Starting phenix.real_space_refine on Mon Apr 6 14:25:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yim_72998/04_2026/9yim_72998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yim_72998/04_2026/9yim_72998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yim_72998/04_2026/9yim_72998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yim_72998/04_2026/9yim_72998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yim_72998/04_2026/9yim_72998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yim_72998/04_2026/9yim_72998.map" } resolution = 2.62 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= 0.001 sd= 0.006 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 10 5.49 5 Mg 5 5.21 5 S 122 5.16 5 C 11987 2.51 5 N 3235 2.21 5 O 3680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19039 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" 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: "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: "Y" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2259 Classifications: {'peptide': 278} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 267} Chain: "Z" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2131 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 260} 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 4.23, per 1000 atoms: 0.22 Number of scatterers: 19039 At special positions: 0 Unit cell: (89.424, 110.124, 227.7, 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 122 16.00 P 10 15.00 Mg 5 11.99 O 3680 8.00 N 3235 7.00 C 11987 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: 1.48 Conformation dependent library (CDL) restraints added in 829.7 milliseconds 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 36 sheets defined 47.4% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.516A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.550A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.014A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.533A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.997A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.699A 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 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.533A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.099A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.582A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.594A 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: 4.037A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.512A 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 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.642A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.761A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 removed outlier: 3.518A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.133A 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 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.597A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.654A 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: 3.952A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.519A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.721A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.762A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.697A 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 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.521A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.266A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.509A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.512A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.578A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.596A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.843A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.546A 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: 3.653A 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 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.653A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.504A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.845A pdb=" N GLY D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.793A 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 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.539A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.667A 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 114 through 126 Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.514A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.649A 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 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.685A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.744A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 286 through 289 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.551A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 28 through 41 Processing helix chain 'Y' and resid 42 through 49 removed outlier: 4.451A pdb=" N LEU Y 46 " --> pdb=" O ASN Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 61 removed outlier: 3.993A pdb=" N ASN Y 58 " --> pdb=" O PHE Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 136 removed outlier: 3.537A pdb=" N SER Y 123 " --> pdb=" O SER Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.874A pdb=" N GLY Y 150 " --> pdb=" O THR Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 167 No H-bonds generated for 'chain 'Y' and resid 165 through 167' Processing helix chain 'Y' and resid 220 through 254 removed outlier: 4.662A pdb=" N SER Y 251 " --> pdb=" O TYR Y 247 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP Y 252 " --> pdb=" O GLN Y 248 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR Y 254 " --> pdb=" O MET Y 250 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 Processing helix chain 'Y' and resid 273 through 277 removed outlier: 3.524A pdb=" N SER Y 276 " --> pdb=" O LYS Y 273 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR Y 277 " --> pdb=" O ILE Y 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 273 through 277' Processing helix chain 'Y' and resid 278 through 282 Processing helix chain 'Z' and resid 3 through 15 Processing helix chain 'Z' and resid 17 through 19 No H-bonds generated for 'chain 'Z' and resid 17 through 19' Processing helix chain 'Z' and resid 20 through 32 Processing helix chain 'Z' and resid 35 through 43 Processing helix chain 'Z' and resid 90 through 112 removed outlier: 3.779A pdb=" N GLU Z 99 " --> pdb=" O LYS Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 208 through 231 Processing helix chain 'Z' and resid 231 through 244 Processing helix chain 'Z' and resid 252 through 271 removed outlier: 3.536A pdb=" N GLN Z 271 " --> pdb=" O LYS Z 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.990A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (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: 6.099A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.730A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.008A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.043A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.755A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.625A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.782A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.861A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.162A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.686A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.238A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'Y' and resid 63 through 65 removed outlier: 3.647A pdb=" N THR Y 63 " --> pdb=" O ILE Y 76 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 86 through 89 removed outlier: 3.637A pdb=" N ASP Y 99 " --> pdb=" O GLU Y 104 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU Y 104 " --> pdb=" O ASP Y 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 86 through 89 Processing sheet with id=AD7, first strand: chain 'Y' and resid 139 through 146 removed outlier: 4.087A pdb=" N THR Y 180 " --> pdb=" O GLN Y 187 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLN Y 187 " --> pdb=" O THR Y 180 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS Z 145 " --> pdb=" O GLN Z 178 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 48 through 52 removed outlier: 4.346A pdb=" N LYS Z 48 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 66 through 67 removed outlier: 4.658A pdb=" N SER Z 73 " --> pdb=" O LYS Z 78 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS Z 78 " --> pdb=" O SER Z 73 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2646 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: 3.59 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4635 1.33 - 1.45: 3801 1.45 - 1.57: 10772 1.57 - 1.69: 16 1.69 - 1.81: 211 Bond restraints: 19435 Sorted by residual: bond pdb=" C ASN E 111 " pdb=" N PRO E 112 " ideal model delta sigma weight residual 1.334 1.353 -0.020 8.40e-03 1.42e+04 5.47e+00 bond pdb=" N ASP Z 251 " pdb=" CA ASP Z 251 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.82e+00 bond pdb=" CB GLU D 334 " pdb=" CG GLU D 334 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.63e+00 bond pdb=" C ALA Z 250 " pdb=" N ASP Z 251 " ideal model delta sigma weight residual 1.332 1.359 -0.026 1.40e-02 5.10e+03 3.48e+00 bond pdb=" CB TRP Z 148 " pdb=" CG TRP Z 148 " ideal model delta sigma weight residual 1.498 1.555 -0.057 3.10e-02 1.04e+03 3.36e+00 ... (remaining 19430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 25724 3.06 - 6.11: 556 6.11 - 9.17: 60 9.17 - 12.22: 7 12.22 - 15.28: 3 Bond angle restraints: 26350 Sorted by residual: angle pdb=" C ALA Z 250 " pdb=" N ASP Z 251 " pdb=" CA ASP Z 251 " ideal model delta sigma weight residual 121.54 136.75 -15.21 1.91e+00 2.74e-01 6.35e+01 angle pdb=" C ILE Y 148 " pdb=" N ASP Y 149 " pdb=" CA ASP Y 149 " ideal model delta sigma weight residual 121.54 133.52 -11.98 1.91e+00 2.74e-01 3.94e+01 angle pdb=" C PHE E 127 " pdb=" N ASN E 128 " pdb=" CA ASN E 128 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.12e+01 angle pdb=" C GLN Z 255 " pdb=" N GLU Z 256 " pdb=" CA GLU Z 256 " ideal model delta sigma weight residual 120.54 127.89 -7.35 1.35e+00 5.49e-01 2.97e+01 angle pdb=" C ASN Z 77 " pdb=" CA ASN Z 77 " pdb=" CB ASN Z 77 " ideal model delta sigma weight residual 116.54 110.61 5.93 1.15e+00 7.56e-01 2.65e+01 ... (remaining 26345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.72: 11040 19.72 - 39.43: 574 39.43 - 59.15: 79 59.15 - 78.86: 15 78.86 - 98.58: 9 Dihedral angle restraints: 11717 sinusoidal: 4758 harmonic: 6959 Sorted by residual: dihedral pdb=" CA LEU Z 35 " pdb=" C LEU Z 35 " pdb=" N CYS Z 36 " pdb=" CA CYS Z 36 " ideal model delta harmonic sigma weight residual -180.00 -147.33 -32.67 0 5.00e+00 4.00e-02 4.27e+01 dihedral pdb=" CA MET D 47 " pdb=" C MET D 47 " pdb=" N GLY D 48 " pdb=" CA GLY D 48 " ideal model delta harmonic sigma weight residual -180.00 -151.26 -28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" C5' ADP D 400 " pdb=" O5' ADP D 400 " pdb=" PA ADP D 400 " pdb=" O2A ADP D 400 " ideal model delta sinusoidal sigma weight residual -60.00 38.58 -98.58 1 2.00e+01 2.50e-03 2.76e+01 ... (remaining 11714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2365 0.075 - 0.151: 473 0.151 - 0.226: 49 0.226 - 0.301: 15 0.301 - 0.376: 9 Chirality restraints: 2911 Sorted by residual: chirality pdb=" CB THR Z 179 " pdb=" CA THR Z 179 " pdb=" OG1 THR Z 179 " pdb=" CG2 THR Z 179 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CG LEU Z 258 " pdb=" CB LEU Z 258 " pdb=" CD1 LEU Z 258 " pdb=" CD2 LEU Z 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.46e+00 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 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 2908 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL Z 32 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO Z 33 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO Z 33 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO Z 33 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 173 " 0.021 2.00e-02 2.50e+03 2.16e-02 1.16e+01 pdb=" CG TRP Y 173 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 173 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 173 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 173 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 173 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 173 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 173 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 173 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 345 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE E 345 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE E 345 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU E 346 " -0.018 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 22 2.65 - 3.21: 15554 3.21 - 3.77: 29013 3.77 - 4.34: 42180 4.34 - 4.90: 69311 Nonbonded interactions: 156080 Sorted by model distance: nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.082 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.092 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.094 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.101 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.105 2.170 ... (remaining 156075 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 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 : 0.005 0.078 19435 Z= 0.258 Angle : 1.044 15.280 26350 Z= 0.564 Chirality : 0.063 0.376 2911 Planarity : 0.009 0.091 3387 Dihedral : 12.396 98.578 7253 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -2.19 (0.15), residues: 2374 helix: -2.42 (0.12), residues: 957 sheet: -0.03 (0.23), residues: 493 loop : -0.89 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 147 TYR 0.033 0.002 TYR E 362 PHE 0.046 0.003 PHE Y 228 TRP 0.057 0.003 TRP Y 173 HIS 0.008 0.002 HIS Y 197 Details of bonding type rmsd covalent geometry : bond 0.00542 (19435) covalent geometry : angle 1.04391 (26350) hydrogen bonds : bond 0.14733 ( 971) hydrogen bonds : angle 7.30218 ( 2646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9184 (mmm) cc_final: 0.8936 (mmm) REVERT: Z 126 HIS cc_start: 0.8842 (m90) cc_final: 0.8620 (m-70) REVERT: Z 163 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8084 (mmm160) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.8645 time to fit residues: 118.2442 Evaluate side-chains 108 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.0870 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS D 41 GLN D 246 GLN E 246 GLN Y 246 ASN Z 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.057189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.041175 restraints weight = 58898.678| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.55 r_work: 0.2736 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19435 Z= 0.115 Angle : 0.565 9.509 26350 Z= 0.284 Chirality : 0.044 0.167 2911 Planarity : 0.005 0.058 3387 Dihedral : 5.938 85.867 2677 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 0.49 % Allowed : 3.37 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2374 helix: -0.18 (0.16), residues: 975 sheet: 0.23 (0.23), residues: 505 loop : -0.17 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 102 TYR 0.010 0.001 TYR D 143 PHE 0.024 0.001 PHE Y 228 TRP 0.026 0.001 TRP Y 173 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00256 (19435) covalent geometry : angle 0.56530 (26350) hydrogen bonds : bond 0.03254 ( 971) hydrogen bonds : angle 4.98220 ( 2646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8614 (mtt) REVERT: E 47 MET cc_start: 0.7418 (mmm) cc_final: 0.6586 (mmt) REVERT: E 283 MET cc_start: 0.9066 (mmm) cc_final: 0.8834 (mmt) REVERT: E 325 MET cc_start: 0.8905 (mmt) cc_final: 0.8679 (mtt) REVERT: Y 250 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8546 (tpp) REVERT: Z 163 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7922 (mmm-85) outliers start: 10 outliers final: 1 residues processed: 115 average time/residue: 0.7596 time to fit residues: 96.5045 Evaluate side-chains 114 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain Y residue 250 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.037018 restraints weight = 59699.538| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.47 r_work: 0.2588 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 19435 Z= 0.381 Angle : 0.714 11.016 26350 Z= 0.362 Chirality : 0.052 0.187 2911 Planarity : 0.005 0.067 3387 Dihedral : 7.005 116.755 2677 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 0.78 % Allowed : 4.73 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2374 helix: 0.50 (0.16), residues: 979 sheet: 0.30 (0.23), residues: 528 loop : -0.07 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 372 TYR 0.023 0.002 TYR C 143 PHE 0.052 0.002 PHE Y 255 TRP 0.027 0.002 TRP Y 173 HIS 0.009 0.002 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00903 (19435) covalent geometry : angle 0.71447 (26350) hydrogen bonds : bond 0.04496 ( 971) hydrogen bonds : angle 4.94627 ( 2646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: E 47 MET cc_start: 0.7609 (mmm) cc_final: 0.6915 (mmt) REVERT: E 283 MET cc_start: 0.9097 (mmm) cc_final: 0.8884 (mmt) REVERT: Y 250 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8698 (tpp) outliers start: 16 outliers final: 4 residues processed: 116 average time/residue: 0.7971 time to fit residues: 101.9662 Evaluate side-chains 115 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain Y residue 250 MET Chi-restraints excluded: chain Z residue 164 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 138 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.054916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.038792 restraints weight = 58972.113| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.47 r_work: 0.2651 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19435 Z= 0.123 Angle : 0.543 8.266 26350 Z= 0.269 Chirality : 0.044 0.163 2911 Planarity : 0.004 0.040 3387 Dihedral : 6.150 101.568 2677 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 0.54 % Allowed : 5.80 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2374 helix: 1.13 (0.17), residues: 979 sheet: 0.35 (0.23), residues: 519 loop : 0.13 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 102 TYR 0.011 0.001 TYR Z 232 PHE 0.015 0.001 PHE Y 255 TRP 0.016 0.002 TRP Y 173 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00284 (19435) covalent geometry : angle 0.54294 (26350) hydrogen bonds : bond 0.02936 ( 971) hydrogen bonds : angle 4.54081 ( 2646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.9331 (mtm) cc_final: 0.9067 (mtp) REVERT: D 364 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: E 47 MET cc_start: 0.7297 (mmm) cc_final: 0.7000 (mmt) REVERT: E 283 MET cc_start: 0.9047 (mmm) cc_final: 0.8836 (mmt) REVERT: E 372 ARG cc_start: 0.8929 (ptt180) cc_final: 0.8695 (tmm-80) REVERT: Z 163 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7959 (mmm-85) outliers start: 11 outliers final: 2 residues processed: 115 average time/residue: 0.7638 time to fit residues: 97.1298 Evaluate side-chains 110 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 138 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.055051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.039034 restraints weight = 58634.331| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.46 r_work: 0.2662 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19435 Z= 0.107 Angle : 0.524 7.795 26350 Z= 0.258 Chirality : 0.043 0.155 2911 Planarity : 0.003 0.045 3387 Dihedral : 5.735 91.564 2677 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 0.78 % Allowed : 6.20 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.18), residues: 2374 helix: 1.47 (0.17), residues: 979 sheet: 0.48 (0.24), residues: 504 loop : 0.17 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 102 TYR 0.010 0.001 TYR Z 232 PHE 0.016 0.001 PHE Y 228 TRP 0.015 0.001 TRP Y 173 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00243 (19435) covalent geometry : angle 0.52445 (26350) hydrogen bonds : bond 0.02762 ( 971) hydrogen bonds : angle 4.38236 ( 2646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.9323 (mtm) cc_final: 0.9060 (mtp) REVERT: D 364 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: E 283 MET cc_start: 0.9033 (mmm) cc_final: 0.8830 (mmt) REVERT: E 372 ARG cc_start: 0.8924 (ptt180) cc_final: 0.8705 (tmm-80) REVERT: Y 102 ARG cc_start: 0.8955 (ptp-110) cc_final: 0.8614 (ptp90) REVERT: Z 88 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (mmm) REVERT: Z 163 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7978 (mmm-85) outliers start: 16 outliers final: 2 residues processed: 116 average time/residue: 0.7906 time to fit residues: 101.1660 Evaluate side-chains 114 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain Z residue 88 MET Chi-restraints excluded: chain Z residue 206 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.053556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.037433 restraints weight = 58773.307| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.44 r_work: 0.2603 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 19435 Z= 0.278 Angle : 0.611 9.275 26350 Z= 0.305 Chirality : 0.048 0.161 2911 Planarity : 0.004 0.050 3387 Dihedral : 6.338 105.252 2677 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 0.78 % Allowed : 6.29 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 2374 helix: 1.37 (0.17), residues: 979 sheet: 0.45 (0.23), residues: 513 loop : 0.21 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 102 TYR 0.011 0.001 TYR Y 199 PHE 0.030 0.002 PHE Y 255 TRP 0.014 0.002 TRP Y 169 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00656 (19435) covalent geometry : angle 0.61144 (26350) hydrogen bonds : bond 0.03671 ( 971) hydrogen bonds : angle 4.59241 ( 2646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9128 (mmt) cc_final: 0.8864 (mmm) REVERT: D 364 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: E 372 ARG cc_start: 0.8954 (ptt180) cc_final: 0.8723 (tmm-80) outliers start: 16 outliers final: 3 residues processed: 117 average time/residue: 0.7671 time to fit residues: 99.1775 Evaluate side-chains 113 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain Z residue 206 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 84 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.054850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.038752 restraints weight = 59156.504| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.50 r_work: 0.2650 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19435 Z= 0.113 Angle : 0.528 8.631 26350 Z= 0.260 Chirality : 0.043 0.161 2911 Planarity : 0.003 0.043 3387 Dihedral : 5.795 92.773 2677 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 0.49 % Allowed : 6.73 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.18), residues: 2374 helix: 1.62 (0.17), residues: 979 sheet: 0.45 (0.23), residues: 514 loop : 0.32 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 102 TYR 0.010 0.001 TYR Z 167 PHE 0.012 0.001 PHE Y 228 TRP 0.013 0.002 TRP Y 169 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00260 (19435) covalent geometry : angle 0.52808 (26350) hydrogen bonds : bond 0.02763 ( 971) hydrogen bonds : angle 4.35549 ( 2646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.9355 (mtm) cc_final: 0.9067 (mtp) REVERT: C 47 MET cc_start: 0.8381 (ppp) cc_final: 0.7361 (pmm) REVERT: D 364 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: E 372 ARG cc_start: 0.8987 (ptt180) cc_final: 0.8731 (tmm-80) REVERT: Z 163 ARG cc_start: 0.8299 (mmm160) cc_final: 0.8053 (mmm-85) outliers start: 10 outliers final: 2 residues processed: 117 average time/residue: 0.7455 time to fit residues: 96.4672 Evaluate side-chains 113 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 164 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 121 optimal weight: 0.0870 chunk 15 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.054145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.038023 restraints weight = 59379.647| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.47 r_work: 0.2625 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19435 Z= 0.186 Angle : 0.561 9.212 26350 Z= 0.277 Chirality : 0.045 0.178 2911 Planarity : 0.004 0.056 3387 Dihedral : 5.914 95.720 2677 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 0.44 % Allowed : 6.98 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2374 helix: 1.63 (0.17), residues: 979 sheet: 0.54 (0.23), residues: 507 loop : 0.33 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Y 102 TYR 0.013 0.001 TYR D 143 PHE 0.020 0.001 PHE Y 255 TRP 0.013 0.002 TRP Y 169 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00438 (19435) covalent geometry : angle 0.56066 (26350) hydrogen bonds : bond 0.03141 ( 971) hydrogen bonds : angle 4.40502 ( 2646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.8381 (ppp) cc_final: 0.8082 (pmm) REVERT: D 364 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: E 372 ARG cc_start: 0.9019 (ptt180) cc_final: 0.8755 (tmm-80) outliers start: 9 outliers final: 2 residues processed: 115 average time/residue: 0.7411 time to fit residues: 94.6853 Evaluate side-chains 113 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 22 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.053144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.037001 restraints weight = 59637.407| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.47 r_work: 0.2588 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19435 Z= 0.317 Angle : 0.646 11.270 26350 Z= 0.321 Chirality : 0.049 0.197 2911 Planarity : 0.004 0.057 3387 Dihedral : 6.506 108.714 2677 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 0.49 % Allowed : 7.07 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2374 helix: 1.44 (0.17), residues: 979 sheet: 0.54 (0.23), residues: 503 loop : 0.19 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 102 TYR 0.015 0.001 TYR D 143 PHE 0.027 0.002 PHE Y 255 TRP 0.014 0.002 TRP Y 169 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00749 (19435) covalent geometry : angle 0.64550 (26350) hydrogen bonds : bond 0.03848 ( 971) hydrogen bonds : angle 4.62228 ( 2646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: C 47 MET cc_start: 0.8497 (ppp) cc_final: 0.8209 (pmm) REVERT: D 44 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8644 (mtm) REVERT: D 364 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: E 372 ARG cc_start: 0.9005 (ptt180) cc_final: 0.8758 (tmm-80) REVERT: Z 163 ARG cc_start: 0.8267 (mmm160) cc_final: 0.7958 (mmm-85) outliers start: 10 outliers final: 3 residues processed: 114 average time/residue: 0.7325 time to fit residues: 92.5209 Evaluate side-chains 111 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.054246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.038198 restraints weight = 58964.686| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.46 r_work: 0.2631 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19435 Z= 0.145 Angle : 0.571 13.347 26350 Z= 0.281 Chirality : 0.044 0.206 2911 Planarity : 0.004 0.050 3387 Dihedral : 6.071 99.608 2677 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 0.29 % Allowed : 7.27 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2374 helix: 1.59 (0.17), residues: 980 sheet: 0.52 (0.23), residues: 507 loop : 0.30 (0.23), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Y 102 TYR 0.012 0.001 TYR D 143 PHE 0.014 0.001 PHE Y 255 TRP 0.015 0.002 TRP Y 169 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00340 (19435) covalent geometry : angle 0.57140 (26350) hydrogen bonds : bond 0.03012 ( 971) hydrogen bonds : angle 4.42666 ( 2646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.8430 (ppp) cc_final: 0.8174 (pmm) REVERT: D 364 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: E 372 ARG cc_start: 0.8986 (ptt180) cc_final: 0.8730 (tmm-80) outliers start: 6 outliers final: 2 residues processed: 111 average time/residue: 0.7615 time to fit residues: 93.6786 Evaluate side-chains 111 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 119 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 181 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.054110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.037945 restraints weight = 59193.596| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.49 r_work: 0.2623 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19435 Z= 0.175 Angle : 0.583 14.404 26350 Z= 0.285 Chirality : 0.045 0.204 2911 Planarity : 0.004 0.050 3387 Dihedral : 6.015 97.509 2677 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 0.39 % Allowed : 7.46 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.18), residues: 2374 helix: 1.63 (0.17), residues: 980 sheet: 0.53 (0.23), residues: 507 loop : 0.32 (0.23), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Y 102 TYR 0.013 0.001 TYR D 143 PHE 0.017 0.001 PHE Y 255 TRP 0.014 0.002 TRP Y 169 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00413 (19435) covalent geometry : angle 0.58279 (26350) hydrogen bonds : bond 0.03119 ( 971) hydrogen bonds : angle 4.42090 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6501.34 seconds wall clock time: 111 minutes 24.86 seconds (6684.86 seconds total)