Starting phenix.real_space_refine on Fri Jun 20 00:25:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcv_28994/06_2025/8fcv_28994.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcv_28994/06_2025/8fcv_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_28994/06_2025/8fcv_28994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcv_28994/06_2025/8fcv_28994.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcv_28994/06_2025/8fcv_28994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcv_28994/06_2025/8fcv_28994.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.890 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 81 5.49 5 Mg 7 5.21 5 S 75 5.16 5 C 14490 2.51 5 N 4031 2.21 5 O 4432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23116 Number of models: 1 Model: "" Number of chains: 17 Chain: "N" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "O" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "P" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2618 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "Q" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2508 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "W" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.67, per 1000 atoms: 0.63 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: 6.34 Conformation dependent library (CDL) restraints added in 2.8 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: 7.96 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: 7.72 Time building geometry restraints manager: 7.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7184 1.34 - 1.46: 3865 1.46 - 1.58: 12410 1.58 - 1.70: 153 1.70 - 1.82: 104 Bond restraints: 23716 Sorted by residual: bond pdb=" N SER V 59 " pdb=" CA SER V 59 " ideal model delta sigma weight residual 1.463 1.436 0.027 1.30e-02 5.92e+03 4.27e+00 bond pdb=" C GLY U 60 " pdb=" O GLY U 60 " ideal model delta sigma weight residual 1.238 1.221 0.017 1.12e-02 7.97e+03 2.24e+00 bond pdb=" CA ASP V 127 " pdb=" CB ASP V 127 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.61e-02 3.86e+03 1.90e+00 bond pdb=" CG ASP V 187 " pdb=" OD1 ASP V 187 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.70e+00 bond pdb=" CB ASP V 187 " pdb=" CG ASP V 187 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.59e+00 ... (remaining 23711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 31578 1.69 - 3.39: 672 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: 11710 17.65 - 35.30: 1731 35.30 - 52.95: 662 52.95 - 70.60: 151 70.60 - 88.25: 24 Dihedral angle restraints: 14278 sinusoidal: 6399 harmonic: 7879 Sorted by residual: dihedral pdb=" CA GLU W 95 " pdb=" C GLU W 95 " pdb=" N ALA W 96 " pdb=" CA ALA W 96 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU P 185 " pdb=" C LEU P 185 " pdb=" N PRO P 186 " pdb=" CA PRO P 186 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP V 187 " pdb=" C ASP V 187 " pdb=" N GLN V 188 " pdb=" CA GLN V 188 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 14275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2684 0.038 - 0.075: 697 0.075 - 0.113: 201 0.113 - 0.150: 45 0.150 - 0.188: 3 Chirality restraints: 3630 Sorted by residual: chirality pdb=" CA ASP W 127 " pdb=" N ASP W 127 " pdb=" C ASP W 127 " pdb=" CB ASP W 127 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA ASP V 127 " pdb=" N ASP V 127 " pdb=" C ASP V 127 " pdb=" CB ASP V 127 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ASP T 127 " pdb=" N ASP T 127 " pdb=" C ASP T 127 " pdb=" CB ASP T 127 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 3627 not shown) Planarity restraints: 3903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE V 126 " 0.012 2.00e-02 2.50e+03 2.12e-02 7.90e+00 pdb=" CG PHE V 126 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE V 126 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE V 126 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE V 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE V 126 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE V 126 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA V 58 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C ALA V 58 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA V 58 " 0.018 2.00e-02 2.50e+03 pdb=" N SER V 59 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 297 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ALA U 297 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA U 297 " 0.014 2.00e-02 2.50e+03 pdb=" N THR U 298 " 0.013 2.00e-02 2.50e+03 ... (remaining 3900 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 59.030 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23716 Z= 0.147 Angle : 0.618 8.469 32391 Z= 0.345 Chirality : 0.039 0.188 3630 Planarity : 0.004 0.054 3903 Dihedral : 19.304 88.253 9186 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.11 % Favored : 95.44 % Rotamer: Outliers : 0.73 % Allowed : 25.63 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2677 helix: 1.11 (0.14), residues: 1564 sheet: -0.73 (0.41), residues: 186 loop : -0.79 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 267 HIS 0.010 0.001 HIS W 162 PHE 0.047 0.001 PHE V 126 TYR 0.019 0.001 TYR P 154 ARG 0.010 0.000 ARG V 131 Details of bonding type rmsd hydrogen bonds : bond 0.17137 ( 1212) hydrogen bonds : angle 5.89098 ( 3330) covalent geometry : bond 0.00274 (23716) covalent geometry : angle 0.61812 (32391) *********************** 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 : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 77 ASN cc_start: 0.8471 (t0) cc_final: 0.8153 (t0) REVERT: P 91 ILE cc_start: 0.5990 (mt) cc_final: 0.5627 (mp) REVERT: P 120 LEU cc_start: 0.8591 (pp) cc_final: 0.8027 (mt) REVERT: P 154 TYR cc_start: 0.8772 (p90) cc_final: 0.8363 (p90) REVERT: P 180 HIS cc_start: 0.8853 (m-70) cc_final: 0.8591 (m-70) REVERT: Q 71 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8412 (mt-10) REVERT: Q 164 HIS cc_start: 0.8400 (t-90) cc_final: 0.8067 (t-90) REVERT: Q 172 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8576 (mm-30) REVERT: Q 321 GLU cc_start: 0.8699 (tt0) cc_final: 0.8272 (tm-30) REVERT: R 138 PHE cc_start: 0.9222 (m-80) cc_final: 0.8489 (m-80) REVERT: R 320 LYS cc_start: 0.8959 (tppt) cc_final: 0.8718 (mtmm) REVERT: R 324 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8128 (tm-30) REVERT: S 9 LEU cc_start: 0.8969 (pt) cc_final: 0.8677 (mm) REVERT: S 121 LEU cc_start: 0.9620 (pt) cc_final: 0.9350 (pp) REVERT: S 124 HIS cc_start: 0.8139 (m90) cc_final: 0.7707 (m90) REVERT: S 128 TYR cc_start: 0.6995 (m-80) cc_final: 0.6656 (m-10) REVERT: S 324 GLU cc_start: 0.8316 (pp20) cc_final: 0.7668 (pp20) REVERT: T 164 HIS cc_start: 0.9037 (t-170) cc_final: 0.8197 (t-90) REVERT: T 189 LEU cc_start: 0.8883 (tp) cc_final: 0.8667 (tp) REVERT: T 210 GLU cc_start: 0.8671 (pt0) cc_final: 0.8124 (tm-30) REVERT: U 25 ASN cc_start: 0.9216 (m-40) cc_final: 0.8578 (m-40) REVERT: U 95 GLU cc_start: 0.7910 (pm20) cc_final: 0.7376 (pm20) REVERT: U 142 ASN cc_start: 0.7027 (m-40) cc_final: 0.6714 (m110) REVERT: U 321 GLU cc_start: 0.9311 (tp30) cc_final: 0.9100 (tp30) REVERT: V 166 ASP cc_start: 0.9050 (t0) cc_final: 0.8842 (m-30) REVERT: W 44 ILE cc_start: 0.9601 (mm) cc_final: 0.9340 (mm) REVERT: W 56 TYR cc_start: 0.6918 (m-10) cc_final: 0.6431 (m-80) REVERT: W 97 ILE cc_start: 0.8472 (pt) cc_final: 0.8222 (tt) REVERT: W 164 HIS cc_start: 0.8358 (t70) cc_final: 0.7850 (p-80) REVERT: W 175 HIS cc_start: 0.8988 (m-70) cc_final: 0.8516 (m-70) REVERT: W 186 GLN cc_start: 0.8279 (tm-30) cc_final: 0.8006 (tm-30) REVERT: W 198 MET cc_start: 0.7822 (mpp) cc_final: 0.7071 (mpp) outliers start: 17 outliers final: 4 residues processed: 346 average time/residue: 1.2106 time to fit residues: 494.4126 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 : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain V residue 301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 248 GLN Q 203 HIS ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 197 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 188 GLN W 203 HIS W 254 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.086588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058968 restraints weight = 73826.213| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.30 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 23716 Z= 0.259 Angle : 0.674 8.774 32391 Z= 0.349 Chirality : 0.043 0.196 3630 Planarity : 0.005 0.046 3903 Dihedral : 16.943 89.376 3879 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.62 % Favored : 96.08 % Rotamer: Outliers : 4.32 % Allowed : 25.12 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2677 helix: 1.27 (0.13), residues: 1612 sheet: -0.93 (0.39), residues: 193 loop : -0.89 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 146 HIS 0.013 0.001 HIS W 254 PHE 0.034 0.002 PHE P 308 TYR 0.025 0.002 TYR U 103 ARG 0.011 0.001 ARG P 276 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 1212) hydrogen bonds : angle 4.48098 ( 3330) covalent geometry : bond 0.00587 (23716) covalent geometry : angle 0.67350 (32391) *********************** 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 302 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 201 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 39 SER cc_start: 0.9191 (t) cc_final: 0.8781 (p) REVERT: P 65 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8610 (tp) REVERT: P 77 ASN cc_start: 0.8244 (t0) cc_final: 0.7823 (t0) REVERT: P 119 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8133 (tm) REVERT: P 135 TYR cc_start: 0.8716 (m-80) cc_final: 0.8379 (m-80) REVERT: P 154 TYR cc_start: 0.8875 (p90) cc_final: 0.8602 (p90) REVERT: P 155 GLU cc_start: 0.8938 (mp0) cc_final: 0.8687 (mp0) REVERT: P 161 PHE cc_start: 0.9253 (m-80) cc_final: 0.9016 (m-80) REVERT: P 180 HIS cc_start: 0.9133 (m-70) cc_final: 0.8701 (m-70) REVERT: Q 41 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.9000 (mmm) REVERT: Q 71 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8515 (mt-10) REVERT: Q 164 HIS cc_start: 0.8576 (t70) cc_final: 0.8282 (t-90) REVERT: Q 172 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8402 (mp0) REVERT: Q 188 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8759 (mm110) REVERT: Q 321 GLU cc_start: 0.8959 (tt0) cc_final: 0.8358 (tm-30) REVERT: R 138 PHE cc_start: 0.9040 (m-80) cc_final: 0.8747 (m-80) REVERT: R 187 ASP cc_start: 0.9192 (m-30) cc_final: 0.8860 (m-30) REVERT: R 318 MET cc_start: 0.8286 (mmt) cc_final: 0.8010 (mtt) REVERT: R 321 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: R 324 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8515 (tp30) REVERT: S 9 LEU cc_start: 0.9020 (pt) cc_final: 0.8792 (mm) REVERT: S 121 LEU cc_start: 0.9649 (pt) cc_final: 0.9289 (pp) REVERT: S 124 HIS cc_start: 0.8173 (m90) cc_final: 0.7631 (m90) REVERT: T 10 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: T 108 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8578 (tp30) REVERT: T 210 GLU cc_start: 0.8754 (pt0) cc_final: 0.8234 (tm-30) REVERT: U 142 ASN cc_start: 0.7131 (m110) cc_final: 0.6831 (m110) REVERT: U 164 HIS cc_start: 0.8553 (t-90) cc_final: 0.8303 (t-90) REVERT: W 41 MET cc_start: 0.9208 (mmm) cc_final: 0.8953 (mmm) REVERT: W 97 ILE cc_start: 0.8714 (pt) cc_final: 0.8477 (tt) REVERT: W 175 HIS cc_start: 0.9094 (m-70) cc_final: 0.8596 (m-70) REVERT: W 188 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8890 (mm110) outliers start: 101 outliers final: 35 residues processed: 285 average time/residue: 1.1886 time to fit residues: 405.0309 Evaluate side-chains 204 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain 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 46 GLU 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 305 LEU Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain S residue 343 LEU Chi-restraints excluded: chain T residue 10 GLU 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 20 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 189 LEU Chi-restraints excluded: chain U residue 286 LYS Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 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 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 Chi-restraints excluded: chain W residue 321 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 196 optimal weight: 0.0670 chunk 93 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 167 optimal weight: 0.0270 chunk 217 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 233 GLN ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 252 GLN T 197 ASN U 25 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 338 ASN V 142 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 188 GLN ** W 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.088829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061125 restraints weight = 73052.525| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.34 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23716 Z= 0.124 Angle : 0.595 9.167 32391 Z= 0.301 Chirality : 0.040 0.213 3630 Planarity : 0.004 0.045 3903 Dihedral : 16.586 82.520 3875 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.47 % Favored : 96.26 % Rotamer: Outliers : 3.64 % Allowed : 25.63 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2677 helix: 1.43 (0.13), residues: 1604 sheet: -1.06 (0.38), residues: 191 loop : -0.86 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 146 HIS 0.012 0.001 HIS P 80 PHE 0.015 0.001 PHE U 126 TYR 0.017 0.001 TYR W 26 ARG 0.006 0.000 ARG P 218 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 1212) hydrogen bonds : angle 4.14645 ( 3330) covalent geometry : bond 0.00270 (23716) covalent geometry : angle 0.59500 (32391) *********************** 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 276 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 191 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 94 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7181 (pmm) REVERT: P 119 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.7765 (tm) REVERT: P 120 LEU cc_start: 0.8382 (pt) cc_final: 0.7714 (mt) REVERT: P 122 TRP cc_start: 0.7823 (m100) cc_final: 0.7543 (m100) REVERT: P 135 TYR cc_start: 0.9117 (m-80) cc_final: 0.8876 (m-80) REVERT: P 154 TYR cc_start: 0.8850 (p90) cc_final: 0.8382 (p90) REVERT: P 155 GLU cc_start: 0.8895 (mp0) cc_final: 0.8567 (mp0) REVERT: P 161 PHE cc_start: 0.9211 (m-80) cc_final: 0.8980 (m-80) REVERT: P 180 HIS cc_start: 0.9172 (m-70) cc_final: 0.8731 (m-70) REVERT: Q 71 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8418 (mt-10) REVERT: Q 164 HIS cc_start: 0.8540 (t70) cc_final: 0.8193 (t-90) REVERT: Q 172 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8394 (mp0) REVERT: Q 188 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8702 (mm110) REVERT: Q 210 GLU cc_start: 0.8956 (mp0) cc_final: 0.8556 (mp0) REVERT: Q 321 GLU cc_start: 0.8955 (tt0) cc_final: 0.8315 (tm-30) REVERT: R 138 PHE cc_start: 0.9091 (m-80) cc_final: 0.8753 (m-10) REVERT: R 187 ASP cc_start: 0.9208 (m-30) cc_final: 0.8845 (m-30) REVERT: R 324 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8323 (tm-30) REVERT: S 9 LEU cc_start: 0.8955 (pt) cc_final: 0.8703 (mm) REVERT: S 128 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: S 302 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8194 (tt) REVERT: T 189 LEU cc_start: 0.9209 (tp) cc_final: 0.8976 (tp) REVERT: T 210 GLU cc_start: 0.8668 (pt0) cc_final: 0.8072 (tm-30) REVERT: U 142 ASN cc_start: 0.7277 (m110) cc_final: 0.6885 (m110) REVERT: U 164 HIS cc_start: 0.8529 (t-90) cc_final: 0.8006 (t-90) REVERT: V 95 GLU cc_start: 0.8080 (pm20) cc_final: 0.7441 (pp20) REVERT: V 105 ASN cc_start: 0.9485 (t0) cc_final: 0.9213 (t0) REVERT: V 198 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8130 (mtm) REVERT: W 41 MET cc_start: 0.9159 (mmm) cc_final: 0.8952 (mmm) REVERT: W 97 ILE cc_start: 0.8692 (pt) cc_final: 0.8389 (tt) REVERT: W 175 HIS cc_start: 0.9026 (m-70) cc_final: 0.8424 (m-70) outliers start: 85 outliers final: 33 residues processed: 258 average time/residue: 0.9399 time to fit residues: 292.6830 Evaluate side-chains 211 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 2.921 ------------------------------------------------------------------------------- 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 94 MET Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 290 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain 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 128 TYR 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 305 LEU 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 339 LEU Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 198 MET 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 102 ARG Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 164 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 106 optimal weight: 0.8980 chunk 257 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN ** 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 = 0.3701 r_free = 0.3701 target = 0.088096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060517 restraints weight = 74080.945| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.28 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23716 Z= 0.139 Angle : 0.569 8.700 32391 Z= 0.290 Chirality : 0.040 0.193 3630 Planarity : 0.004 0.044 3903 Dihedral : 16.276 86.390 3874 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.29 % Favored : 96.45 % Rotamer: Outliers : 3.55 % Allowed : 25.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2677 helix: 1.52 (0.13), residues: 1604 sheet: -1.19 (0.37), residues: 196 loop : -0.80 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 146 HIS 0.005 0.001 HIS W 175 PHE 0.031 0.001 PHE W 126 TYR 0.025 0.001 TYR U 103 ARG 0.005 0.000 ARG S 131 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1212) hydrogen bonds : angle 4.00124 ( 3330) covalent geometry : bond 0.00312 (23716) covalent geometry : angle 0.56905 (32391) *********************** 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 273 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 190 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 94 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7399 (pmm) REVERT: P 119 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.7659 (tm) REVERT: P 120 LEU cc_start: 0.8492 (pt) cc_final: 0.7802 (mt) REVERT: P 154 TYR cc_start: 0.8857 (p90) cc_final: 0.8445 (p90) REVERT: P 155 GLU cc_start: 0.8934 (mp0) cc_final: 0.8463 (mp0) REVERT: P 161 PHE cc_start: 0.9205 (m-80) cc_final: 0.8998 (m-80) REVERT: P 180 HIS cc_start: 0.9214 (m-70) cc_final: 0.8741 (m-70) REVERT: Q 41 MET cc_start: 0.9326 (mmm) cc_final: 0.9116 (mmm) REVERT: Q 71 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8301 (mt-10) REVERT: Q 164 HIS cc_start: 0.8545 (t70) cc_final: 0.8189 (t-90) REVERT: Q 172 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8627 (mp0) REVERT: Q 188 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8681 (mm110) REVERT: Q 210 GLU cc_start: 0.8963 (mp0) cc_final: 0.8598 (mp0) REVERT: Q 321 GLU cc_start: 0.8996 (tt0) cc_final: 0.8348 (tm-30) REVERT: R 18 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8566 (mp0) REVERT: R 138 PHE cc_start: 0.9121 (m-80) cc_final: 0.8747 (m-10) REVERT: R 172 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8811 (mt-10) REVERT: R 188 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8901 (mm-40) REVERT: R 324 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8386 (tp30) REVERT: S 9 LEU cc_start: 0.8965 (pt) cc_final: 0.8690 (mm) REVERT: S 102 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8230 (ttm110) REVERT: S 128 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7217 (m-80) REVERT: S 166 ASP cc_start: 0.8764 (m-30) cc_final: 0.8438 (m-30) REVERT: T 10 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8701 (tm-30) REVERT: T 189 LEU cc_start: 0.9220 (tp) cc_final: 0.8993 (tp) REVERT: T 210 GLU cc_start: 0.8722 (pt0) cc_final: 0.8085 (tm-30) REVERT: U 19 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8560 (mtm180) REVERT: U 24 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8186 (pp20) REVERT: V 95 GLU cc_start: 0.8201 (pm20) cc_final: 0.7818 (pp20) REVERT: V 105 ASN cc_start: 0.9467 (t0) cc_final: 0.9180 (t0) REVERT: W 41 MET cc_start: 0.9173 (mmm) cc_final: 0.8867 (mmm) REVERT: W 97 ILE cc_start: 0.8560 (pt) cc_final: 0.8265 (tt) REVERT: W 175 HIS cc_start: 0.9020 (m-70) cc_final: 0.8416 (m-70) outliers start: 83 outliers final: 41 residues processed: 259 average time/residue: 1.0080 time to fit residues: 312.3148 Evaluate side-chains 216 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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 69 ASP Chi-restraints excluded: chain P residue 75 SER 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 Q residue 56 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 192 LEU 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 172 GLU 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 S residue 305 LEU Chi-restraints excluded: chain T residue 10 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 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 189 LEU Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 339 LEU 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 315 CYS 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 164 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 10.0000 chunk 256 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 160 optimal weight: 0.0970 chunk 19 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 0.0010 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 HIS ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 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 = 0.3715 r_free = 0.3715 target = 0.088728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062111 restraints weight = 72798.322| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.22 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23716 Z= 0.113 Angle : 0.574 10.387 32391 Z= 0.288 Chirality : 0.039 0.198 3630 Planarity : 0.004 0.044 3903 Dihedral : 16.055 79.711 3874 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.59 % Favored : 96.15 % Rotamer: Outliers : 3.21 % Allowed : 27.13 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2677 helix: 1.51 (0.13), residues: 1616 sheet: -1.15 (0.37), residues: 196 loop : -0.70 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 122 HIS 0.004 0.001 HIS V 30 PHE 0.021 0.001 PHE S 126 TYR 0.013 0.001 TYR S 56 ARG 0.005 0.000 ARG S 223 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 1212) hydrogen bonds : angle 3.85800 ( 3330) covalent geometry : bond 0.00245 (23716) covalent geometry : angle 0.57423 (32391) *********************** 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 270 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 195 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 94 MET cc_start: 0.8218 (pmt) cc_final: 0.7527 (pmm) REVERT: P 119 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.7711 (tm) REVERT: P 120 LEU cc_start: 0.8524 (pt) cc_final: 0.7745 (mt) REVERT: P 122 TRP cc_start: 0.7481 (m100) cc_final: 0.6835 (m100) REVERT: P 134 ASN cc_start: 0.9551 (p0) cc_final: 0.9061 (t0) REVERT: P 135 TYR cc_start: 0.8974 (m-80) cc_final: 0.8641 (m-80) REVERT: P 154 TYR cc_start: 0.8799 (p90) cc_final: 0.8401 (p90) REVERT: P 155 GLU cc_start: 0.8942 (mp0) cc_final: 0.8654 (mp0) REVERT: P 161 PHE cc_start: 0.9244 (m-80) cc_final: 0.9043 (m-80) REVERT: P 173 ARG cc_start: 0.9176 (tpp80) cc_final: 0.8869 (ttm-80) REVERT: P 180 HIS cc_start: 0.9213 (m-70) cc_final: 0.8720 (m-70) REVERT: Q 71 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8356 (mt-10) REVERT: Q 164 HIS cc_start: 0.8529 (t70) cc_final: 0.8193 (t-90) REVERT: Q 172 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8618 (mp0) REVERT: Q 188 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8646 (mm110) REVERT: Q 210 GLU cc_start: 0.8968 (mp0) cc_final: 0.8631 (mp0) REVERT: Q 215 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6731 (ppt90) REVERT: Q 321 GLU cc_start: 0.8993 (tt0) cc_final: 0.8342 (tm-30) REVERT: R 18 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8571 (mp0) REVERT: R 82 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8380 (pp) REVERT: R 138 PHE cc_start: 0.9117 (m-80) cc_final: 0.8735 (m-10) REVERT: R 172 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8852 (mt-10) REVERT: R 324 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8316 (tm-30) REVERT: S 9 LEU cc_start: 0.8973 (pt) cc_final: 0.8716 (mm) REVERT: S 102 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8442 (mmm160) REVERT: S 128 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: S 166 ASP cc_start: 0.8769 (m-30) cc_final: 0.8472 (m-30) REVERT: T 10 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8736 (tm-30) REVERT: T 146 LYS cc_start: 0.8193 (tptt) cc_final: 0.7848 (tptt) REVERT: T 189 LEU cc_start: 0.9188 (tp) cc_final: 0.8964 (tp) REVERT: T 210 GLU cc_start: 0.8656 (pt0) cc_final: 0.8092 (tm-30) REVERT: U 19 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8602 (mtm180) REVERT: U 24 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8343 (pp20) REVERT: U 146 LYS cc_start: 0.9240 (mppt) cc_final: 0.8977 (mtpt) REVERT: U 338 ASN cc_start: 0.9296 (m-40) cc_final: 0.9085 (m110) REVERT: V 105 ASN cc_start: 0.9453 (t0) cc_final: 0.9140 (t0) REVERT: V 128 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: W 41 MET cc_start: 0.9178 (mmm) cc_final: 0.8901 (mmm) REVERT: W 97 ILE cc_start: 0.8471 (pt) cc_final: 0.8202 (tt) REVERT: W 175 HIS cc_start: 0.9034 (m-70) cc_final: 0.8491 (m-70) outliers start: 75 outliers final: 33 residues processed: 257 average time/residue: 1.0220 time to fit residues: 316.6633 Evaluate side-chains 213 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 2.769 ------------------------------------------------------------------------------- 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 75 SER 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 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 82 LEU Chi-restraints excluded: chain R residue 172 GLU 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 S residue 305 LEU Chi-restraints excluded: chain T residue 10 GLU 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 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 144 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 162 HIS T 25 ASN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060915 restraints weight = 73082.769| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.24 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23716 Z= 0.134 Angle : 0.577 10.537 32391 Z= 0.289 Chirality : 0.040 0.189 3630 Planarity : 0.004 0.043 3903 Dihedral : 15.966 74.078 3874 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.55 % Favored : 96.19 % Rotamer: Outliers : 3.34 % Allowed : 26.83 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2677 helix: 1.62 (0.13), residues: 1599 sheet: -1.08 (0.37), residues: 196 loop : -0.71 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 122 HIS 0.004 0.001 HIS W 175 PHE 0.044 0.001 PHE W 126 TYR 0.027 0.001 TYR U 103 ARG 0.005 0.000 ARG V 131 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 1212) hydrogen bonds : angle 3.82205 ( 3330) covalent geometry : bond 0.00302 (23716) covalent geometry : angle 0.57671 (32391) *********************** 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 261 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 183 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 94 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7934 (pmm) REVERT: P 118 THR cc_start: 0.7315 (t) cc_final: 0.6668 (m) REVERT: P 120 LEU cc_start: 0.8488 (pt) cc_final: 0.7837 (mt) REVERT: P 135 TYR cc_start: 0.9049 (m-80) cc_final: 0.8842 (m-80) REVERT: P 154 TYR cc_start: 0.8834 (p90) cc_final: 0.8412 (p90) REVERT: P 155 GLU cc_start: 0.8974 (mp0) cc_final: 0.8695 (mp0) REVERT: P 180 HIS cc_start: 0.9222 (m-70) cc_final: 0.8724 (m-70) REVERT: Q 71 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8526 (mt-10) REVERT: Q 95 GLU cc_start: 0.7905 (pm20) cc_final: 0.7685 (pm20) REVERT: Q 164 HIS cc_start: 0.8528 (t70) cc_final: 0.8212 (t-90) REVERT: Q 172 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8641 (mp0) REVERT: Q 188 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8685 (mm110) REVERT: Q 210 GLU cc_start: 0.9007 (mp0) cc_final: 0.8663 (mp0) REVERT: Q 321 GLU cc_start: 0.9014 (tt0) cc_final: 0.8378 (tm-30) REVERT: R 18 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: R 82 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8417 (pp) REVERT: R 138 PHE cc_start: 0.9168 (m-80) cc_final: 0.8784 (m-10) REVERT: R 324 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8313 (tm-30) REVERT: S 9 LEU cc_start: 0.8995 (pt) cc_final: 0.8750 (mm) REVERT: S 102 ARG cc_start: 0.8719 (ttm110) cc_final: 0.8256 (ttm110) REVERT: S 128 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: S 166 ASP cc_start: 0.8769 (m-30) cc_final: 0.8455 (m-30) REVERT: T 10 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8711 (tm-30) REVERT: T 146 LYS cc_start: 0.8219 (tptt) cc_final: 0.7968 (tptt) REVERT: T 189 LEU cc_start: 0.9220 (tp) cc_final: 0.8985 (tp) REVERT: T 210 GLU cc_start: 0.8677 (pt0) cc_final: 0.8106 (tm-30) REVERT: U 19 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8627 (mtm180) REVERT: U 25 ASN cc_start: 0.8924 (m110) cc_final: 0.8584 (m-40) REVERT: U 338 ASN cc_start: 0.9298 (m-40) cc_final: 0.9080 (m110) REVERT: V 41 MET cc_start: 0.9124 (tpp) cc_final: 0.8762 (mmm) REVERT: V 105 ASN cc_start: 0.9446 (t0) cc_final: 0.9142 (t0) REVERT: V 128 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: W 41 MET cc_start: 0.9178 (mmm) cc_final: 0.8890 (mmm) REVERT: W 97 ILE cc_start: 0.8437 (pt) cc_final: 0.8065 (tt) REVERT: W 175 HIS cc_start: 0.9082 (m-70) cc_final: 0.8557 (m-70) outliers start: 78 outliers final: 36 residues processed: 249 average time/residue: 1.0182 time to fit residues: 303.8257 Evaluate side-chains 211 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 2.562 ------------------------------------------------------------------------------- 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 75 SER 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 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 Q residue 301 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 82 LEU 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 S residue 305 LEU Chi-restraints excluded: chain T residue 10 GLU 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 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 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 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 189 LEU Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 260 THR 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 27 optimal weight: 6.9990 chunk 206 optimal weight: 0.0980 chunk 233 optimal weight: 5.9990 chunk 160 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 162 HIS Q 188 GLN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.088636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061149 restraints weight = 74478.447| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.38 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23716 Z= 0.120 Angle : 0.580 9.198 32391 Z= 0.289 Chirality : 0.040 0.193 3630 Planarity : 0.004 0.043 3903 Dihedral : 15.895 75.837 3873 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.36 % Favored : 96.38 % Rotamer: Outliers : 3.08 % Allowed : 27.17 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2677 helix: 1.60 (0.13), residues: 1610 sheet: -1.04 (0.37), residues: 196 loop : -0.71 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 122 HIS 0.004 0.001 HIS V 30 PHE 0.030 0.001 PHE W 126 TYR 0.024 0.001 TYR W 109 ARG 0.006 0.000 ARG V 131 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 1212) hydrogen bonds : angle 3.75511 ( 3330) covalent geometry : bond 0.00270 (23716) covalent geometry : angle 0.58026 (32391) *********************** 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 260 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8792 (tt) REVERT: P 94 MET cc_start: 0.8238 (pmt) cc_final: 0.7950 (pmm) REVERT: P 118 THR cc_start: 0.7454 (t) cc_final: 0.7118 (m) REVERT: P 120 LEU cc_start: 0.8583 (pt) cc_final: 0.7954 (mt) REVERT: P 134 ASN cc_start: 0.9565 (p0) cc_final: 0.9107 (t0) REVERT: P 135 TYR cc_start: 0.9044 (m-80) cc_final: 0.8656 (m-80) REVERT: P 154 TYR cc_start: 0.8840 (p90) cc_final: 0.8390 (p90) REVERT: P 155 GLU cc_start: 0.8994 (mp0) cc_final: 0.8705 (mp0) REVERT: P 180 HIS cc_start: 0.9208 (m-70) cc_final: 0.8693 (m-70) REVERT: P 298 GLU cc_start: 0.8693 (tp30) cc_final: 0.8163 (mm-30) REVERT: Q 71 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8474 (mt-10) REVERT: Q 164 HIS cc_start: 0.8527 (t70) cc_final: 0.8236 (t-90) REVERT: Q 172 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8644 (mp0) REVERT: Q 198 MET cc_start: 0.8841 (mpm) cc_final: 0.8177 (tmm) REVERT: Q 210 GLU cc_start: 0.9026 (mp0) cc_final: 0.8683 (mp0) REVERT: Q 215 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6826 (ppt90) REVERT: Q 321 GLU cc_start: 0.9006 (tt0) cc_final: 0.8371 (tm-30) REVERT: R 18 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: R 82 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8406 (pp) REVERT: R 138 PHE cc_start: 0.9168 (m-80) cc_final: 0.8778 (m-10) REVERT: R 190 ASP cc_start: 0.8782 (m-30) cc_final: 0.8445 (m-30) REVERT: R 324 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8329 (tm-30) REVERT: S 9 LEU cc_start: 0.8987 (pt) cc_final: 0.8750 (mm) REVERT: S 102 ARG cc_start: 0.8723 (ttm110) cc_final: 0.8259 (ttm110) REVERT: S 128 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: S 166 ASP cc_start: 0.8810 (m-30) cc_final: 0.8523 (m-30) REVERT: T 146 LYS cc_start: 0.8118 (tptt) cc_final: 0.7860 (tptt) REVERT: T 189 LEU cc_start: 0.9193 (tp) cc_final: 0.8963 (tp) REVERT: T 210 GLU cc_start: 0.8653 (pt0) cc_final: 0.8095 (tm-30) REVERT: U 19 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8558 (mtm180) REVERT: U 24 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7971 (pp20) REVERT: U 144 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: U 145 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8557 (p) REVERT: U 338 ASN cc_start: 0.9287 (m-40) cc_final: 0.9067 (m110) REVERT: V 41 MET cc_start: 0.9111 (tpp) cc_final: 0.8777 (mmm) REVERT: V 105 ASN cc_start: 0.9461 (t0) cc_final: 0.9146 (t0) REVERT: V 128 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: W 41 MET cc_start: 0.9179 (mmm) cc_final: 0.8879 (mmm) REVERT: W 97 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8071 (tt) REVERT: W 175 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8601 (m-70) REVERT: W 262 ASN cc_start: 0.9146 (t0) cc_final: 0.8939 (t0) outliers start: 72 outliers final: 39 residues processed: 252 average time/residue: 0.9971 time to fit residues: 303.1958 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 : 2.901 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain P residue 127 TYR 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 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 74 LEU 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 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 266 HIS Chi-restraints excluded: chain S residue 305 LEU 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 144 GLU Chi-restraints excluded: chain U residue 145 SER 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 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 W residue 40 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 175 HIS Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 195 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 HIS R 188 GLN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 105 ASN ** U 203 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.087859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060353 restraints weight = 74659.302| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.34 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3086 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= 0.130 Angle : 0.582 10.119 32391 Z= 0.291 Chirality : 0.040 0.186 3630 Planarity : 0.004 0.043 3903 Dihedral : 15.866 76.156 3873 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.74 % Favored : 96.00 % Rotamer: Outliers : 2.82 % Allowed : 27.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2677 helix: 1.70 (0.13), residues: 1600 sheet: -1.00 (0.38), residues: 196 loop : -0.75 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 146 HIS 0.009 0.001 HIS P 80 PHE 0.027 0.001 PHE W 126 TYR 0.027 0.001 TYR U 103 ARG 0.012 0.000 ARG U 131 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1212) hydrogen bonds : angle 3.73048 ( 3330) covalent geometry : bond 0.00294 (23716) covalent geometry : angle 0.58200 (32391) *********************** 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 250 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 184 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 94 MET cc_start: 0.8472 (pmt) cc_final: 0.8027 (pmm) REVERT: P 118 THR cc_start: 0.7617 (t) cc_final: 0.7123 (m) REVERT: P 120 LEU cc_start: 0.8631 (pt) cc_final: 0.8033 (mt) REVERT: P 125 MET cc_start: 0.6437 (pmm) cc_final: 0.6102 (pmm) REVERT: P 134 ASN cc_start: 0.9558 (p0) cc_final: 0.9131 (t0) REVERT: P 135 TYR cc_start: 0.9066 (m-80) cc_final: 0.8675 (m-80) REVERT: P 154 TYR cc_start: 0.8879 (p90) cc_final: 0.8375 (p90) REVERT: P 155 GLU cc_start: 0.8985 (mp0) cc_final: 0.8684 (mp0) REVERT: P 180 HIS cc_start: 0.9200 (m-70) cc_final: 0.8704 (m-70) REVERT: Q 71 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8513 (mt-10) REVERT: Q 164 HIS cc_start: 0.8560 (t70) cc_final: 0.8327 (t-90) REVERT: Q 172 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8666 (mp0) REVERT: Q 188 GLN cc_start: 0.8974 (mm110) cc_final: 0.8652 (mm110) REVERT: Q 198 MET cc_start: 0.8812 (mpm) cc_final: 0.8141 (tmm) REVERT: Q 210 GLU cc_start: 0.8987 (mp0) cc_final: 0.8622 (mp0) REVERT: Q 215 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6819 (ppt90) REVERT: Q 321 GLU cc_start: 0.9011 (tt0) cc_final: 0.8382 (tm-30) REVERT: R 18 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: R 138 PHE cc_start: 0.9179 (m-80) cc_final: 0.8812 (m-10) REVERT: R 324 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8309 (tm-30) REVERT: S 9 LEU cc_start: 0.9003 (pt) cc_final: 0.8796 (mm) REVERT: S 102 ARG cc_start: 0.8718 (ttm110) cc_final: 0.8264 (ttm110) REVERT: S 128 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: S 166 ASP cc_start: 0.8829 (m-30) cc_final: 0.8541 (m-30) REVERT: T 146 LYS cc_start: 0.8113 (tptt) cc_final: 0.7848 (tptt) REVERT: T 189 LEU cc_start: 0.9204 (tp) cc_final: 0.8976 (tp) REVERT: T 210 GLU cc_start: 0.8686 (pt0) cc_final: 0.8120 (tm-30) REVERT: U 19 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8648 (mtm180) REVERT: U 24 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8028 (pp20) REVERT: U 59 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.8065 (t) REVERT: U 338 ASN cc_start: 0.9281 (m-40) cc_final: 0.9058 (m110) REVERT: V 41 MET cc_start: 0.9105 (tpp) cc_final: 0.8794 (mmm) REVERT: V 105 ASN cc_start: 0.9428 (t0) cc_final: 0.9103 (t0) REVERT: V 128 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: W 41 MET cc_start: 0.9187 (mmm) cc_final: 0.8882 (mmm) REVERT: W 262 ASN cc_start: 0.9128 (t0) cc_final: 0.8902 (t0) outliers start: 66 outliers final: 38 residues processed: 241 average time/residue: 0.9353 time to fit residues: 274.0840 Evaluate side-chains 217 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 2.860 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain P residue 98 THR Chi-restraints excluded: chain P residue 127 TYR 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 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 74 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 275 LEU 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 266 HIS Chi-restraints excluded: chain S residue 305 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 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 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 W residue 40 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 180 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** U 203 HIS ** 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 = 0.3648 r_free = 0.3648 target = 0.085326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.058202 restraints weight = 74722.377| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.17 r_work: 0.2818 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23716 Z= 0.224 Angle : 0.646 9.572 32391 Z= 0.327 Chirality : 0.042 0.208 3630 Planarity : 0.004 0.042 3903 Dihedral : 16.123 77.432 3873 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.04 % Rotamer: Outliers : 2.65 % Allowed : 28.11 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2677 helix: 1.57 (0.13), residues: 1606 sheet: -0.95 (0.39), residues: 191 loop : -0.62 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 146 HIS 0.010 0.001 HIS P 80 PHE 0.036 0.002 PHE W 138 TYR 0.025 0.002 TYR S 56 ARG 0.007 0.000 ARG V 131 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 1212) hydrogen bonds : angle 3.91165 ( 3330) covalent geometry : bond 0.00511 (23716) covalent geometry : angle 0.64565 (32391) *********************** 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 234 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 172 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 39 SER cc_start: 0.9213 (t) cc_final: 0.8944 (p) REVERT: P 65 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8908 (tt) REVERT: P 94 MET cc_start: 0.8519 (pmt) cc_final: 0.7740 (pmm) REVERT: P 119 LEU cc_start: 0.8583 (mm) cc_final: 0.7721 (tm) REVERT: P 120 LEU cc_start: 0.8573 (pt) cc_final: 0.7697 (mt) REVERT: P 125 MET cc_start: 0.7267 (pmm) cc_final: 0.6827 (pmm) REVERT: P 135 TYR cc_start: 0.9125 (m-80) cc_final: 0.8915 (m-80) REVERT: P 147 MET cc_start: 0.8110 (ttt) cc_final: 0.7888 (ttt) REVERT: P 154 TYR cc_start: 0.8992 (p90) cc_final: 0.8608 (p90) REVERT: P 155 GLU cc_start: 0.9038 (mp0) cc_final: 0.8786 (mp0) REVERT: P 166 PHE cc_start: 0.9416 (m-80) cc_final: 0.9055 (m-80) REVERT: P 180 HIS cc_start: 0.9128 (m-70) cc_final: 0.8630 (m-70) REVERT: Q 71 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8678 (mt-10) REVERT: Q 164 HIS cc_start: 0.8789 (t70) cc_final: 0.8557 (t-90) REVERT: Q 172 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8841 (mp0) REVERT: Q 188 GLN cc_start: 0.8930 (mm110) cc_final: 0.8615 (mm110) REVERT: Q 198 MET cc_start: 0.9112 (mpm) cc_final: 0.8190 (tmm) REVERT: Q 321 GLU cc_start: 0.9108 (tt0) cc_final: 0.8469 (tm-30) REVERT: R 18 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: R 138 PHE cc_start: 0.9262 (m-80) cc_final: 0.8915 (m-10) REVERT: R 324 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8589 (tm-30) REVERT: S 102 ARG cc_start: 0.9069 (ttm110) cc_final: 0.8713 (ttm110) REVERT: S 166 ASP cc_start: 0.9254 (m-30) cc_final: 0.8976 (m-30) REVERT: T 10 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: T 89 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8578 (m) REVERT: T 118 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7176 (tm-30) REVERT: T 141 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8794 (mm) REVERT: T 210 GLU cc_start: 0.9016 (pt0) cc_final: 0.8288 (tm-30) REVERT: U 24 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8542 (pp20) REVERT: U 25 ASN cc_start: 0.9133 (m110) cc_final: 0.8721 (m110) REVERT: U 146 LYS cc_start: 0.9323 (mppt) cc_final: 0.9072 (mmmt) REVERT: U 338 ASN cc_start: 0.9371 (m-40) cc_final: 0.9016 (m110) REVERT: V 41 MET cc_start: 0.9263 (tpp) cc_final: 0.9027 (mmm) REVERT: V 105 ASN cc_start: 0.9509 (t0) cc_final: 0.9227 (t0) REVERT: V 234 CYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8218 (t) REVERT: V 338 ASN cc_start: 0.9635 (t0) cc_final: 0.9331 (t0) REVERT: W 41 MET cc_start: 0.9255 (mmm) cc_final: 0.8956 (mmm) REVERT: W 97 ILE cc_start: 0.8541 (pt) cc_final: 0.8042 (tt) outliers start: 62 outliers final: 35 residues processed: 229 average time/residue: 1.2294 time to fit residues: 344.0793 Evaluate side-chains 200 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain P residue 98 THR Chi-restraints excluded: chain P residue 127 TYR 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 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 68 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 305 LEU Chi-restraints excluded: chain T residue 10 GLU Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 89 VAL 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 W residue 40 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 164 HIS Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 52 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 213 optimal weight: 0.4980 chunk 263 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN T 25 ASN ** U 203 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.087500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060357 restraints weight = 73214.880| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.19 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23716 Z= 0.123 Angle : 0.623 12.586 32391 Z= 0.310 Chirality : 0.040 0.236 3630 Planarity : 0.004 0.045 3903 Dihedral : 15.945 78.565 3873 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.74 % Favored : 96.00 % Rotamer: Outliers : 1.88 % Allowed : 29.40 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2677 helix: 1.62 (0.13), residues: 1593 sheet: -1.01 (0.39), residues: 196 loop : -0.63 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 122 HIS 0.010 0.001 HIS P 80 PHE 0.025 0.001 PHE W 126 TYR 0.027 0.001 TYR T 103 ARG 0.009 0.000 ARG V 131 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 1212) hydrogen bonds : angle 3.79556 ( 3330) covalent geometry : bond 0.00277 (23716) covalent geometry : angle 0.62333 (32391) ********************** 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 222 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8834 (tt) REVERT: P 94 MET cc_start: 0.8495 (pmt) cc_final: 0.7953 (pmm) REVERT: P 120 LEU cc_start: 0.8629 (pt) cc_final: 0.8162 (mt) REVERT: P 125 MET cc_start: 0.7030 (pmm) cc_final: 0.6770 (pmm) REVERT: P 134 ASN cc_start: 0.9557 (p0) cc_final: 0.9141 (t0) REVERT: P 135 TYR cc_start: 0.9055 (m-80) cc_final: 0.8536 (m-80) REVERT: P 154 TYR cc_start: 0.8877 (p90) cc_final: 0.8334 (p90) REVERT: P 155 GLU cc_start: 0.8968 (mp0) cc_final: 0.8653 (mp0) REVERT: P 166 PHE cc_start: 0.9048 (m-80) cc_final: 0.6809 (m-80) REVERT: P 173 ARG cc_start: 0.9173 (tpp80) cc_final: 0.8877 (ttm-80) REVERT: P 180 HIS cc_start: 0.9068 (m-70) cc_final: 0.8525 (m-70) REVERT: P 188 MET cc_start: 0.7942 (mmm) cc_final: 0.7403 (mmm) REVERT: P 298 GLU cc_start: 0.8767 (tp30) cc_final: 0.8216 (mm-30) REVERT: Q 71 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8391 (mt-10) REVERT: Q 164 HIS cc_start: 0.8530 (t70) cc_final: 0.8278 (t-90) REVERT: Q 172 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8648 (mp0) REVERT: Q 188 GLN cc_start: 0.8992 (mm110) cc_final: 0.8646 (mm110) REVERT: Q 198 MET cc_start: 0.8843 (mpm) cc_final: 0.8132 (tmm) REVERT: Q 321 GLU cc_start: 0.9020 (tt0) cc_final: 0.8391 (tm-30) REVERT: R 18 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: R 138 PHE cc_start: 0.9250 (m-80) cc_final: 0.8877 (m-10) REVERT: R 324 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8349 (tm-30) REVERT: S 102 ARG cc_start: 0.8721 (ttm110) cc_final: 0.8240 (ttm110) REVERT: S 128 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: S 166 ASP cc_start: 0.8796 (m-30) cc_final: 0.8521 (m-30) REVERT: T 210 GLU cc_start: 0.8715 (pt0) cc_final: 0.8114 (tm-30) REVERT: T 283 ASP cc_start: 0.8933 (m-30) cc_final: 0.8394 (t0) REVERT: U 19 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8677 (mtm180) REVERT: U 24 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8100 (pp20) REVERT: U 25 ASN cc_start: 0.8868 (m110) cc_final: 0.8347 (m110) REVERT: U 146 LYS cc_start: 0.9205 (mppt) cc_final: 0.8972 (mmmt) REVERT: U 338 ASN cc_start: 0.9292 (m-40) cc_final: 0.8873 (m110) REVERT: V 41 MET cc_start: 0.9102 (tpp) cc_final: 0.8759 (mmm) REVERT: V 95 GLU cc_start: 0.8050 (pm20) cc_final: 0.7745 (pm20) REVERT: V 105 ASN cc_start: 0.9444 (t0) cc_final: 0.9124 (t0) REVERT: V 234 CYS cc_start: 0.8794 (m) cc_final: 0.8066 (t) REVERT: V 338 ASN cc_start: 0.9612 (t0) cc_final: 0.9293 (t0) REVERT: W 41 MET cc_start: 0.9193 (mmm) cc_final: 0.8902 (mmm) REVERT: W 97 ILE cc_start: 0.8450 (pt) cc_final: 0.8039 (tt) REVERT: W 198 MET cc_start: 0.8127 (mtm) cc_final: 0.7402 (mtp) outliers start: 44 outliers final: 33 residues processed: 218 average time/residue: 1.2671 time to fit residues: 336.5038 Evaluate side-chains 202 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 222 GLN 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 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 S residue 305 LEU Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 89 VAL 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 W residue 40 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 105 ASN Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 235 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 162 HIS R 188 GLN S 30 HIS S 142 ASN 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** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.087727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060687 restraints weight = 73395.509| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.17 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3431 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= 0.123 Angle : 0.623 12.614 32391 Z= 0.310 Chirality : 0.040 0.232 3630 Planarity : 0.004 0.044 3903 Dihedral : 15.819 79.309 3873 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.62 % Favored : 96.12 % Rotamer: Outliers : 2.10 % Allowed : 29.44 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2677 helix: 1.64 (0.13), residues: 1593 sheet: -1.03 (0.39), residues: 196 loop : -0.63 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 122 HIS 0.010 0.001 HIS P 80 PHE 0.040 0.001 PHE W 126 TYR 0.020 0.001 TYR Q 109 ARG 0.008 0.000 ARG V 131 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1212) hydrogen bonds : angle 3.75767 ( 3330) covalent geometry : bond 0.00277 (23716) covalent geometry : angle 0.62317 (32391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13832.77 seconds wall clock time: 244 minutes 37.06 seconds (14677.06 seconds total)