 0.8946 (m-80) REVERT: P 166 PHE cc_start: 0.8530 (m-80) cc_final: 0.6076 (m-80) REVERT: P 173 ARG cc_start: 0.9263 (tpp80) cc_final: 0.8669 (ttm-80) REVERT: P 180 HIS cc_start: 0.9113 (m-70) cc_final: 0.8742 (m-70) REVERT: Q 41 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8869 (mmm) REVERT: Q 71 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8449 (mt-10) REVERT: Q 164 HIS cc_start: 0.8513 (t70) cc_final: 0.8165 (t-90) REVERT: Q 172 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8317 (mp0) REVERT: Q 188 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8607 (mm110) REVERT: Q 321 GLU cc_start: 0.8858 (tt0) cc_final: 0.8325 (tm-30) REVERT: R 138 PHE cc_start: 0.8993 (m-80) cc_final: 0.8698 (m-80) REVERT: R 321 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8478 (pp20) REVERT: R 324 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8322 (tm-30) REVERT: S 9 LEU cc_start: 0.8936 (pt) cc_final: 0.8702 (mm) REVERT: S 24 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8767 (tm-30) REVERT: S 124 HIS cc_start: 0.8091 (m90) cc_final: 0.7888 (m170) REVERT: S 302 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7701 (tp) REVERT: S 306 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8655 (mp10) REVERT: T 108 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8503 (tp30) REVERT: T 189 LEU cc_start: 0.9205 (tp) cc_final: 0.8947 (tp) REVERT: T 210 GLU cc_start: 0.8675 (pt0) cc_final: 0.8117 (tm-30) REVERT: U 25 ASN cc_start: 0.9133 (m-40) cc_final: 0.8565 (m-40) REVERT: U 95 GLU cc_start: 0.8112 (pm20) cc_final: 0.7891 (pm20) REVERT: U 142 ASN cc_start: 0.7272 (m-40) cc_final: 0.6958 (m110) REVERT: U 338 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8936 (m110) REVERT: V 24 GLU cc_start: 0.9254 (tp30) cc_final: 0.9009 (tp30) REVERT: W 41 MET cc_start: 0.9172 (mmm) cc_final: 0.8954 (mmm) REVERT: W 56 TYR cc_start: 0.7246 (m-80) cc_final: 0.6600 (m-80) REVERT: W 97 ILE cc_start: 0.8520 (pt) cc_final: 0.8280 (tt) REVERT: W 175 HIS cc_start: 0.9029 (m-70) cc_final: 0.8555 (m-70) REVERT: W 186 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8192 (tm-30) outliers start: 87 outliers final: 26 residues processed: 277 average time/residue: 0.4871 time to fit residues: 161.1577 Evaluate side-chains 204 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 217 TYR Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 213 THR Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 343 LEU Chi-restraints excluded: chain T residue 108 GLU 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 198 MET Chi-restraints excluded: chain U residue 286 LYS Chi-restraints excluded: chain U residue 338 ASN Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 102 ARG Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 260 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 215 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 203 HIS ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 338 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.087554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059692 restraints weight = 74162.231| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.37 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23716 Z= 0.229 Angle : 0.639 8.893 32391 Z= 0.332 Chirality : 0.043 0.200 3630 Planarity : 0.004 0.063 3903 Dihedral : 15.717 63.398 3660 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.62 % Favored : 96.08 % Rotamer: Outliers : 3.94 % Allowed : 25.29 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.17), residues: 2677 helix: 1.30 (0.13), residues: 1611 sheet: -1.03 (0.38), residues: 193 loop : -0.85 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 184 TYR 0.023 0.001 TYR U 103 PHE 0.022 0.002 PHE S 126 TRP 0.014 0.001 TRP V 106 HIS 0.014 0.001 HIS W 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (23716) covalent geometry : angle 0.63918 / 0.33 (32391) hydrogen bonds : bond 0.04682 / 5.08 ( 1212) hydrogen bonds : angle 4.38202 / 5.26 ( 3330) *********************** 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 271 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 179 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 94 MET cc_start: 0.7979 (pmt) cc_final: 0.7162 (pmm) REVERT: P 119 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7645 (tm) REVERT: P 120 LEU cc_start: 0.8298 (pt) cc_final: 0.7630 (mt) REVERT: P 122 TRP cc_start: 0.7825 (m100) cc_final: 0.7374 (m100) REVERT: P 154 TYR cc_start: 0.8817 (p90) cc_final: 0.8465 (p90) REVERT: P 155 GLU cc_start: 0.8907 (mp0) cc_final: 0.8377 (mp0) REVERT: P 180 HIS cc_start: 0.9188 (m-70) cc_final: 0.8761 (m-70) REVERT: Q 71 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8573 (mt-10) REVERT: Q 164 HIS cc_start: 0.8563 (t70) cc_final: 0.8237 (t-90) REVERT: Q 172 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8426 (mp0) REVERT: Q 188 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8653 (mm110) REVERT: Q 321 GLU cc_start: 0.8923 (tt0) cc_final: 0.8327 (tm-30) REVERT: R 137 ASN cc_start: 0.8906 (p0) cc_final: 0.8705 (p0) REVERT: R 138 PHE cc_start: 0.9029 (m-80) cc_final: 0.8712 (m-10) REVERT: R 187 ASP cc_start: 0.9174 (m-30) cc_final: 0.8861 (m-30) REVERT: R 318 MET cc_start: 0.8333 (mmt) cc_final: 0.8116 (mtt) REVERT: R 321 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8439 (tm-30) REVERT: R 324 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8459 (tm-30) REVERT: S 9 LEU cc_start: 0.8989 (pt) cc_final: 0.8751 (mm) REVERT: S 128 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: S 306 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8658 (mp10) REVERT: T 108 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8546 (tp30) REVERT: T 210 GLU cc_start: 0.8725 (pt0) cc_final: 0.8234 (tm-30) REVERT: T 289 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9111 (tt) REVERT: T 293 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8932 (mm) REVERT: U 24 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8084 (pp20) REVERT: U 25 ASN cc_start: 0.8984 (m-40) cc_final: 0.8394 (m-40) REVERT: U 142 ASN cc_start: 0.7161 (m110) cc_final: 0.6795 (m110) REVERT: V 24 GLU cc_start: 0.9248 (tp30) cc_final: 0.9016 (tp30) REVERT: V 95 GLU cc_start: 0.8095 (pm20) cc_final: 0.7783 (pp20) REVERT: W 41 MET cc_start: 0.9179 (mmm) cc_final: 0.8975 (mmm) REVERT: W 56 TYR cc_start: 0.7433 (m-80) cc_final: 0.6698 (m-80) REVERT: W 97 ILE cc_start: 0.8687 (pt) cc_final: 0.8371 (tt) REVERT: W 175 HIS cc_start: 0.9073 (m-70) cc_final: 0.8552 (m-70) REVERT: W 188 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8917 (mm110) REVERT: W 198 MET cc_start: 0.7533 (mpp) cc_final: 0.7217 (mtm) outliers start: 92 outliers final: 34 residues processed: 256 average time/residue: 0.4705 time to fit residues: 145.4765 Evaluate side-chains 207 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 80 HIS Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 343 LEU Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 315 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 65 THR Chi-restraints excluded: chain W residue 102 ARG Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 226 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 152 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 188 optimal weight: 0.1980 chunk 159 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 252 GLN T 197 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.088196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060155 restraints weight = 73728.767| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.38 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23716 Z= 0.141 Angle : 0.589 8.894 32391 Z= 0.300 Chirality : 0.041 0.221 3630 Planarity : 0.004 0.044 3903 Dihedral : 15.657 63.789 3657 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.51 % Favored : 96.23 % Rotamer: Outliers : 3.25 % Allowed : 26.06 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2677 helix: 1.38 (0.13), residues: 1611 sheet: -1.09 (0.38), residues: 191 loop : -0.84 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 131 TYR 0.024 0.001 TYR U 103 PHE 0.015 0.001 PHE U 126 TRP 0.011 0.001 TRP P 122 HIS 0.007 0.001 HIS W 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (23716) covalent geometry : angle 0.58949 / 0.30 (32391) hydrogen bonds : bond 0.04113 / 4.43 ( 1212) hydrogen bonds : angle 4.18916 / 5.05 ( 3330) *********************** 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 262 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 186 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 57 MET cc_start: 0.7940 (pp-130) cc_final: 0.7738 (pp-130) REVERT: P 94 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7190 (pmm) REVERT: P 119 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7669 (tm) REVERT: P 120 LEU cc_start: 0.8350 (pt) cc_final: 0.7702 (mt) REVERT: P 122 TRP cc_start: 0.7527 (m100) cc_final: 0.7121 (m100) REVERT: P 154 TYR cc_start: 0.8834 (p90) cc_final: 0.8415 (p90) REVERT: P 155 GLU cc_start: 0.8922 (mp0) cc_final: 0.8497 (mp0) REVERT: P 180 HIS cc_start: 0.9174 (m-70) cc_final: 0.8721 (m-70) REVERT: Q 56 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: Q 71 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8464 (mt-10) REVERT: Q 164 HIS cc_start: 0.8582 (t70) cc_final: 0.8237 (t-90) REVERT: Q 172 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8356 (mp0) REVERT: Q 188 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8629 (mm110) REVERT: Q 210 GLU cc_start: 0.8967 (mp0) cc_final: 0.8657 (mp0) REVERT: Q 321 GLU cc_start: 0.8931 (tt0) cc_final: 0.8317 (tm-30) REVERT: R 137 ASN cc_start: 0.8802 (p0) cc_final: 0.8589 (p0) REVERT: R 138 PHE cc_start: 0.9042 (m-80) cc_final: 0.8705 (m-10) REVERT: R 188 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8780 (mm-40) REVERT: R 324 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8327 (tm-30) REVERT: S 9 LEU cc_start: 0.8970 (pt) cc_final: 0.8728 (mm) REVERT: S 102 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8404 (mmm160) REVERT: S 128 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: T 108 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8513 (tp30) REVERT: T 189 LEU cc_start: 0.9208 (tp) cc_final: 0.9000 (tp) REVERT: T 210 GLU cc_start: 0.8699 (pt0) cc_final: 0.8093 (tm-30) REVERT: T 318 MET cc_start: 0.8442 (mtt) cc_final: 0.8193 (mmm) REVERT: U 25 ASN cc_start: 0.8998 (m-40) cc_final: 0.8740 (m-40) REVERT: U 142 ASN cc_start: 0.7143 (m110) cc_final: 0.6747 (m110) REVERT: U 146 LYS cc_start: 0.9326 (mppt) cc_final: 0.9077 (mtpt) REVERT: V 24 GLU cc_start: 0.9227 (tp30) cc_final: 0.8989 (tp30) REVERT: V 95 GLU cc_start: 0.8146 (pm20) cc_final: 0.7749 (pp20) REVERT: V 142 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7385 (p0) REVERT: W 41 MET cc_start: 0.9164 (mmm) cc_final: 0.8898 (mmm) REVERT: W 97 ILE cc_start: 0.8689 (pt) cc_final: 0.8377 (tt) REVERT: W 175 HIS cc_start: 0.9033 (m-70) cc_final: 0.8488 (m-70) REVERT: W 262 ASN cc_start: 0.9259 (t0) cc_final: 0.9046 (t0) outliers start: 76 outliers final: 39 residues processed: 244 average time/residue: 0.4758 time to fit residues: 139.7899 Evaluate side-chains 211 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 217 TYR Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain P residue 290 VAL Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain T residue 305 LEU 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 198 MET Chi-restraints excluded: chain U residue 286 LYS Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 260 THR Chi-restraints excluded: chain W residue 304 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 102 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 241 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 30 optimal weight: 40.0000 chunk 234 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN U 203 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.086424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058455 restraints weight = 73974.731| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.33 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23716 Z= 0.223 Angle : 0.622 9.063 32391 Z= 0.317 Chirality : 0.042 0.171 3630 Planarity : 0.004 0.094 3903 Dihedral : 15.644 63.982 3657 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.62 % Favored : 96.12 % Rotamer: Outliers : 3.85 % Allowed : 25.97 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2677 helix: 1.37 (0.13), residues: 1621 sheet: -1.17 (0.37), residues: 191 loop : -0.77 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG W 102 TYR 0.023 0.001 TYR U 103 PHE 0.035 0.002 PHE W 126 TRP 0.014 0.001 TRP P 122 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (23716) covalent geometry : angle 0.62218 / 0.32 (32391) hydrogen bonds : bond 0.04258 / 4.60 ( 1212) hydrogen bonds : angle 4.12708 / 4.98 ( 3330) *********************** 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 to be fit. rotamer outliers: 90 poor density : 174 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8663 (tp) REVERT: P 94 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7200 (pmm) REVERT: P 119 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7570 (tm) REVERT: P 120 LEU cc_start: 0.8394 (pt) cc_final: 0.7729 (mt) REVERT: P 122 TRP cc_start: 0.7478 (m100) cc_final: 0.6729 (m100) REVERT: P 147 MET cc_start: 0.8482 (tmt) cc_final: 0.8001 (tmt) REVERT: P 154 TYR cc_start: 0.8915 (p90) cc_final: 0.8501 (p90) REVERT: P 155 GLU cc_start: 0.8973 (mp0) cc_final: 0.8696 (mp0) REVERT: P 180 HIS cc_start: 0.9161 (m-70) cc_final: 0.8675 (m-70) REVERT: Q 56 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: Q 71 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8479 (mt-10) REVERT: Q 164 HIS cc_start: 0.8618 (t70) cc_final: 0.8283 (t-90) REVERT: Q 172 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8669 (mp0) REVERT: Q 188 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8666 (mm110) REVERT: Q 210 GLU cc_start: 0.8946 (mp0) cc_final: 0.8632 (mp0) REVERT: Q 321 GLU cc_start: 0.8979 (tt0) cc_final: 0.8355 (tm-30) REVERT: R 18 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: R 137 ASN cc_start: 0.8861 (p0) cc_final: 0.8642 (p0) REVERT: R 138 PHE cc_start: 0.9070 (m-80) cc_final: 0.8711 (m-10) REVERT: R 187 ASP cc_start: 0.9178 (m-30) cc_final: 0.8883 (m-30) REVERT: R 324 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8368 (tm-30) REVERT: S 9 LEU cc_start: 0.8997 (pt) cc_final: 0.8707 (mm) REVERT: S 102 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8327 (ttm110) REVERT: S 128 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: T 210 GLU cc_start: 0.8738 (pt0) cc_final: 0.8027 (tm-30) REVERT: U 19 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8497 (mtm180) REVERT: U 24 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8154 (pp20) REVERT: U 25 ASN cc_start: 0.9128 (m-40) cc_final: 0.8464 (m-40) REVERT: U 142 ASN cc_start: 0.7234 (m110) cc_final: 0.6857 (m110) REVERT: V 41 MET cc_start: 0.9129 (tpp) cc_final: 0.8799 (mmm) REVERT: V 95 GLU cc_start: 0.8387 (pm20) cc_final: 0.7906 (pp20) REVERT: W 41 MET cc_start: 0.9204 (mmm) cc_final: 0.8993 (mmm) REVERT: W 97 ILE cc_start: 0.8752 (pt) cc_final: 0.8368 (tt) REVERT: W 131 ARG cc_start: 0.8227 (mpt180) cc_final: 0.7818 (mmp80) REVERT: W 175 HIS cc_start: 0.9048 (m-70) cc_final: 0.8455 (m-70) REVERT: W 188 GLN cc_start: 0.9245 (mp-120) cc_final: 0.8970 (mm110) REVERT: W 198 MET cc_start: 0.7686 (mtm) cc_final: 0.7435 (mtm) REVERT: W 262 ASN cc_start: 0.9280 (t0) cc_final: 0.9069 (t0) outliers start: 90 outliers final: 48 residues processed: 251 average time/residue: 0.5114 time to fit residues: 152.3094 Evaluate side-chains 214 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain P residue 290 VAL Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER 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 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 189 LEU 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 145 SER 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 234 CYS Chi-restraints excluded: chain V residue 275 LEU 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 65 THR Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 221 LEU Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 260 THR Chi-restraints excluded: chain W residue 263 LEU Chi-restraints excluded: chain W residue 304 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 124 HIS ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.087744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.060107 restraints weight = 74102.176| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.34 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2583 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= 0.126 Angle : 0.604 10.467 32391 Z= 0.302 Chirality : 0.041 0.217 3630 Planarity : 0.004 0.047 3903 Dihedral : 15.577 64.134 3657 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.74 % Favored : 96.00 % Rotamer: Outliers : 3.21 % Allowed : 27.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.17), residues: 2677 helix: 1.45 (0.13), residues: 1615 sheet: -1.25 (0.37), residues: 196 loop : -0.75 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 131 TYR 0.024 0.001 TYR U 103 PHE 0.024 0.001 PHE P 161 TRP 0.013 0.001 TRP P 146 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (23716) covalent geometry : angle 0.60388 / 0.30 (32391) hydrogen bonds : bond 0.03799 / 4.08 ( 1212) hydrogen bonds : angle 3.97510 / 4.82 ( 3330) *********************** 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 257 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 182 time to evaluate : 0.897 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 94 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7379 (pmm) REVERT: P 119 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7571 (tm) REVERT: P 120 LEU cc_start: 0.8444 (pt) cc_final: 0.7789 (mt) REVERT: P 122 TRP cc_start: 0.7557 (m100) cc_final: 0.6914 (m100) REVERT: P 147 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7923 (tmt) REVERT: P 154 TYR cc_start: 0.8833 (p90) cc_final: 0.8427 (p90) REVERT: P 155 GLU cc_start: 0.8999 (mp0) cc_final: 0.8613 (mp0) REVERT: P 166 PHE cc_start: 0.9026 (m-80) cc_final: 0.8815 (m-80) REVERT: P 180 HIS cc_start: 0.9172 (m-70) cc_final: 0.8680 (m-70) REVERT: Q 56 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: Q 71 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8435 (mt-10) REVERT: Q 164 HIS cc_start: 0.8614 (t70) cc_final: 0.8303 (t-90) REVERT: Q 172 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8637 (mp0) REVERT: Q 188 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8616 (mm110) REVERT: Q 210 GLU cc_start: 0.8980 (mp0) cc_final: 0.8636 (mp0) REVERT: Q 321 GLU cc_start: 0.8966 (tt0) cc_final: 0.8338 (tm-30) REVERT: R 18 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: R 82 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8381 (pp) REVERT: R 137 ASN cc_start: 0.8860 (p0) cc_final: 0.8649 (p0) REVERT: R 138 PHE cc_start: 0.9078 (m-80) cc_final: 0.8732 (m-10) REVERT: R 187 ASP cc_start: 0.9230 (m-30) cc_final: 0.8898 (m-30) REVERT: R 324 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8312 (tm-30) REVERT: S 9 LEU cc_start: 0.8985 (pt) cc_final: 0.8703 (mm) REVERT: S 102 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8124 (ttm110) REVERT: S 128 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: T 108 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: T 189 LEU cc_start: 0.9183 (tp) cc_final: 0.8982 (tp) REVERT: T 210 GLU cc_start: 0.8766 (pt0) cc_final: 0.8064 (tm-30) REVERT: U 19 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8501 (mtm180) REVERT: U 24 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8199 (pp20) REVERT: U 95 GLU cc_start: 0.7860 (pm20) cc_final: 0.7229 (pm20) REVERT: U 146 LYS cc_start: 0.9275 (mppt) cc_final: 0.8996 (mtpt) REVERT: V 41 MET cc_start: 0.9101 (tpp) cc_final: 0.8786 (mmm) REVERT: V 128 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: W 41 MET cc_start: 0.9182 (mmm) cc_final: 0.8922 (mmm) REVERT: W 97 ILE cc_start: 0.8637 (pt) cc_final: 0.8248 (tt) REVERT: W 102 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6571 (ppt170) REVERT: W 103 TYR cc_start: 0.8927 (m-80) cc_final: 0.8332 (m-80) REVERT: W 175 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8444 (m-70) REVERT: W 188 GLN cc_start: 0.9191 (mp-120) cc_final: 0.8924 (mm110) REVERT: W 262 ASN cc_start: 0.9236 (t0) cc_final: 0.9008 (t0) outliers start: 75 outliers final: 38 residues processed: 241 average time/residue: 0.4928 time to fit residues: 142.2218 Evaluate side-chains 221 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 147 MET Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain T residue 285 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 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU 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 102 ARG Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 175 HIS Chi-restraints excluded: chain W residue 260 THR Chi-restraints excluded: chain W residue 304 ASP Chi-restraints excluded: chain W residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 141 optimal weight: 0.0980 chunk 205 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 162 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.087822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060189 restraints weight = 73348.316| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.31 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23716 Z= 0.127 Angle : 0.592 9.625 32391 Z= 0.296 Chirality : 0.041 0.200 3630 Planarity : 0.004 0.045 3903 Dihedral : 15.487 64.191 3657 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.04 % Rotamer: Outliers : 3.00 % Allowed : 27.21 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.17), residues: 2677 helix: 1.51 (0.13), residues: 1614 sheet: -1.24 (0.37), residues: 196 loop : -0.76 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 131 TYR 0.024 0.001 TYR U 103 PHE 0.048 0.001 PHE W 126 TRP 0.013 0.001 TRP P 146 HIS 0.005 0.001 HIS W 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (23716) covalent geometry : angle 0.59153 / 0.30 (32391) hydrogen bonds : bond 0.03744 / 4.02 ( 1212) hydrogen bonds : angle 3.90616 / 4.74 ( 3330) *********************** 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 249 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 179 time to evaluate : 0.860 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: 0.9092 (OUTLIER) cc_final: 0.8660 (tp) REVERT: P 94 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7359 (pmm) REVERT: P 119 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7474 (tm) REVERT: P 120 LEU cc_start: 0.8476 (pt) cc_final: 0.7779 (mt) REVERT: P 122 TRP cc_start: 0.7648 (m100) cc_final: 0.6930 (m100) REVERT: P 147 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7886 (tmt) REVERT: P 154 TYR cc_start: 0.8844 (p90) cc_final: 0.8383 (p90) REVERT: P 155 GLU cc_start: 0.9010 (mp0) cc_final: 0.8729 (mp0) REVERT: P 180 HIS cc_start: 0.9197 (m-70) cc_final: 0.8697 (m-70) REVERT: Q 56 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: Q 71 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8452 (mt-10) REVERT: Q 95 GLU cc_start: 0.7843 (pm20) cc_final: 0.7495 (pm20) REVERT: Q 164 HIS cc_start: 0.8601 (t70) cc_final: 0.8296 (t-90) REVERT: Q 172 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8644 (mp0) REVERT: Q 188 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8623 (mm110) REVERT: Q 198 MET cc_start: 0.8868 (mpm) cc_final: 0.8166 (tmm) REVERT: Q 210 GLU cc_start: 0.8972 (mp0) cc_final: 0.8612 (mp0) REVERT: Q 321 GLU cc_start: 0.8972 (tt0) cc_final: 0.8342 (tm-30) REVERT: R 18 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8564 (mp0) REVERT: R 82 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8414 (pp) REVERT: R 137 ASN cc_start: 0.8856 (p0) cc_final: 0.8637 (p0) REVERT: R 138 PHE cc_start: 0.9077 (m-80) cc_final: 0.8740 (m-10) REVERT: R 324 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8366 (tm-30) REVERT: S 9 LEU cc_start: 0.9004 (pt) cc_final: 0.8735 (mm) REVERT: S 102 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8255 (ttm110) REVERT: S 128 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: T 189 LEU cc_start: 0.9201 (tp) cc_final: 0.8998 (tp) REVERT: T 210 GLU cc_start: 0.8732 (pt0) cc_final: 0.8066 (tm-30) REVERT: U 19 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8549 (mtm180) REVERT: U 25 ASN cc_start: 0.9117 (m-40) cc_final: 0.8791 (m-40) REVERT: V 41 MET cc_start: 0.9090 (tpp) cc_final: 0.8766 (mmm) REVERT: V 128 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: W 41 MET cc_start: 0.9178 (mmm) cc_final: 0.8854 (mmm) REVERT: W 97 ILE cc_start: 0.8523 (pt) cc_final: 0.8142 (tt) REVERT: W 131 ARG cc_start: 0.8258 (mpt180) cc_final: 0.8021 (mmt90) REVERT: W 175 HIS cc_start: 0.9076 (m-70) cc_final: 0.8510 (m-70) REVERT: W 188 GLN cc_start: 0.9164 (mp-120) cc_final: 0.8898 (mm110) REVERT: W 262 ASN cc_start: 0.9228 (t0) cc_final: 0.8958 (t0) outliers start: 70 outliers final: 37 residues processed: 236 average time/residue: 0.5135 time to fit residues: 144.1571 Evaluate side-chains 214 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 147 MET Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain Q residue 260 THR 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 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 225 SER 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 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 250 optimal weight: 0.0670 chunk 272 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 162 HIS ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.086988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060096 restraints weight = 72669.035| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.14 r_work: 0.2871 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23716 Z= 0.153 Angle : 0.616 12.307 32391 Z= 0.309 Chirality : 0.041 0.185 3630 Planarity : 0.004 0.045 3903 Dihedral : 15.452 64.473 3656 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.66 % Favored : 96.08 % Rotamer: Outliers : 3.12 % Allowed : 27.39 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2677 helix: 1.50 (0.13), residues: 1622 sheet: -1.18 (0.37), residues: 196 loop : -0.72 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG U 131 TYR 0.024 0.001 TYR U 103 PHE 0.037 0.001 PHE W 126 TRP 0.015 0.001 TRP P 146 HIS 0.004 0.001 HIS W 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (23716) covalent geometry : angle 0.61641 / 0.31 (32391) hydrogen bonds : bond 0.03771 / 4.04 ( 1212) hydrogen bonds : angle 3.88670 / 4.73 ( 3330) *********************** 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 252 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 179 time to evaluate : 0.887 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: 0.9134 (OUTLIER) cc_final: 0.8767 (tp) REVERT: P 94 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7609 (pmm) REVERT: P 118 THR cc_start: 0.7456 (t) cc_final: 0.6346 (m) REVERT: P 119 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7547 (tm) REVERT: P 120 LEU cc_start: 0.8461 (pt) cc_final: 0.7790 (mt) REVERT: P 122 TRP cc_start: 0.7791 (m100) cc_final: 0.7131 (m100) REVERT: P 147 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7876 (tmt) REVERT: P 154 TYR cc_start: 0.8941 (p90) cc_final: 0.8425 (p90) REVERT: P 155 GLU cc_start: 0.9040 (mp0) cc_final: 0.8752 (mp0) REVERT: P 166 PHE cc_start: 0.9382 (m-80) cc_final: 0.7960 (m-80) REVERT: P 180 HIS cc_start: 0.9168 (m-70) cc_final: 0.8668 (m-70) REVERT: Q 56 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: Q 71 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8637 (mt-10) REVERT: Q 164 HIS cc_start: 0.8798 (t70) cc_final: 0.8524 (t-90) REVERT: Q 172 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8806 (mp0) REVERT: Q 188 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8491 (mm110) REVERT: Q 198 MET cc_start: 0.9125 (mpm) cc_final: 0.8244 (tmm) REVERT: Q 321 GLU cc_start: 0.9061 (tt0) cc_final: 0.8425 (tm-30) REVERT: R 18 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: R 82 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8325 (pp) REVERT: R 138 PHE cc_start: 0.9128 (m-80) cc_final: 0.8770 (m-10) REVERT: R 190 ASP cc_start: 0.8871 (m-30) cc_final: 0.8543 (m-30) REVERT: R 324 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8579 (tm-30) REVERT: S 9 LEU cc_start: 0.9017 (pt) cc_final: 0.8741 (mm) REVERT: S 102 ARG cc_start: 0.9063 (ttm110) cc_final: 0.8610 (ttm110) REVERT: S 128 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: S 166 ASP cc_start: 0.9230 (m-30) cc_final: 0.8959 (m-30) REVERT: T 189 LEU cc_start: 0.9307 (tp) cc_final: 0.9089 (tp) REVERT: T 210 GLU cc_start: 0.8974 (pt0) cc_final: 0.8260 (tm-30) REVERT: U 19 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8563 (mtm180) REVERT: U 24 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8399 (pp20) REVERT: U 25 ASN cc_start: 0.9382 (m-40) cc_final: 0.8781 (m-40) REVERT: U 95 GLU cc_start: 0.8402 (pm20) cc_final: 0.7830 (pm20) REVERT: U 146 LYS cc_start: 0.9366 (mppt) cc_final: 0.9109 (mtpt) REVERT: V 95 GLU cc_start: 0.8801 (pm20) cc_final: 0.8075 (pp20) REVERT: V 128 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: W 41 MET cc_start: 0.9229 (mmm) cc_final: 0.8923 (mmm) REVERT: W 56 TYR cc_start: 0.7535 (m-80) cc_final: 0.7311 (m-80) REVERT: W 97 ILE cc_start: 0.8475 (pt) cc_final: 0.8051 (tt) REVERT: W 175 HIS cc_start: 0.9191 (m-70) cc_final: 0.8668 (m-70) REVERT: W 188 GLN cc_start: 0.9287 (mp-120) cc_final: 0.8989 (mm110) REVERT: W 262 ASN cc_start: 0.9246 (t0) cc_final: 0.8991 (t0) outliers start: 73 outliers final: 42 residues processed: 238 average time/residue: 0.4811 time to fit residues: 137.3793 Evaluate side-chains 216 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 147 MET Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 25 ASN Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain T residue 285 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 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 123 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 160 optimal weight: 0.0070 chunk 222 optimal weight: 8.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 162 HIS ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.086418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.058512 restraints weight = 74598.782| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.36 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23716 Z= 0.202 Angle : 0.631 11.151 32391 Z= 0.320 Chirality : 0.042 0.179 3630 Planarity : 0.004 0.046 3903 Dihedral : 15.465 64.848 3656 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.77 % Favored : 95.97 % Rotamer: Outliers : 2.91 % Allowed : 27.81 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2677 helix: 1.54 (0.13), residues: 1615 sheet: -1.15 (0.38), residues: 196 loop : -0.75 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG U 131 TYR 0.023 0.001 TYR S 56 PHE 0.034 0.001 PHE W 126 TRP 0.018 0.001 TRP P 146 HIS 0.005 0.001 HIS W 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (23716) covalent geometry : angle 0.63108 / 0.32 (32391) hydrogen bonds : bond 0.03962 / 4.27 ( 1212) hydrogen bonds : angle 3.94385 / 4.80 ( 3330) *********************** 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 237 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 169 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 57 MET cc_start: 0.8107 (tmm) cc_final: 0.7699 (tmm) REVERT: P 65 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8715 (tp) REVERT: P 94 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7475 (pmm) REVERT: P 118 THR cc_start: 0.7486 (t) cc_final: 0.6444 (m) REVERT: P 119 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7496 (tm) REVERT: P 120 LEU cc_start: 0.8559 (pt) cc_final: 0.7949 (mt) REVERT: P 122 TRP cc_start: 0.7886 (m100) cc_final: 0.7147 (m100) REVERT: P 147 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7795 (tmt) REVERT: P 154 TYR cc_start: 0.8866 (p90) cc_final: 0.8407 (p90) REVERT: P 155 GLU cc_start: 0.9013 (mp0) cc_final: 0.8708 (mp0) REVERT: P 180 HIS cc_start: 0.9169 (m-70) cc_final: 0.8663 (m-70) REVERT: Q 56 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: Q 71 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8455 (mt-10) REVERT: Q 164 HIS cc_start: 0.8625 (t70) cc_final: 0.8329 (t-90) REVERT: Q 172 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8690 (mp0) REVERT: Q 188 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8674 (mm110) REVERT: Q 321 GLU cc_start: 0.9036 (tt0) cc_final: 0.8409 (tm-30) REVERT: R 18 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: R 82 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8384 (pp) REVERT: R 138 PHE cc_start: 0.9157 (m-80) cc_final: 0.8747 (m-10) REVERT: R 324 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8393 (tm-30) REVERT: S 102 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8251 (ttm110) REVERT: S 128 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: S 166 ASP cc_start: 0.8792 (m-30) cc_final: 0.8495 (m-30) REVERT: T 89 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8434 (m) REVERT: T 210 GLU cc_start: 0.8791 (pt0) cc_final: 0.8082 (tm-30) REVERT: U 19 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8542 (mtm180) REVERT: U 24 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8098 (pp20) REVERT: U 25 ASN cc_start: 0.9185 (m-40) cc_final: 0.8504 (m-40) REVERT: U 95 GLU cc_start: 0.7832 (pm20) cc_final: 0.7282 (pm20) REVERT: U 146 LYS cc_start: 0.9254 (mppt) cc_final: 0.9021 (mtpt) REVERT: V 41 MET cc_start: 0.8928 (mmm) cc_final: 0.8660 (mmm) REVERT: V 95 GLU cc_start: 0.8195 (pm20) cc_final: 0.7458 (pp20) REVERT: V 128 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: W 41 MET cc_start: 0.9214 (mmm) cc_final: 0.8954 (mmm) REVERT: W 97 ILE cc_start: 0.8650 (pt) cc_final: 0.8249 (tt) REVERT: W 175 HIS cc_start: 0.9137 (m-70) cc_final: 0.8629 (m-70) REVERT: W 188 GLN cc_start: 0.9207 (mp-120) cc_final: 0.8898 (mm110) REVERT: W 262 ASN cc_start: 0.9233 (t0) cc_final: 0.8961 (t0) outliers start: 68 outliers final: 45 residues processed: 226 average time/residue: 0.4598 time to fit residues: 124.5403 Evaluate side-chains 215 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 147 MET Chi-restraints excluded: chain P residue 167 CYS Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain Q residue 260 THR 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 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 89 VAL 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 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain W residue 260 THR Chi-restraints excluded: chain W residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 250 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 144 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 40.0000 chunk 264 optimal weight: 9.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.086556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.058726 restraints weight = 74038.294| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.32 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23716 Z= 0.164 Angle : 0.629 12.423 32391 Z= 0.317 Chirality : 0.041 0.188 3630 Planarity : 0.004 0.046 3903 Dihedral : 15.455 65.302 3656 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.04 % Rotamer: Outliers : 2.48 % Allowed : 28.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2677 helix: 1.56 (0.13), residues: 1599 sheet: -1.14 (0.38), residues: 196 loop : -0.67 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG U 131 TYR 0.023 0.001 TYR U 103 PHE 0.033 0.001 PHE W 126 TRP 0.019 0.001 TRP P 146 HIS 0.008 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (23716) covalent geometry : angle 0.62929 / 0.32 (32391) hydrogen bonds : bond 0.03817 / 4.11 ( 1212) hydrogen bonds : angle 3.93175 / 4.80 ( 3330) ********************** 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 224 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 57 MET cc_start: 0.8062 (tmm) cc_final: 0.7628 (tmm) REVERT: P 65 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8752 (tp) REVERT: P 94 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7537 (pmm) REVERT: P 110 MET cc_start: 0.9206 (pmm) cc_final: 0.8982 (pmm) REVERT: P 118 THR cc_start: 0.7560 (t) cc_final: 0.6568 (m) REVERT: P 119 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7517 (tm) REVERT: P 120 LEU cc_start: 0.8602 (pt) cc_final: 0.7827 (mt) REVERT: P 122 TRP cc_start: 0.8097 (m100) cc_final: 0.7280 (m100) REVERT: P 147 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7673 (tmt) REVERT: P 154 TYR cc_start: 0.8840 (p90) cc_final: 0.8382 (p90) REVERT: P 155 GLU cc_start: 0.9007 (mp0) cc_final: 0.8724 (mp0) REVERT: P 180 HIS cc_start: 0.9165 (m-70) cc_final: 0.8654 (m-70) REVERT: P 188 MET cc_start: 0.7624 (mmm) cc_final: 0.7095 (mmm) REVERT: Q 56 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: Q 71 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8448 (mt-10) REVERT: Q 164 HIS cc_start: 0.8608 (t70) cc_final: 0.8368 (t-90) REVERT: Q 172 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8690 (mp0) REVERT: Q 188 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8662 (mm110) REVERT: Q 198 MET cc_start: 0.8842 (mpm) cc_final: 0.8506 (ttt) REVERT: Q 321 GLU cc_start: 0.9032 (tt0) cc_final: 0.8405 (tm-30) REVERT: R 18 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: R 82 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8376 (pp) REVERT: R 138 PHE cc_start: 0.9172 (m-80) cc_final: 0.8755 (m-10) REVERT: R 324 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8406 (tm-30) REVERT: S 102 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8263 (ttm110) REVERT: S 128 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: S 166 ASP cc_start: 0.8798 (m-30) cc_final: 0.8493 (m-30) REVERT: T 89 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8467 (m) REVERT: T 210 GLU cc_start: 0.8808 (pt0) cc_final: 0.8159 (tm-30) REVERT: T 283 ASP cc_start: 0.8904 (m-30) cc_final: 0.8419 (t0) REVERT: U 19 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8539 (mtm180) REVERT: U 24 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8087 (pp20) REVERT: U 25 ASN cc_start: 0.9221 (m-40) cc_final: 0.8539 (m-40) REVERT: U 95 GLU cc_start: 0.7853 (pm20) cc_final: 0.7259 (pm20) REVERT: U 146 LYS cc_start: 0.9258 (mppt) cc_final: 0.9034 (mtpt) REVERT: V 41 MET cc_start: 0.8952 (mmm) cc_final: 0.8693 (mmm) REVERT: V 95 GLU cc_start: 0.8201 (pm20) cc_final: 0.7520 (pp20) REVERT: V 128 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: W 41 MET cc_start: 0.9207 (mmm) cc_final: 0.8891 (mmm) REVERT: W 97 ILE cc_start: 0.8648 (pt) cc_final: 0.8174 (tt) REVERT: W 175 HIS cc_start: 0.9105 (m-70) cc_final: 0.8596 (m-70) REVERT: W 188 GLN cc_start: 0.9203 (mp-120) cc_final: 0.8878 (mm110) REVERT: W 262 ASN cc_start: 0.9234 (t0) cc_final: 0.8978 (t0) outliers start: 58 outliers final: 41 residues processed: 215 average time/residue: 0.4325 time to fit residues: 111.9714 Evaluate side-chains 213 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 147 MET Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain Q residue 260 THR 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 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 285 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 192 LEU Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain W residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 115 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 245 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.058126 restraints weight = 74053.121| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.35 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23716 Z= 0.202 Angle : 0.645 11.275 32391 Z= 0.326 Chirality : 0.042 0.178 3630 Planarity : 0.004 0.046 3903 Dihedral : 15.459 65.811 3656 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.62 % Favored : 96.12 % Rotamer: Outliers : 2.48 % Allowed : 28.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2677 helix: 1.55 (0.13), residues: 1598 sheet: -1.14 (0.39), residues: 196 loop : -0.70 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 131 TYR 0.022 0.001 TYR U 103 PHE 0.032 0.002 PHE W 126 TRP 0.024 0.001 TRP P 146 HIS 0.007 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (23716) covalent geometry : angle 0.64477 / 0.33 (32391) hydrogen bonds : bond 0.04013 / 4.29 ( 1212) hydrogen bonds : angle 3.96380 / 4.84 ( 3330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6020.58 seconds wall clock time: 104 minutes 16.11 seconds (6256.11 seconds total)