Starting phenix.real_space_refine on Fri Aug 7 04:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zzk_75004/08_2026/9zzk_75004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zzk_75004/08_2026/9zzk_75004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zzk_75004/08_2026/9zzk_75004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zzk_75004/08_2026/9zzk_75004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zzk_75004/08_2026/9zzk_75004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zzk_75004/08_2026/9zzk_75004.map" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 13 5.49 5 Mg 6 5.21 5 S 131 5.16 5 C 11839 2.51 5 N 3181 2.21 5 O 3621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18791 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2830 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1359 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2830 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" 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: 3.91, per 1000 atoms: 0.21 Number of scatterers: 18791 At special positions: 0 Unit cell: (87.731, 100.415, 214.571, 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 131 16.00 P 13 15.00 Mg 6 11.99 O 3621 8.00 N 3181 7.00 C 11839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 749.4 milliseconds 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 34 sheets defined 47.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.801A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.708A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.046A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.685A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.584A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.007A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.681A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.523A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.820A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.536A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.820A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.761A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.581A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.768A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.792A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.914A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.081A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 4.061A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.949A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.558A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.535A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.762A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.818A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.686A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.625A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.637A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.501A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 306 removed outlier: 4.111A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.756A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.584A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.925A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.676A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.849A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.959A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.540A pdb=" N PHE D 266 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.540A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.589A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 302 through 306' Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.862A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.868A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.692A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 4.008A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.508A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 205 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.871A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 263 through 267 removed outlier: 3.534A pdb=" N PHE E 266 " --> pdb=" O GLN E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.551A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.542A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.818A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 208 removed outlier: 3.599A pdb=" N LEU M 203 " --> pdb=" O ILE M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 236 Processing helix chain 'M' and resid 253 through 265 Processing helix chain 'M' and resid 281 through 291 removed outlier: 3.784A pdb=" N ALA M 291 " --> pdb=" O ALA M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 322 removed outlier: 3.706A pdb=" N GLU M 315 " --> pdb=" O GLY M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 363 removed outlier: 4.744A pdb=" N GLN M 355 " --> pdb=" O ASN M 351 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG M 356 " --> pdb=" O MET M 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 92 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.502A pdb=" N GLU O 125 " --> pdb=" O GLN O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 145 Processing helix chain 'O' and resid 181 through 197 Processing helix chain 'O' and resid 205 through 217 removed outlier: 3.809A pdb=" N CYS O 217 " --> pdb=" O LYS O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 233 removed outlier: 3.765A pdb=" N ALA O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER O 233 " --> pdb=" O THR O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 255 removed outlier: 3.520A pdb=" N ARG O 254 " --> pdb=" O GLY O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 263 removed outlier: 4.255A pdb=" N PHE O 262 " --> pdb=" O PRO O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 267 removed outlier: 3.510A pdb=" N ILE O 267 " --> pdb=" O PRO O 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 264 through 267' Processing helix chain 'O' and resid 273 through 284 Processing helix chain 'O' and resid 289 through 295 removed outlier: 3.589A pdb=" N ALA O 295 " --> pdb=" O LYS O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 321 removed outlier: 3.756A pdb=" N ARG O 312 " --> pdb=" O GLY O 308 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 348 removed outlier: 3.526A pdb=" N GLY O 343 " --> pdb=" O VAL O 339 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 366 Processing helix chain 'O' and resid 367 through 369 No H-bonds generated for 'chain 'O' and resid 367 through 369' Processing helix chain 'O' and resid 370 through 375 removed outlier: 3.857A pdb=" N CYS O 374 " --> pdb=" O VAL O 370 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE O 375 " --> pdb=" O HIS O 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 370 through 375' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.576A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 7.456A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.965A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 357 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.085A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.034A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB5, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.609A pdb=" N ILE C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.070A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.116A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC2, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.215A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.416A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.301A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'M' and resid 215 through 217 removed outlier: 3.650A pdb=" N SER M 246 " --> pdb=" O VAL M 216 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN M 274 " --> pdb=" O PHE M 245 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL M 273 " --> pdb=" O GLU M 300 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG M 302 " --> pdb=" O VAL M 273 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 8 through 11 Processing sheet with id=AD4, first strand: chain 'O' and resid 35 through 38 Processing sheet with id=AD5, first strand: chain 'O' and resid 103 through 107 removed outlier: 3.734A pdb=" N GLU O 107 " --> pdb=" O ALA O 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 176 through 178 removed outlier: 6.048A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN O 297 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 238 through 241 825 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 1.77 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: 5743 1.34 - 1.46: 4479 1.46 - 1.59: 8716 1.59 - 1.71: 18 1.71 - 1.84: 231 Bond restraints: 19187 Sorted by residual: bond pdb=" CB MET B 44 " pdb=" CG MET B 44 " ideal model delta sigma weight residual 1.520 1.420 0.100 3.00e-02 1.11e+03 1.12e+01 bond pdb=" CA PRO A 332 " pdb=" C PRO A 332 " ideal model delta sigma weight residual 1.517 1.499 0.018 6.70e-03 2.23e+04 7.45e+00 bond pdb=" C ARG C 116 " pdb=" N GLU C 117 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.31e-02 5.83e+03 4.90e+00 bond pdb=" CB GLN A 354 " pdb=" CG GLN A 354 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.75e+00 bond pdb=" CB GLU C 270 " pdb=" CG GLU C 270 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.43e+00 ... (remaining 19182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 25719 4.88 - 9.76: 277 9.76 - 14.64: 34 14.64 - 19.52: 5 19.52 - 24.40: 1 Bond angle restraints: 26036 Sorted by residual: angle pdb=" CA LEU O 171 " pdb=" CB LEU O 171 " pdb=" CG LEU O 171 " ideal model delta sigma weight residual 116.30 140.70 -24.40 3.50e+00 8.16e-02 4.86e+01 angle pdb=" N GLY B 46 " pdb=" CA GLY B 46 " pdb=" C GLY B 46 " ideal model delta sigma weight residual 113.18 129.20 -16.02 2.37e+00 1.78e-01 4.57e+01 angle pdb=" CA GLU O 167 " pdb=" CB GLU O 167 " pdb=" CG GLU O 167 " ideal model delta sigma weight residual 114.10 125.91 -11.81 2.00e+00 2.50e-01 3.49e+01 angle pdb=" CA GLU C 117 " pdb=" CB GLU C 117 " pdb=" CG GLU C 117 " ideal model delta sigma weight residual 114.10 125.72 -11.62 2.00e+00 2.50e-01 3.38e+01 angle pdb=" C SER M 208 " pdb=" N ASN M 209 " pdb=" CA ASN M 209 " ideal model delta sigma weight residual 122.82 131.03 -8.21 1.42e+00 4.96e-01 3.35e+01 ... (remaining 26031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.15: 10817 20.15 - 40.29: 672 40.29 - 60.44: 77 60.44 - 80.59: 23 80.59 - 100.73: 5 Dihedral angle restraints: 11594 sinusoidal: 4708 harmonic: 6886 Sorted by residual: dihedral pdb=" CA VAL M 198 " pdb=" C VAL M 198 " pdb=" N ILE M 199 " pdb=" CA ILE M 199 " ideal model delta harmonic sigma weight residual 180.00 118.57 61.43 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA MET B 44 " pdb=" C MET B 44 " pdb=" N VAL B 45 " pdb=" CA VAL B 45 " ideal model delta harmonic sigma weight residual -180.00 -141.99 -38.01 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA ILE M 199 " pdb=" C ILE M 199 " pdb=" N GLU M 200 " pdb=" CA GLU M 200 " ideal model delta harmonic sigma weight residual 180.00 -143.88 -36.12 0 5.00e+00 4.00e-02 5.22e+01 ... (remaining 11591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 2849 0.172 - 0.343: 60 0.343 - 0.515: 2 0.515 - 0.686: 0 0.686 - 0.858: 1 Chirality restraints: 2912 Sorted by residual: chirality pdb=" CG LEU O 171 " pdb=" CB LEU O 171 " pdb=" CD1 LEU O 171 " pdb=" CD2 LEU O 171 " both_signs ideal model delta sigma weight residual False -2.59 -1.73 -0.86 2.00e-01 2.50e+01 1.84e+01 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CB ILE B 64 " pdb=" CA ILE B 64 " pdb=" CG1 ILE B 64 " pdb=" CG2 ILE B 64 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 2909 not shown) Planarity restraints: 3327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN M 357 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" CD GLN M 357 " 0.061 2.00e-02 2.50e+03 pdb=" OE1 GLN M 357 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 GLN M 357 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 356 " 0.028 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP O 356 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP O 356 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP O 356 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP O 356 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 356 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP O 356 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 356 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 356 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP O 356 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 303 " 0.023 2.00e-02 2.50e+03 2.61e-02 1.19e+01 pdb=" CG PHE M 303 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE M 303 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE M 303 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE M 303 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE M 303 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE M 303 " 0.002 2.00e-02 2.50e+03 ... (remaining 3324 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 49 2.65 - 3.21: 15671 3.21 - 3.78: 29728 3.78 - 4.34: 41021 4.34 - 4.90: 65893 Nonbonded interactions: 152362 Sorted by model distance: nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.090 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.092 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.096 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.101 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.134 2.170 ... (remaining 152357 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 'A' and resid 5 through 375) selection = (chain 'B' and (resid 5 through 39 or resid 50 through 375)) selection = (chain 'C' and (resid 5 through 39 or resid 50 through 375)) selection = (chain 'D' and (resid 5 through 39 or resid 50 through 375)) selection = (chain 'E' and (resid 5 through 39 or resid 50 through 375)) selection = (chain 'O' and resid 5 through 375) } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.320 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.006 0.100 19187 Z= 0.297 Angle : 1.297 24.405 26036 Z= 0.662 Chirality : 0.069 0.858 2912 Planarity : 0.010 0.085 3327 Dihedral : 13.111 100.733 7174 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.15), residues: 2342 helix: -2.68 (0.11), residues: 991 sheet: -0.18 (0.26), residues: 400 loop : -0.99 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 28 TYR 0.033 0.003 TYR B 143 PHE 0.061 0.003 PHE M 303 TRP 0.059 0.004 TRP O 356 HIS 0.012 0.002 HIS E 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.30 (19187) covalent geometry : angle 1.29738 / 0.66 (26036) hydrogen bonds : bond 0.16302 / 10.56 ( 819) hydrogen bonds : angle 7.45079 / 5.16 ( 2220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9323 (tpt) cc_final: 0.8934 (tpp) REVERT: A 83 GLU cc_start: 0.8632 (tp30) cc_final: 0.8281 (mm-30) REVERT: A 104 LEU cc_start: 0.9147 (mt) cc_final: 0.8891 (mt) REVERT: A 123 MET cc_start: 0.9340 (mmp) cc_final: 0.9110 (mmp) REVERT: A 154 ASP cc_start: 0.8847 (t0) cc_final: 0.8423 (p0) REVERT: A 239 SER cc_start: 0.8866 (p) cc_final: 0.8657 (m) REVERT: A 283 MET cc_start: 0.9273 (mmm) cc_final: 0.8935 (mmm) REVERT: A 305 MET cc_start: 0.9012 (mmm) cc_final: 0.8349 (mmm) REVERT: A 328 LYS cc_start: 0.9173 (mppt) cc_final: 0.8872 (mppt) REVERT: B 121 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8867 (tm-30) REVERT: B 127 PHE cc_start: 0.8890 (m-80) cc_final: 0.8491 (m-80) REVERT: B 132 MET cc_start: 0.8368 (tmm) cc_final: 0.7699 (tmm) REVERT: B 269 MET cc_start: 0.7845 (mmm) cc_final: 0.7284 (mtt) REVERT: B 283 MET cc_start: 0.9472 (mmm) cc_final: 0.9187 (mmm) REVERT: B 284 LYS cc_start: 0.9624 (ptmt) cc_final: 0.9400 (ttpt) REVERT: B 305 MET cc_start: 0.7805 (mmp) cc_final: 0.7376 (mmm) REVERT: C 44 MET cc_start: 0.7395 (tpt) cc_final: 0.6878 (tpp) REVERT: C 119 MET cc_start: 0.9031 (ptp) cc_final: 0.8709 (ptp) REVERT: C 153 LEU cc_start: 0.9346 (tt) cc_final: 0.9051 (pt) REVERT: C 154 ASP cc_start: 0.8845 (t0) cc_final: 0.8612 (t0) REVERT: C 265 SER cc_start: 0.9510 (p) cc_final: 0.9146 (t) REVERT: C 305 MET cc_start: 0.9041 (mmp) cc_final: 0.8716 (mmm) REVERT: D 65 LEU cc_start: 0.8777 (mm) cc_final: 0.8540 (tp) REVERT: D 82 MET cc_start: 0.8705 (tpt) cc_final: 0.7381 (tmm) REVERT: D 119 MET cc_start: 0.9047 (mtm) cc_final: 0.8742 (mtm) REVERT: D 283 MET cc_start: 0.9196 (mmm) cc_final: 0.8610 (mmm) REVERT: E 44 MET cc_start: 0.8860 (mtp) cc_final: 0.8382 (mtt) REVERT: E 132 MET cc_start: 0.8782 (ppp) cc_final: 0.8491 (ppp) REVERT: E 176 MET cc_start: 0.8193 (mmm) cc_final: 0.7993 (mmm) REVERT: E 184 ASP cc_start: 0.9353 (m-30) cc_final: 0.9151 (m-30) REVERT: E 185 LEU cc_start: 0.9437 (mt) cc_final: 0.9065 (mt) REVERT: E 192 ILE cc_start: 0.9588 (pt) cc_final: 0.9184 (mm) REVERT: E 283 MET cc_start: 0.9153 (mmm) cc_final: 0.8888 (mmm) REVERT: E 313 MET cc_start: 0.9449 (tpp) cc_final: 0.9040 (tpp) REVERT: M 262 GLU cc_start: 0.8971 (pt0) cc_final: 0.8719 (pp20) REVERT: M 269 HIS cc_start: 0.6532 (t-90) cc_final: 0.6315 (t-90) REVERT: M 310 MET cc_start: 0.6670 (tpt) cc_final: 0.5756 (tmm) REVERT: O 82 MET cc_start: 0.3386 (mmt) cc_final: 0.2438 (mmt) REVERT: O 283 MET cc_start: 0.7784 (mmm) cc_final: 0.7528 (mmm) REVERT: O 299 MET cc_start: 0.7896 (mmm) cc_final: 0.6450 (tpp) REVERT: O 325 MET cc_start: 0.5604 (mmm) cc_final: 0.5271 (mpp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1233 time to fit residues: 48.8969 Evaluate side-chains 188 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS B 41 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS C 371 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 371 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS M 220 ASN M 304 HIS M 357 GLN O 296 ASN O 297 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.068496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048380 restraints weight = 106770.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.049794 restraints weight = 60098.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.050755 restraints weight = 39896.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051356 restraints weight = 29924.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.051738 restraints weight = 24541.064| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19187 Z= 0.224 Angle : 0.707 9.253 26036 Z= 0.358 Chirality : 0.045 0.172 2912 Planarity : 0.006 0.057 3327 Dihedral : 6.768 89.412 2684 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.20 % Rotamer: Outliers : 0.20 % Allowed : 2.08 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2342 helix: -0.60 (0.15), residues: 1009 sheet: -0.03 (0.26), residues: 420 loop : 0.04 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 147 TYR 0.020 0.002 TYR B 166 PHE 0.015 0.002 PHE E 21 TRP 0.020 0.002 TRP O 356 HIS 0.010 0.002 HIS O 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (19187) covalent geometry : angle 0.70700 / 0.36 (26036) hydrogen bonds : bond 0.03532 / 2.32 ( 819) hydrogen bonds : angle 5.04962 / 3.48 ( 2220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 212 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.9170 (mmp) cc_final: 0.8846 (mmm) REVERT: A 154 ASP cc_start: 0.8646 (t0) cc_final: 0.8314 (p0) REVERT: A 257 CYS cc_start: 0.8093 (t) cc_final: 0.7876 (t) REVERT: A 313 MET cc_start: 0.9298 (tpt) cc_final: 0.8959 (tpp) REVERT: B 127 PHE cc_start: 0.8810 (m-80) cc_final: 0.8513 (m-80) REVERT: B 187 ASP cc_start: 0.9376 (m-30) cc_final: 0.9174 (m-30) REVERT: B 257 CYS cc_start: 0.8692 (t) cc_final: 0.8492 (t) REVERT: B 269 MET cc_start: 0.8160 (mmm) cc_final: 0.7566 (mtt) REVERT: B 299 MET cc_start: 0.8796 (tpp) cc_final: 0.8275 (tpp) REVERT: B 305 MET cc_start: 0.7934 (mmp) cc_final: 0.7550 (mmp) REVERT: B 355 MET cc_start: 0.9086 (pmm) cc_final: 0.8614 (pmm) REVERT: C 44 MET cc_start: 0.7531 (tpt) cc_final: 0.7147 (tpp) REVERT: C 82 MET cc_start: 0.9093 (tpt) cc_final: 0.8801 (tpp) REVERT: C 104 LEU cc_start: 0.9232 (tp) cc_final: 0.8962 (tp) REVERT: C 119 MET cc_start: 0.8969 (ptp) cc_final: 0.8638 (ptm) REVERT: C 154 ASP cc_start: 0.8931 (t0) cc_final: 0.8587 (t0) REVERT: C 176 MET cc_start: 0.9222 (mmm) cc_final: 0.8561 (mmm) REVERT: C 190 MET cc_start: 0.9320 (mtm) cc_final: 0.8950 (mtp) REVERT: C 269 MET cc_start: 0.8292 (mmm) cc_final: 0.7635 (mtt) REVERT: C 283 MET cc_start: 0.9383 (mmm) cc_final: 0.8927 (tpp) REVERT: D 82 MET cc_start: 0.9139 (tpt) cc_final: 0.8032 (tmm) REVERT: D 119 MET cc_start: 0.9077 (mtm) cc_final: 0.8683 (mtp) REVERT: D 190 MET cc_start: 0.9180 (mtm) cc_final: 0.8942 (mtm) REVERT: D 299 MET cc_start: 0.8833 (tpp) cc_final: 0.8432 (tpp) REVERT: E 44 MET cc_start: 0.8718 (mtp) cc_final: 0.8382 (mtt) REVERT: E 80 ASP cc_start: 0.8823 (m-30) cc_final: 0.8410 (p0) REVERT: E 185 LEU cc_start: 0.9566 (mt) cc_final: 0.9209 (mt) REVERT: M 262 GLU cc_start: 0.9220 (pt0) cc_final: 0.8904 (pp20) REVERT: M 263 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7975 (mpp) REVERT: M 269 HIS cc_start: 0.6701 (t-90) cc_final: 0.6377 (t-90) REVERT: M 283 LYS cc_start: 0.8071 (ptmm) cc_final: 0.7810 (ptmm) REVERT: M 289 MET cc_start: 0.7171 (ppp) cc_final: 0.6670 (ppp) REVERT: M 308 HIS cc_start: 0.5318 (t-170) cc_final: 0.4972 (p90) REVERT: M 310 MET cc_start: 0.6934 (tpt) cc_final: 0.6260 (tpt) REVERT: M 335 PHE cc_start: 0.8923 (m-80) cc_final: 0.8683 (m-80) REVERT: O 82 MET cc_start: 0.3212 (mmt) cc_final: 0.1909 (mmm) REVERT: O 110 LEU cc_start: 0.7722 (mm) cc_final: 0.7500 (mp) REVERT: O 227 MET cc_start: 0.3343 (mmp) cc_final: 0.3123 (mmp) REVERT: O 299 MET cc_start: 0.8205 (mmm) cc_final: 0.6784 (tpp) REVERT: O 305 MET cc_start: 0.7100 (mmm) cc_final: 0.6697 (mmm) REVERT: O 325 MET cc_start: 0.7000 (mmm) cc_final: 0.6503 (mmm) outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.1246 time to fit residues: 41.9958 Evaluate side-chains 168 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 118 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 201 optimal weight: 40.0000 chunk 225 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN M 306 GLN O 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.066984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046565 restraints weight = 106360.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047771 restraints weight = 60469.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.048691 restraints weight = 40484.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049317 restraints weight = 30452.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.049699 restraints weight = 25096.146| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19187 Z= 0.186 Angle : 0.641 7.543 26036 Z= 0.320 Chirality : 0.045 0.164 2912 Planarity : 0.005 0.076 3327 Dihedral : 6.439 87.271 2684 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2342 helix: 0.22 (0.16), residues: 1000 sheet: 0.26 (0.27), residues: 409 loop : 0.17 (0.22), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 28 TYR 0.017 0.001 TYR B 143 PHE 0.011 0.001 PHE M 303 TRP 0.010 0.001 TRP C 79 HIS 0.006 0.001 HIS O 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (19187) covalent geometry : angle 0.64112 / 0.32 (26036) hydrogen bonds : bond 0.03295 / 2.15 ( 819) hydrogen bonds : angle 4.75991 / 3.28 ( 2220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9545 (mtm) cc_final: 0.9246 (mtt) REVERT: A 123 MET cc_start: 0.9246 (mmp) cc_final: 0.8919 (mmm) REVERT: A 154 ASP cc_start: 0.8512 (t0) cc_final: 0.8250 (p0) REVERT: A 283 MET cc_start: 0.9326 (mmm) cc_final: 0.9062 (mmm) REVERT: A 313 MET cc_start: 0.9119 (tpt) cc_final: 0.8726 (tpp) REVERT: B 11 ASP cc_start: 0.8583 (t0) cc_final: 0.8173 (t0) REVERT: B 44 MET cc_start: 0.6700 (mmp) cc_final: 0.6432 (mmp) REVERT: B 119 MET cc_start: 0.9112 (mpp) cc_final: 0.8570 (mmm) REVERT: B 127 PHE cc_start: 0.8783 (m-80) cc_final: 0.8538 (m-80) REVERT: B 269 MET cc_start: 0.8154 (mmm) cc_final: 0.7671 (mtt) REVERT: B 299 MET cc_start: 0.8744 (tpp) cc_final: 0.8459 (mmm) REVERT: B 355 MET cc_start: 0.9151 (pmm) cc_final: 0.8572 (pmm) REVERT: C 44 MET cc_start: 0.7553 (tpt) cc_final: 0.7016 (tpp) REVERT: C 104 LEU cc_start: 0.9282 (tp) cc_final: 0.9077 (tp) REVERT: C 119 MET cc_start: 0.9016 (ptp) cc_final: 0.8547 (ptm) REVERT: C 154 ASP cc_start: 0.9013 (t0) cc_final: 0.8659 (t0) REVERT: C 190 MET cc_start: 0.9301 (mtm) cc_final: 0.9020 (mtp) REVERT: C 283 MET cc_start: 0.9395 (mmm) cc_final: 0.9000 (tpp) REVERT: D 82 MET cc_start: 0.9121 (tpt) cc_final: 0.7940 (tmm) REVERT: D 119 MET cc_start: 0.9062 (mtm) cc_final: 0.8745 (mtp) REVERT: D 176 MET cc_start: 0.8075 (ptp) cc_final: 0.7661 (mtm) REVERT: D 292 ASP cc_start: 0.8787 (m-30) cc_final: 0.8332 (t0) REVERT: D 299 MET cc_start: 0.8930 (tpp) cc_final: 0.8317 (tpp) REVERT: E 10 CYS cc_start: 0.7606 (t) cc_final: 0.7101 (t) REVERT: E 44 MET cc_start: 0.8720 (mtp) cc_final: 0.8420 (mtt) REVERT: E 80 ASP cc_start: 0.8818 (m-30) cc_final: 0.8410 (p0) REVERT: E 185 LEU cc_start: 0.9535 (mt) cc_final: 0.9139 (mt) REVERT: E 226 GLU cc_start: 0.8901 (tt0) cc_final: 0.8697 (tm-30) REVERT: M 262 GLU cc_start: 0.9178 (pt0) cc_final: 0.8846 (pp20) REVERT: M 283 LYS cc_start: 0.8170 (ptmm) cc_final: 0.7915 (ptmm) REVERT: M 289 MET cc_start: 0.7229 (ppp) cc_final: 0.6814 (ppp) REVERT: M 335 PHE cc_start: 0.8911 (m-80) cc_final: 0.7775 (m-80) REVERT: O 82 MET cc_start: 0.3522 (mmt) cc_final: 0.2299 (mmm) REVERT: O 299 MET cc_start: 0.8337 (mmm) cc_final: 0.7062 (tpp) REVERT: O 305 MET cc_start: 0.7351 (mmm) cc_final: 0.7008 (mmm) REVERT: O 325 MET cc_start: 0.7205 (mmm) cc_final: 0.6811 (mmm) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.1100 time to fit residues: 35.2835 Evaluate side-chains 163 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 114 optimal weight: 0.0870 chunk 164 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN O 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.066481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046383 restraints weight = 105885.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.047526 restraints weight = 60067.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048443 restraints weight = 39642.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049061 restraints weight = 29632.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049397 restraints weight = 24378.380| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19187 Z= 0.166 Angle : 0.613 9.417 26036 Z= 0.303 Chirality : 0.044 0.160 2912 Planarity : 0.004 0.063 3327 Dihedral : 6.166 83.085 2684 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2342 helix: 0.57 (0.17), residues: 997 sheet: 0.16 (0.26), residues: 437 loop : 0.40 (0.23), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 28 TYR 0.012 0.001 TYR B 143 PHE 0.024 0.001 PHE M 335 TRP 0.011 0.001 TRP E 79 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (19187) covalent geometry : angle 0.61272 / 0.30 (26036) hydrogen bonds : bond 0.03056 / 2.01 ( 819) hydrogen bonds : angle 4.60468 / 3.18 ( 2220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.9279 (mmp) cc_final: 0.8954 (mmm) REVERT: A 313 MET cc_start: 0.9108 (tpt) cc_final: 0.8692 (tpp) REVERT: B 119 MET cc_start: 0.9124 (mpp) cc_final: 0.8659 (mpp) REVERT: B 269 MET cc_start: 0.8153 (mmm) cc_final: 0.7610 (mtt) REVERT: C 44 MET cc_start: 0.7526 (tpt) cc_final: 0.7053 (tpp) REVERT: C 82 MET cc_start: 0.9017 (tpt) cc_final: 0.8815 (tpp) REVERT: C 104 LEU cc_start: 0.9281 (tp) cc_final: 0.9051 (tp) REVERT: C 119 MET cc_start: 0.9011 (ptp) cc_final: 0.8510 (ptm) REVERT: C 154 ASP cc_start: 0.8953 (t0) cc_final: 0.8557 (t0) REVERT: C 190 MET cc_start: 0.9323 (mtm) cc_final: 0.9007 (mtp) REVERT: C 283 MET cc_start: 0.9375 (mmm) cc_final: 0.9009 (tpp) REVERT: D 82 MET cc_start: 0.9067 (tpt) cc_final: 0.8036 (tmm) REVERT: D 292 ASP cc_start: 0.8724 (m-30) cc_final: 0.8339 (t0) REVERT: D 299 MET cc_start: 0.9001 (tpp) cc_final: 0.8475 (tpp) REVERT: E 10 CYS cc_start: 0.7602 (t) cc_final: 0.7113 (t) REVERT: E 44 MET cc_start: 0.8677 (mtp) cc_final: 0.8444 (mtm) REVERT: E 80 ASP cc_start: 0.8842 (m-30) cc_final: 0.8354 (p0) REVERT: E 185 LEU cc_start: 0.9479 (mt) cc_final: 0.9060 (mt) REVERT: E 227 MET cc_start: 0.9380 (mmm) cc_final: 0.9167 (mmm) REVERT: E 299 MET cc_start: 0.8848 (ttm) cc_final: 0.8644 (ttp) REVERT: M 283 LYS cc_start: 0.8420 (ptmm) cc_final: 0.8137 (ptmm) REVERT: M 289 MET cc_start: 0.7420 (ppp) cc_final: 0.6979 (ppp) REVERT: M 333 TYR cc_start: 0.8933 (t80) cc_final: 0.8701 (t80) REVERT: M 335 PHE cc_start: 0.8404 (m-80) cc_final: 0.7897 (m-80) REVERT: O 82 MET cc_start: 0.3799 (mmt) cc_final: 0.2626 (mmm) REVERT: O 161 HIS cc_start: 0.8389 (m-70) cc_final: 0.8177 (m-70) REVERT: O 299 MET cc_start: 0.8504 (mmm) cc_final: 0.7374 (tpp) REVERT: O 305 MET cc_start: 0.7287 (mmm) cc_final: 0.6915 (mmm) REVERT: O 325 MET cc_start: 0.7476 (mmm) cc_final: 0.7103 (mmm) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1149 time to fit residues: 35.7257 Evaluate side-chains 162 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 107 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.067421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046751 restraints weight = 105074.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048031 restraints weight = 59038.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.048922 restraints weight = 39696.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.049488 restraints weight = 30408.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.049822 restraints weight = 25228.693| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19187 Z= 0.120 Angle : 0.590 7.935 26036 Z= 0.287 Chirality : 0.044 0.159 2912 Planarity : 0.004 0.056 3327 Dihedral : 5.998 79.754 2684 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 0.05 % Allowed : 1.39 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2342 helix: 0.79 (0.17), residues: 992 sheet: 0.25 (0.26), residues: 424 loop : 0.45 (0.23), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 28 TYR 0.011 0.001 TYR B 143 PHE 0.015 0.001 PHE M 303 TRP 0.013 0.001 TRP B 356 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19187) covalent geometry : angle 0.59002 / 0.29 (26036) hydrogen bonds : bond 0.02822 / 1.87 ( 819) hydrogen bonds : angle 4.44385 / 3.05 ( 2220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 CYS cc_start: 0.8313 (t) cc_final: 0.8075 (t) REVERT: A 313 MET cc_start: 0.9175 (tpt) cc_final: 0.8726 (tpp) REVERT: B 119 MET cc_start: 0.9077 (mpp) cc_final: 0.8583 (mmm) REVERT: B 269 MET cc_start: 0.8119 (mmm) cc_final: 0.7562 (mtt) REVERT: B 299 MET cc_start: 0.8797 (mmm) cc_final: 0.8154 (mmm) REVERT: B 355 MET cc_start: 0.9056 (pmm) cc_final: 0.8765 (pmm) REVERT: C 44 MET cc_start: 0.7520 (tpt) cc_final: 0.7036 (tpp) REVERT: C 104 LEU cc_start: 0.9281 (tp) cc_final: 0.9062 (tp) REVERT: C 119 MET cc_start: 0.8964 (ptp) cc_final: 0.8477 (ptm) REVERT: C 154 ASP cc_start: 0.8880 (t0) cc_final: 0.8406 (t0) REVERT: C 190 MET cc_start: 0.9261 (mtm) cc_final: 0.9053 (mtp) REVERT: C 283 MET cc_start: 0.9371 (mmm) cc_final: 0.9028 (tpp) REVERT: D 82 MET cc_start: 0.9051 (tpt) cc_final: 0.8051 (tmm) REVERT: D 292 ASP cc_start: 0.8715 (m-30) cc_final: 0.8378 (t0) REVERT: D 299 MET cc_start: 0.8998 (tpp) cc_final: 0.8346 (tpp) REVERT: E 10 CYS cc_start: 0.7522 (t) cc_final: 0.6977 (t) REVERT: E 80 ASP cc_start: 0.8852 (m-30) cc_final: 0.8371 (p0) REVERT: E 185 LEU cc_start: 0.9423 (mt) cc_final: 0.9060 (mt) REVERT: E 226 GLU cc_start: 0.9005 (tt0) cc_final: 0.8658 (tt0) REVERT: E 299 MET cc_start: 0.8993 (ttm) cc_final: 0.8776 (ttp) REVERT: M 262 GLU cc_start: 0.9079 (pt0) cc_final: 0.8763 (pp20) REVERT: M 283 LYS cc_start: 0.8274 (ptmm) cc_final: 0.8049 (ptmm) REVERT: M 289 MET cc_start: 0.7610 (ppp) cc_final: 0.7120 (ppp) REVERT: M 335 PHE cc_start: 0.8399 (m-80) cc_final: 0.7919 (m-80) REVERT: O 82 MET cc_start: 0.3429 (mmt) cc_final: 0.2247 (mmm) REVERT: O 161 HIS cc_start: 0.8372 (m-70) cc_final: 0.8155 (m-70) REVERT: O 299 MET cc_start: 0.8578 (mmm) cc_final: 0.7458 (tpp) REVERT: O 305 MET cc_start: 0.7345 (mmm) cc_final: 0.7029 (mmm) REVERT: O 325 MET cc_start: 0.7476 (mmm) cc_final: 0.7152 (mmm) outliers start: 1 outliers final: 1 residues processed: 206 average time/residue: 0.1112 time to fit residues: 36.1520 Evaluate side-chains 160 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 198 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 209 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN M 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.062735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.042781 restraints weight = 110602.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043975 restraints weight = 62330.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044833 restraints weight = 41844.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045290 restraints weight = 31771.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045682 restraints weight = 26893.804| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 19187 Z= 0.391 Angle : 0.866 8.770 26036 Z= 0.434 Chirality : 0.049 0.208 2912 Planarity : 0.005 0.046 3327 Dihedral : 6.560 79.773 2684 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2342 helix: 0.15 (0.16), residues: 1010 sheet: 0.00 (0.25), residues: 449 loop : -0.12 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 290 TYR 0.019 0.002 TYR A 91 PHE 0.018 0.002 PHE B 223 TRP 0.051 0.004 TRP O 356 HIS 0.010 0.002 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.39 (19187) covalent geometry : angle 0.86579 / 0.43 (26036) hydrogen bonds : bond 0.04106 / 2.69 ( 819) hydrogen bonds : angle 5.28823 / 3.62 ( 2220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9351 (tpt) cc_final: 0.9124 (tpp) REVERT: A 123 MET cc_start: 0.9511 (mmp) cc_final: 0.9083 (mmp) REVERT: A 257 CYS cc_start: 0.8114 (t) cc_final: 0.7792 (t) REVERT: A 313 MET cc_start: 0.9251 (tpt) cc_final: 0.8762 (tpp) REVERT: B 176 MET cc_start: 0.8858 (mmp) cc_final: 0.8551 (mmm) REVERT: B 190 MET cc_start: 0.9240 (tmm) cc_final: 0.8997 (tmm) REVERT: B 236 LEU cc_start: 0.9473 (mp) cc_final: 0.9045 (tp) REVERT: B 269 MET cc_start: 0.8186 (mmm) cc_final: 0.7786 (mtt) REVERT: B 299 MET cc_start: 0.8826 (mmm) cc_final: 0.8242 (mmm) REVERT: B 325 MET cc_start: 0.8912 (mmm) cc_final: 0.8362 (mmt) REVERT: C 44 MET cc_start: 0.7771 (tpt) cc_final: 0.7216 (tpp) REVERT: C 119 MET cc_start: 0.9098 (ptp) cc_final: 0.8892 (ppp) REVERT: C 123 MET cc_start: 0.9370 (mmp) cc_final: 0.9085 (mmp) REVERT: C 154 ASP cc_start: 0.9021 (t0) cc_final: 0.8489 (t0) REVERT: C 190 MET cc_start: 0.9321 (mtm) cc_final: 0.9109 (mtp) REVERT: C 283 MET cc_start: 0.9433 (mmm) cc_final: 0.9151 (tpp) REVERT: D 47 MET cc_start: 0.7141 (ppp) cc_final: 0.6851 (ppp) REVERT: D 82 MET cc_start: 0.9446 (tpt) cc_final: 0.9090 (mmm) REVERT: D 269 MET cc_start: 0.8646 (mtp) cc_final: 0.8429 (mtm) REVERT: D 283 MET cc_start: 0.9435 (mmp) cc_final: 0.9185 (mmm) REVERT: D 292 ASP cc_start: 0.8965 (m-30) cc_final: 0.8456 (t0) REVERT: D 299 MET cc_start: 0.8887 (tpp) cc_final: 0.8347 (tpp) REVERT: E 10 CYS cc_start: 0.8147 (t) cc_final: 0.7781 (t) REVERT: E 80 ASP cc_start: 0.9091 (m-30) cc_final: 0.8616 (p0) REVERT: E 299 MET cc_start: 0.8849 (ttm) cc_final: 0.8471 (ttp) REVERT: M 283 LYS cc_start: 0.8482 (ptmm) cc_final: 0.8158 (ptmm) REVERT: M 289 MET cc_start: 0.7763 (ppp) cc_final: 0.7266 (ppp) REVERT: M 333 TYR cc_start: 0.9081 (t80) cc_final: 0.8848 (t80) REVERT: M 335 PHE cc_start: 0.8552 (m-80) cc_final: 0.8217 (m-80) REVERT: O 82 MET cc_start: 0.3585 (mmt) cc_final: 0.2531 (mmm) REVERT: O 299 MET cc_start: 0.8728 (mmm) cc_final: 0.7908 (tpp) REVERT: O 305 MET cc_start: 0.7520 (mmm) cc_final: 0.7198 (mmm) REVERT: O 325 MET cc_start: 0.7893 (mmm) cc_final: 0.7637 (mmm) REVERT: O 355 MET cc_start: 0.8305 (mmp) cc_final: 0.7005 (tpt) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1221 time to fit residues: 34.4087 Evaluate side-chains 148 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 1.9990 chunk 106 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 0.0770 chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN M 251 HIS ** O 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.066159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046125 restraints weight = 105243.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.047316 restraints weight = 58404.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048289 restraints weight = 38676.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048802 restraints weight = 28865.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049218 restraints weight = 24193.793| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19187 Z= 0.111 Angle : 0.644 12.679 26036 Z= 0.313 Chirality : 0.045 0.152 2912 Planarity : 0.005 0.097 3327 Dihedral : 6.179 74.924 2684 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2342 helix: 0.70 (0.17), residues: 1000 sheet: 0.11 (0.26), residues: 424 loop : 0.18 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 312 TYR 0.012 0.001 TYR B 143 PHE 0.019 0.001 PHE O 223 TRP 0.040 0.002 TRP O 356 HIS 0.005 0.001 HIS M 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (19187) covalent geometry : angle 0.64438 / 0.31 (26036) hydrogen bonds : bond 0.03057 / 2.04 ( 819) hydrogen bonds : angle 4.59176 / 3.16 ( 2220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.673 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: A 82 MET cc_start: 0.9303 (tpt) cc_final: 0.9069 (tpp) REVERT: A 119 MET cc_start: 0.9550 (mtm) cc_final: 0.9241 (ptp) REVERT: A 123 MET cc_start: 0.9407 (mmp) cc_final: 0.9015 (mmp) REVERT: A 257 CYS cc_start: 0.8294 (t) cc_final: 0.8019 (t) REVERT: A 313 MET cc_start: 0.9318 (tpt) cc_final: 0.8856 (tpp) REVERT: B 82 MET cc_start: 0.8742 (tpt) cc_final: 0.8494 (tpp) REVERT: B 86 TRP cc_start: 0.9473 (m-10) cc_final: 0.8761 (m-10) REVERT: B 176 MET cc_start: 0.8854 (mmp) cc_final: 0.8463 (mmm) REVERT: B 190 MET cc_start: 0.9218 (tmm) cc_final: 0.9009 (tmm) REVERT: B 236 LEU cc_start: 0.9449 (mp) cc_final: 0.9015 (tp) REVERT: B 269 MET cc_start: 0.8166 (mmm) cc_final: 0.7745 (mtt) REVERT: B 299 MET cc_start: 0.8716 (mmm) cc_final: 0.8003 (mmm) REVERT: B 325 MET cc_start: 0.8835 (mmm) cc_final: 0.8279 (mmt) REVERT: C 44 MET cc_start: 0.7578 (tpt) cc_final: 0.6926 (tpp) REVERT: C 82 MET cc_start: 0.8919 (tpt) cc_final: 0.8688 (tpp) REVERT: C 104 LEU cc_start: 0.9356 (tp) cc_final: 0.9133 (tp) REVERT: C 154 ASP cc_start: 0.8832 (t0) cc_final: 0.8240 (t0) REVERT: C 283 MET cc_start: 0.9427 (mmm) cc_final: 0.9112 (tpp) REVERT: D 47 MET cc_start: 0.6970 (ppp) cc_final: 0.6702 (ppp) REVERT: D 82 MET cc_start: 0.9463 (tpt) cc_final: 0.8733 (tmm) REVERT: D 123 MET cc_start: 0.9519 (mmm) cc_final: 0.8615 (mmm) REVERT: D 184 ASP cc_start: 0.9325 (m-30) cc_final: 0.9007 (m-30) REVERT: D 269 MET cc_start: 0.8558 (mtp) cc_final: 0.8304 (mtm) REVERT: D 283 MET cc_start: 0.9425 (mmp) cc_final: 0.9180 (mmm) REVERT: D 292 ASP cc_start: 0.8821 (m-30) cc_final: 0.8372 (t0) REVERT: D 299 MET cc_start: 0.8805 (tpp) cc_final: 0.8066 (tpp) REVERT: D 305 MET cc_start: 0.9280 (mmt) cc_final: 0.8931 (mmm) REVERT: D 325 MET cc_start: 0.7818 (tpp) cc_final: 0.7475 (mmt) REVERT: E 10 CYS cc_start: 0.7775 (t) cc_final: 0.7353 (t) REVERT: E 80 ASP cc_start: 0.8840 (m-30) cc_final: 0.8337 (p0) REVERT: E 132 MET cc_start: 0.9000 (ppp) cc_final: 0.8576 (ppp) REVERT: E 226 GLU cc_start: 0.8937 (tt0) cc_final: 0.8509 (tt0) REVERT: E 299 MET cc_start: 0.8999 (ttm) cc_final: 0.8712 (ttp) REVERT: M 262 GLU cc_start: 0.9040 (pt0) cc_final: 0.8776 (pp20) REVERT: M 283 LYS cc_start: 0.8408 (ptmm) cc_final: 0.8076 (ptmm) REVERT: M 289 MET cc_start: 0.7721 (ppp) cc_final: 0.7294 (ppp) REVERT: M 310 MET cc_start: 0.7804 (tpt) cc_final: 0.7155 (mmm) REVERT: M 335 PHE cc_start: 0.8549 (m-80) cc_final: 0.7882 (m-80) REVERT: O 82 MET cc_start: 0.3402 (mmt) cc_final: 0.2371 (mmm) REVERT: O 176 MET cc_start: 0.8585 (tpt) cc_final: 0.8079 (ptp) REVERT: O 299 MET cc_start: 0.8700 (mmm) cc_final: 0.7763 (tpp) REVERT: O 305 MET cc_start: 0.7397 (mmm) cc_final: 0.7073 (mmm) REVERT: O 355 MET cc_start: 0.8407 (mmp) cc_final: 0.7679 (tpp) REVERT: O 356 TRP cc_start: 0.6667 (m-90) cc_final: 0.6454 (m-90) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1165 time to fit residues: 37.1735 Evaluate side-chains 159 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 187 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 200 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 185 optimal weight: 0.0040 chunk 44 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS D 246 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN O 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.065930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045821 restraints weight = 105651.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047149 restraints weight = 58815.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048052 restraints weight = 39123.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048629 restraints weight = 29550.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.048954 restraints weight = 24406.738| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19187 Z= 0.121 Angle : 0.632 11.312 26036 Z= 0.305 Chirality : 0.045 0.193 2912 Planarity : 0.004 0.079 3327 Dihedral : 5.952 72.056 2684 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2342 helix: 0.86 (0.17), residues: 992 sheet: 0.07 (0.26), residues: 426 loop : 0.35 (0.23), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 341 TYR 0.010 0.001 TYR B 166 PHE 0.020 0.001 PHE O 223 TRP 0.033 0.002 TRP O 356 HIS 0.008 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (19187) covalent geometry : angle 0.63244 / 0.31 (26036) hydrogen bonds : bond 0.02932 / 1.97 ( 819) hydrogen bonds : angle 4.49769 / 3.09 ( 2220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.496 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: A 82 MET cc_start: 0.9321 (tpt) cc_final: 0.9075 (tpp) REVERT: A 123 MET cc_start: 0.9403 (mmp) cc_final: 0.9089 (mmp) REVERT: A 257 CYS cc_start: 0.8480 (t) cc_final: 0.8190 (t) REVERT: A 305 MET cc_start: 0.8686 (mmt) cc_final: 0.7988 (mmp) REVERT: A 313 MET cc_start: 0.9302 (tpt) cc_final: 0.8842 (tpp) REVERT: B 82 MET cc_start: 0.8689 (tpt) cc_final: 0.8457 (tpp) REVERT: B 86 TRP cc_start: 0.9502 (m-10) cc_final: 0.8693 (m-10) REVERT: B 119 MET cc_start: 0.9058 (mpp) cc_final: 0.8697 (mpp) REVERT: B 123 MET cc_start: 0.9245 (mmt) cc_final: 0.8784 (mmt) REVERT: B 176 MET cc_start: 0.8836 (mmp) cc_final: 0.8472 (mmm) REVERT: B 190 MET cc_start: 0.9203 (tmm) cc_final: 0.8987 (tpt) REVERT: B 236 LEU cc_start: 0.9438 (mp) cc_final: 0.9003 (tp) REVERT: B 269 MET cc_start: 0.8151 (mmm) cc_final: 0.7715 (mtt) REVERT: B 299 MET cc_start: 0.8764 (mmm) cc_final: 0.8025 (mmm) REVERT: B 325 MET cc_start: 0.8744 (mmm) cc_final: 0.8210 (mmt) REVERT: C 44 MET cc_start: 0.7624 (tpt) cc_final: 0.6976 (tpp) REVERT: C 104 LEU cc_start: 0.9318 (tp) cc_final: 0.9086 (tp) REVERT: C 154 ASP cc_start: 0.8826 (t0) cc_final: 0.8242 (t0) REVERT: C 283 MET cc_start: 0.9409 (mmm) cc_final: 0.9081 (tpp) REVERT: D 47 MET cc_start: 0.7002 (ppp) cc_final: 0.6798 (ppp) REVERT: D 82 MET cc_start: 0.9450 (tpt) cc_final: 0.8645 (tmm) REVERT: D 123 MET cc_start: 0.9541 (mmm) cc_final: 0.8649 (mmm) REVERT: D 184 ASP cc_start: 0.9326 (m-30) cc_final: 0.9004 (m-30) REVERT: D 269 MET cc_start: 0.8562 (mtp) cc_final: 0.8273 (mtm) REVERT: D 283 MET cc_start: 0.9426 (mmp) cc_final: 0.9180 (mmm) REVERT: D 292 ASP cc_start: 0.8824 (m-30) cc_final: 0.8458 (t0) REVERT: D 299 MET cc_start: 0.8853 (tpp) cc_final: 0.8339 (tpp) REVERT: D 305 MET cc_start: 0.9291 (mmt) cc_final: 0.8961 (mmm) REVERT: D 325 MET cc_start: 0.7841 (tpp) cc_final: 0.7506 (mmt) REVERT: E 10 CYS cc_start: 0.7826 (t) cc_final: 0.7409 (t) REVERT: E 80 ASP cc_start: 0.8874 (m-30) cc_final: 0.8353 (p0) REVERT: E 299 MET cc_start: 0.8977 (ttm) cc_final: 0.8710 (ttp) REVERT: M 262 GLU cc_start: 0.9054 (pt0) cc_final: 0.8825 (pp20) REVERT: M 283 LYS cc_start: 0.8489 (ptmm) cc_final: 0.8121 (ptmm) REVERT: M 289 MET cc_start: 0.7802 (ppp) cc_final: 0.7233 (ppp) REVERT: M 310 MET cc_start: 0.7962 (tpt) cc_final: 0.7439 (mmm) REVERT: M 335 PHE cc_start: 0.8453 (m-80) cc_final: 0.7750 (m-80) REVERT: O 82 MET cc_start: 0.3363 (mmt) cc_final: 0.2292 (mmm) REVERT: O 176 MET cc_start: 0.8664 (tpt) cc_final: 0.8158 (ptp) REVERT: O 283 MET cc_start: 0.9361 (tpp) cc_final: 0.8629 (mmm) REVERT: O 299 MET cc_start: 0.8723 (mmm) cc_final: 0.7829 (tpp) REVERT: O 305 MET cc_start: 0.7387 (mmm) cc_final: 0.6839 (mmm) REVERT: O 355 MET cc_start: 0.8373 (mmp) cc_final: 0.7679 (tpp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1147 time to fit residues: 35.0588 Evaluate side-chains 156 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 82 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 213 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 223 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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 = 0.3489 r_free = 0.3489 target = 0.064427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.044187 restraints weight = 106316.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045524 restraints weight = 58940.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.046370 restraints weight = 39408.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046937 restraints weight = 29941.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047249 restraints weight = 24867.206| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19187 Z= 0.204 Angle : 0.699 11.182 26036 Z= 0.342 Chirality : 0.046 0.191 2912 Planarity : 0.005 0.066 3327 Dihedral : 5.984 69.653 2684 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2342 helix: 0.73 (0.17), residues: 998 sheet: -0.07 (0.26), residues: 433 loop : 0.23 (0.23), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 341 TYR 0.014 0.001 TYR B 166 PHE 0.017 0.002 PHE M 279 TRP 0.027 0.002 TRP O 356 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (19187) covalent geometry : angle 0.69866 / 0.34 (26036) hydrogen bonds : bond 0.03206 / 2.10 ( 819) hydrogen bonds : angle 4.71577 / 3.24 ( 2220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9336 (tpt) cc_final: 0.9106 (tpp) REVERT: A 123 MET cc_start: 0.9512 (mmp) cc_final: 0.9145 (mmp) REVERT: A 257 CYS cc_start: 0.8379 (t) cc_final: 0.8039 (t) REVERT: A 313 MET cc_start: 0.9293 (tpt) cc_final: 0.8812 (tpp) REVERT: B 82 MET cc_start: 0.8703 (tpt) cc_final: 0.8445 (tpp) REVERT: B 86 TRP cc_start: 0.9467 (m-10) cc_final: 0.8587 (m-10) REVERT: B 119 MET cc_start: 0.9128 (mpp) cc_final: 0.8648 (mmm) REVERT: B 123 MET cc_start: 0.9272 (mmt) cc_final: 0.8820 (mmt) REVERT: B 176 MET cc_start: 0.8790 (mmp) cc_final: 0.8433 (mmm) REVERT: B 190 MET cc_start: 0.9212 (tmm) cc_final: 0.8946 (tpt) REVERT: B 236 LEU cc_start: 0.9455 (mp) cc_final: 0.9010 (tp) REVERT: B 269 MET cc_start: 0.8173 (mmm) cc_final: 0.7747 (mtt) REVERT: B 299 MET cc_start: 0.8711 (mmm) cc_final: 0.8001 (mmm) REVERT: B 325 MET cc_start: 0.8865 (mmm) cc_final: 0.8395 (mmt) REVERT: C 44 MET cc_start: 0.7713 (tpt) cc_final: 0.7040 (tpp) REVERT: C 104 LEU cc_start: 0.9324 (tp) cc_final: 0.9085 (tp) REVERT: C 154 ASP cc_start: 0.8901 (t0) cc_final: 0.8365 (t0) REVERT: C 227 MET cc_start: 0.9473 (tpp) cc_final: 0.9133 (tpp) REVERT: C 283 MET cc_start: 0.9405 (mmm) cc_final: 0.9107 (tpp) REVERT: D 47 MET cc_start: 0.7137 (ppp) cc_final: 0.6897 (ppp) REVERT: D 82 MET cc_start: 0.9431 (tpt) cc_final: 0.8701 (tmm) REVERT: D 123 MET cc_start: 0.9532 (mmm) cc_final: 0.8567 (mmm) REVERT: D 184 ASP cc_start: 0.9290 (m-30) cc_final: 0.8967 (m-30) REVERT: D 269 MET cc_start: 0.8603 (mtp) cc_final: 0.8341 (mtm) REVERT: D 283 MET cc_start: 0.9448 (mmp) cc_final: 0.9201 (mmm) REVERT: D 292 ASP cc_start: 0.8852 (m-30) cc_final: 0.8512 (t0) REVERT: D 299 MET cc_start: 0.8852 (tpp) cc_final: 0.8327 (tpp) REVERT: D 305 MET cc_start: 0.9258 (mmt) cc_final: 0.8944 (mmm) REVERT: D 325 MET cc_start: 0.8119 (tpp) cc_final: 0.7758 (mmt) REVERT: E 10 CYS cc_start: 0.8033 (t) cc_final: 0.7628 (t) REVERT: E 80 ASP cc_start: 0.8975 (m-30) cc_final: 0.8454 (p0) REVERT: E 82 MET cc_start: 0.8840 (tpt) cc_final: 0.8564 (tpt) REVERT: E 269 MET cc_start: 0.8594 (mmm) cc_final: 0.8072 (mmm) REVERT: E 299 MET cc_start: 0.8954 (ttm) cc_final: 0.8659 (ttp) REVERT: M 283 LYS cc_start: 0.8464 (ptmm) cc_final: 0.8146 (ptmm) REVERT: M 289 MET cc_start: 0.7692 (ppp) cc_final: 0.7079 (ppp) REVERT: M 310 MET cc_start: 0.8061 (tpt) cc_final: 0.7320 (mmm) REVERT: M 335 PHE cc_start: 0.8540 (m-80) cc_final: 0.8065 (m-80) REVERT: M 342 MET cc_start: 0.7945 (ptm) cc_final: 0.7668 (ptm) REVERT: O 82 MET cc_start: 0.3518 (mmt) cc_final: 0.2446 (mmm) REVERT: O 176 MET cc_start: 0.8606 (tpt) cc_final: 0.8028 (ptm) REVERT: O 299 MET cc_start: 0.8746 (mmm) cc_final: 0.7920 (tpp) REVERT: O 305 MET cc_start: 0.7486 (mmm) cc_final: 0.6953 (mmm) REVERT: O 355 MET cc_start: 0.8317 (mmp) cc_final: 0.7473 (tpp) REVERT: O 356 TRP cc_start: 0.6284 (m-90) cc_final: 0.5764 (m-90) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1182 time to fit residues: 34.6626 Evaluate side-chains 153 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 228 optimal weight: 9.9990 chunk 151 optimal weight: 0.0060 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 HIS ** O 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 = 0.3539 r_free = 0.3539 target = 0.065898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045779 restraints weight = 104859.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047133 restraints weight = 58216.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048030 restraints weight = 38676.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.048591 restraints weight = 29145.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.048917 restraints weight = 24099.033| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19187 Z= 0.114 Angle : 0.648 11.036 26036 Z= 0.312 Chirality : 0.045 0.178 2912 Planarity : 0.004 0.055 3327 Dihedral : 5.813 66.598 2684 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2342 helix: 0.85 (0.17), residues: 997 sheet: 0.04 (0.26), residues: 426 loop : 0.32 (0.23), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 341 TYR 0.011 0.001 TYR B 143 PHE 0.019 0.001 PHE M 303 TRP 0.028 0.002 TRP O 356 HIS 0.005 0.001 HIS O 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (19187) covalent geometry : angle 0.64808 / 0.31 (26036) hydrogen bonds : bond 0.02859 / 1.88 ( 819) hydrogen bonds : angle 4.51362 / 3.11 ( 2220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.687 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: A 82 MET cc_start: 0.9346 (tpt) cc_final: 0.9108 (tpp) REVERT: A 119 MET cc_start: 0.9543 (mtm) cc_final: 0.9286 (ptp) REVERT: A 123 MET cc_start: 0.9476 (mmp) cc_final: 0.9113 (mmp) REVERT: A 257 CYS cc_start: 0.8423 (t) cc_final: 0.8085 (t) REVERT: A 313 MET cc_start: 0.9299 (tpt) cc_final: 0.8834 (tpp) REVERT: B 86 TRP cc_start: 0.9459 (m-10) cc_final: 0.8570 (m-10) REVERT: B 123 MET cc_start: 0.9250 (mmt) cc_final: 0.8808 (mmt) REVERT: B 176 MET cc_start: 0.8803 (mmp) cc_final: 0.8407 (mmm) REVERT: B 190 MET cc_start: 0.9207 (tmm) cc_final: 0.8996 (tpt) REVERT: B 236 LEU cc_start: 0.9444 (mp) cc_final: 0.8974 (tt) REVERT: B 269 MET cc_start: 0.8144 (mmm) cc_final: 0.7667 (mtt) REVERT: B 299 MET cc_start: 0.8787 (mmm) cc_final: 0.8172 (mmm) REVERT: B 325 MET cc_start: 0.8827 (mmm) cc_final: 0.8353 (mmt) REVERT: C 44 MET cc_start: 0.7711 (tpt) cc_final: 0.7059 (tpp) REVERT: C 104 LEU cc_start: 0.9333 (tp) cc_final: 0.9104 (tp) REVERT: C 154 ASP cc_start: 0.8802 (t0) cc_final: 0.8214 (t0) REVERT: C 227 MET cc_start: 0.9453 (tpp) cc_final: 0.9106 (tpp) REVERT: C 283 MET cc_start: 0.9411 (mmm) cc_final: 0.9070 (tpp) REVERT: D 47 MET cc_start: 0.7116 (ppp) cc_final: 0.6882 (ppp) REVERT: D 82 MET cc_start: 0.9434 (tpt) cc_final: 0.8620 (tmm) REVERT: D 123 MET cc_start: 0.9530 (mmm) cc_final: 0.8682 (mmm) REVERT: D 184 ASP cc_start: 0.9340 (m-30) cc_final: 0.9015 (m-30) REVERT: D 269 MET cc_start: 0.8591 (mtp) cc_final: 0.8305 (mtm) REVERT: D 283 MET cc_start: 0.9500 (mmp) cc_final: 0.9248 (mmm) REVERT: D 299 MET cc_start: 0.8871 (tpp) cc_final: 0.8092 (tpp) REVERT: D 305 MET cc_start: 0.9287 (mmt) cc_final: 0.9017 (mmm) REVERT: E 10 CYS cc_start: 0.7862 (t) cc_final: 0.7456 (t) REVERT: E 82 MET cc_start: 0.8744 (tpt) cc_final: 0.8502 (tpt) REVERT: E 269 MET cc_start: 0.8613 (mmm) cc_final: 0.8060 (mmm) REVERT: E 299 MET cc_start: 0.8967 (ttm) cc_final: 0.8698 (ttp) REVERT: M 283 LYS cc_start: 0.8570 (ptmm) cc_final: 0.8175 (ptmm) REVERT: M 289 MET cc_start: 0.7675 (ppp) cc_final: 0.7353 (ppp) REVERT: M 310 MET cc_start: 0.8032 (tpt) cc_final: 0.7685 (mmm) REVERT: M 335 PHE cc_start: 0.8724 (m-80) cc_final: 0.8062 (m-80) REVERT: M 342 MET cc_start: 0.7817 (ptm) cc_final: 0.7529 (ptm) REVERT: O 82 MET cc_start: 0.3317 (mmt) cc_final: 0.2323 (mmm) REVERT: O 176 MET cc_start: 0.8925 (tpt) cc_final: 0.8454 (ptp) REVERT: O 283 MET cc_start: 0.9354 (tpp) cc_final: 0.8605 (mmm) REVERT: O 299 MET cc_start: 0.8681 (mmm) cc_final: 0.7788 (tpp) REVERT: O 305 MET cc_start: 0.7430 (mmm) cc_final: 0.6894 (mmm) REVERT: O 355 MET cc_start: 0.8431 (mmp) cc_final: 0.7741 (tpp) REVERT: O 356 TRP cc_start: 0.5953 (m-90) cc_final: 0.5432 (m-90) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1164 time to fit residues: 34.5155 Evaluate side-chains 154 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 65 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.064507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044590 restraints weight = 108145.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.045886 restraints weight = 60405.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046756 restraints weight = 40357.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047284 restraints weight = 30574.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.047587 restraints weight = 25398.520| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19187 Z= 0.190 Angle : 0.680 10.572 26036 Z= 0.332 Chirality : 0.046 0.174 2912 Planarity : 0.004 0.051 3327 Dihedral : 5.807 63.662 2684 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2342 helix: 0.80 (0.17), residues: 996 sheet: -0.02 (0.26), residues: 433 loop : 0.28 (0.23), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 302 TYR 0.012 0.001 TYR B 166 PHE 0.016 0.001 PHE M 303 TRP 0.025 0.002 TRP O 356 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (19187) covalent geometry : angle 0.68007 / 0.33 (26036) hydrogen bonds : bond 0.03074 / 2.02 ( 819) hydrogen bonds : angle 4.64411 / 3.19 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.36 seconds wall clock time: 53 minutes 13.14 seconds (3193.14 seconds total)