Starting phenix.real_space_refine on Fri Jul 3 03:49:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dnh_27572/07_2026/8dnh_27572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnh_27572/07_2026/8dnh_27572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2026/8dnh_27572.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2026/8dnh_27572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2026/8dnh_27572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2026/8dnh_27572.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2026/8dnh_27572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2026/8dnh_27572.cif" } resolution = 2.99 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= 0.009 sd= 0.043 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 8 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 7432 2.51 5 N 1980 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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} Time building chain proxies: 2.28, per 1000 atoms: 0.19 Number of scatterers: 11796 At special positions: 0 Unit cell: (81.081, 104.247, 171.963, 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 88 16.00 P 8 15.00 Mg 4 11.99 O 2284 8.00 N 1980 7.00 C 7432 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: 0.70 Conformation dependent library (CDL) restraints added in 446.1 milliseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 24 sheets defined 50.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.605A pdb=" N MET A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 4.281A pdb=" N ARG A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 171 through 174 removed outlier: 3.542A pdb=" N ILE A 174 " --> pdb=" O PRO A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.700A pdb=" N CYS A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'A' and resid 284 through 287 removed outlier: 6.287A pdb=" N ASP A 287 " --> pdb=" O CYS A 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.698A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 4.260A pdb=" N TYR A 305 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.616A pdb=" N GLN A 352 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.038A pdb=" N ARG A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 77 through 91 removed outlier: 3.605A pdb=" N MET B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 4.281A pdb=" N ARG B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 171 through 174 removed outlier: 3.543A pdb=" N ILE B 174 " --> pdb=" O PRO B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 180 through 192 Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 221 through 232 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.700A pdb=" N CYS B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'B' and resid 284 through 287 removed outlier: 6.287A pdb=" N ASP B 287 " --> pdb=" O CYS B 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 284 through 287' Processing helix chain 'B' and resid 288 through 294 removed outlier: 3.697A pdb=" N ALA B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.260A pdb=" N TYR B 305 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.617A pdb=" N GLN B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.059A pdb=" N ARG B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 77 through 91 removed outlier: 3.605A pdb=" N MET C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 4.281A pdb=" N ARG C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 171 through 174 removed outlier: 3.543A pdb=" N ILE C 174 " --> pdb=" O PRO C 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 174' Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 221 through 232 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.700A pdb=" N CYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 272 through 283 Processing helix chain 'C' and resid 284 through 287 removed outlier: 6.287A pdb=" N ASP C 287 " --> pdb=" O CYS C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.697A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 removed outlier: 4.261A pdb=" N TYR C 305 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.616A pdb=" N GLN C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 365 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.039A pdb=" N ARG C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 77 through 91 removed outlier: 3.604A pdb=" N MET D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 4.281A pdb=" N ARG D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 171 through 174 removed outlier: 3.544A pdb=" N ILE D 174 " --> pdb=" O PRO D 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 180 through 192 Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 221 through 232 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.701A pdb=" N CYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 262 through 266 Processing helix chain 'D' and resid 272 through 283 Processing helix chain 'D' and resid 284 through 287 removed outlier: 6.287A pdb=" N ASP D 287 " --> pdb=" O CYS D 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 284 through 287' Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.698A pdb=" N ALA D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 4.262A pdb=" N TYR D 305 " --> pdb=" O THR D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 333 through 335 No H-bonds generated for 'chain 'D' and resid 333 through 335' Processing helix chain 'D' and resid 336 through 347 Processing helix chain 'D' and resid 348 through 352 removed outlier: 3.616A pdb=" N GLN D 352 " --> pdb=" O SER D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 365 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.039A pdb=" N ARG D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.687A pdb=" N PHE A 30 " --> pdb=" O CYS A 16 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A 103 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 9 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR A 105 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ASN A 11 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 132 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 131 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.517A pdb=" N ARG A 36 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.554A pdb=" N LEU A 175 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 162 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 151 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 164 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 149 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR A 296 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.554A pdb=" N LEU A 175 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN C 40 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.668A pdb=" N LYS A 237 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.688A pdb=" N PHE B 30 " --> pdb=" O CYS B 16 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 103 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 9 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR B 105 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN B 11 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 132 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B 131 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.516A pdb=" N ARG B 36 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB1, first strand: chain 'B' and resid 168 through 169 removed outlier: 3.554A pdb=" N LEU B 175 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 168 through 169 removed outlier: 3.604A pdb=" N VAL B 162 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 151 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 164 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 149 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR B 296 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.668A pdb=" N LYS B 237 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.687A pdb=" N PHE C 30 " --> pdb=" O CYS C 16 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU C 103 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 9 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR C 105 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN C 11 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 132 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 131 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.517A pdb=" N ARG C 36 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AB7, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.554A pdb=" N LEU C 175 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.604A pdb=" N VAL C 162 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 151 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 164 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C 149 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR C 296 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.668A pdb=" N LYS C 237 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.687A pdb=" N PHE D 30 " --> pdb=" O CYS D 16 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 103 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 9 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR D 105 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN D 11 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 132 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D 131 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.518A pdb=" N ARG D 36 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 70 through 71 Processing sheet with id=AC4, first strand: chain 'D' and resid 168 through 169 removed outlier: 3.554A pdb=" N LEU D 175 " --> pdb=" O THR D 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 168 through 169 removed outlier: 3.605A pdb=" N VAL D 162 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 151 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 164 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 149 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR D 296 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.668A pdb=" N LYS D 237 " --> pdb=" O ILE D 249 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1416 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: 1.69 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1976 1.31 - 1.44: 3136 1.44 - 1.56: 6776 1.56 - 1.69: 12 1.69 - 1.81: 152 Bond restraints: 12052 Sorted by residual: bond pdb=" C HIC D 72 " pdb=" O HIC D 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C HIC B 72 " pdb=" O HIC B 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C HIC C 72 " pdb=" O HIC C 72 " ideal model delta sigma weight residual 1.231 1.357 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C HIC A 72 " pdb=" O HIC A 72 " ideal model delta sigma weight residual 1.231 1.357 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CA SER C 367 " pdb=" CB SER C 367 " ideal model delta sigma weight residual 1.537 1.484 0.053 1.38e-02 5.25e+03 1.46e+01 ... (remaining 12047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 15496 1.73 - 3.47: 690 3.47 - 5.20: 120 5.20 - 6.93: 30 6.93 - 8.67: 16 Bond angle restraints: 16352 Sorted by residual: angle pdb=" N PRO B 242 " pdb=" CA PRO B 242 " pdb=" C PRO B 242 " ideal model delta sigma weight residual 113.84 122.51 -8.67 1.30e+00 5.92e-01 4.44e+01 angle pdb=" C PRO A 366 " pdb=" CA PRO A 366 " pdb=" CB PRO A 366 " ideal model delta sigma weight residual 112.89 105.66 7.23 1.31e+00 5.83e-01 3.05e+01 angle pdb=" C PRO C 366 " pdb=" CA PRO C 366 " pdb=" CB PRO C 366 " ideal model delta sigma weight residual 112.89 105.67 7.22 1.31e+00 5.83e-01 3.04e+01 angle pdb=" C PRO D 366 " pdb=" CA PRO D 366 " pdb=" CB PRO D 366 " ideal model delta sigma weight residual 112.89 105.69 7.20 1.31e+00 5.83e-01 3.02e+01 angle pdb=" N ASP B 362 " pdb=" CA ASP B 362 " pdb=" C ASP B 362 " ideal model delta sigma weight residual 114.12 107.29 6.83 1.39e+00 5.18e-01 2.41e+01 ... (remaining 16347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.88: 6949 31.88 - 63.76: 274 63.76 - 95.65: 17 95.65 - 127.53: 0 127.53 - 159.41: 12 Dihedral angle restraints: 7252 sinusoidal: 2932 harmonic: 4320 Sorted by residual: dihedral pdb=" CH3 ACE C 0 " pdb=" C ACE C 0 " pdb=" N ASP C 1 " pdb=" CA ASP C 1 " ideal model delta sinusoidal sigma weight residual -180.00 -133.06 -46.94 1 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CH3 ACE B 0 " pdb=" C ACE B 0 " pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sinusoidal sigma weight residual -180.00 -133.07 -46.93 1 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CH3 ACE D 0 " pdb=" C ACE D 0 " pdb=" N ASP D 1 " pdb=" CA ASP D 1 " ideal model delta sinusoidal sigma weight residual -180.00 -133.07 -46.93 1 5.00e+00 4.00e-02 1.22e+02 ... (remaining 7249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1576 0.085 - 0.170: 216 0.170 - 0.255: 19 0.255 - 0.340: 0 0.340 - 0.425: 1 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA PRO B 242 " pdb=" N PRO B 242 " pdb=" C PRO B 242 " pdb=" CB PRO B 242 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA GLU B 240 " pdb=" N GLU B 240 " pdb=" C GLU B 240 " pdb=" CB GLU B 240 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE C 368 " pdb=" N ILE C 368 " pdb=" C ILE C 368 " pdb=" CB ILE C 368 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1809 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE B 0 " -0.075 2.00e-02 2.50e+03 2.28e-01 6.51e+02 pdb=" O ACE B 0 " -0.002 2.00e-02 2.50e+03 pdb=" CH3 ACE B 0 " 0.187 2.00e-02 2.50e+03 pdb=" N ASP B 1 " -0.382 2.00e-02 2.50e+03 pdb=" CA ASP B 1 " 0.272 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 0 " -0.074 2.00e-02 2.50e+03 2.28e-01 6.51e+02 pdb=" O ACE D 0 " -0.003 2.00e-02 2.50e+03 pdb=" CH3 ACE D 0 " 0.187 2.00e-02 2.50e+03 pdb=" N ASP D 1 " -0.382 2.00e-02 2.50e+03 pdb=" CA ASP D 1 " 0.272 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE C 0 " -0.074 2.00e-02 2.50e+03 2.28e-01 6.51e+02 pdb=" O ACE C 0 " -0.002 2.00e-02 2.50e+03 pdb=" CH3 ACE C 0 " 0.187 2.00e-02 2.50e+03 pdb=" N ASP C 1 " -0.382 2.00e-02 2.50e+03 pdb=" CA ASP C 1 " 0.272 2.00e-02 2.50e+03 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 303 2.70 - 3.25: 10689 3.25 - 3.80: 16644 3.80 - 4.35: 21342 4.35 - 4.90: 37451 Nonbonded interactions: 86429 Sorted by model distance: nonbonded pdb=" O ASP D 243 " pdb=" OD1 ASP D 243 " model vdw 2.150 3.040 nonbonded pdb=" O SER B 32 " pdb=" OG SER B 32 " model vdw 2.333 3.040 nonbonded pdb=" O SER D 32 " pdb=" OG SER D 32 " model vdw 2.333 3.040 nonbonded pdb=" O SER C 32 " pdb=" OG SER C 32 " model vdw 2.334 3.040 nonbonded pdb=" O SER A 32 " pdb=" OG SER A 32 " model vdw 2.334 3.040 ... (remaining 86424 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 0.127 12052 Z= 0.340 Angle : 0.875 8.665 16352 Z= 0.534 Chirality : 0.058 0.425 1812 Planarity : 0.011 0.228 2096 Dihedral : 17.003 159.410 4484 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.16 % Allowed : 11.39 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.22), residues: 1476 helix: 0.70 (0.22), residues: 584 sheet: 0.56 (0.36), residues: 220 loop : -0.13 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.012 0.001 TYR B 336 PHE 0.013 0.001 PHE A 89 TRP 0.018 0.003 TRP A 78 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.34 (12052) covalent geometry : angle 0.87453 / 0.53 (16352) hydrogen bonds : bond 0.29847 / 20.06 ( 531) hydrogen bonds : angle 6.10769 / 4.28 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 264 time to evaluate : 0.415 Fit side-chains REVERT: A 43 MET cc_start: 0.4364 (mmp) cc_final: 0.3568 (mtm) REVERT: A 67 LYS cc_start: 0.7200 (mttm) cc_final: 0.6879 (ptpt) REVERT: A 190 LYS cc_start: 0.6942 (ttmt) cc_final: 0.6206 (mttt) REVERT: A 240 GLU cc_start: 0.6330 (mt-10) cc_final: 0.5319 (pm20) REVERT: A 270 SER cc_start: 0.7023 (t) cc_final: 0.6822 (t) REVERT: A 287 ASP cc_start: 0.6812 (t70) cc_final: 0.6322 (t70) REVERT: A 295 ASN cc_start: 0.7701 (m-40) cc_final: 0.7381 (m-40) REVERT: A 312 MET cc_start: 0.8364 (tpp) cc_final: 0.8134 (tpt) REVERT: A 327 LYS cc_start: 0.6915 (mttp) cc_final: 0.6439 (pttt) REVERT: A 344 ILE cc_start: 0.6118 (mt) cc_final: 0.5896 (mp) REVERT: A 369 VAL cc_start: 0.7060 (t) cc_final: 0.6779 (p) REVERT: B 46 MET cc_start: 0.2908 (mmm) cc_final: 0.2389 (tmm) REVERT: B 49 LYS cc_start: 0.7633 (mtpp) cc_final: 0.6842 (mptt) REVERT: B 94 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6796 (mtm110) REVERT: B 116 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6418 (mt-10) REVERT: B 124 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6420 (OUTLIER) REVERT: B 205 ARG cc_start: 0.6808 (ttm170) cc_final: 0.6606 (ttp80) REVERT: B 222 PHE cc_start: 0.7782 (t80) cc_final: 0.7462 (t80) REVERT: B 223 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6347 (mm-30) REVERT: B 271 CYS cc_start: 0.8531 (m) cc_final: 0.7548 (m) REVERT: B 273 ILE cc_start: 0.7402 (mm) cc_final: 0.7123 (tt) REVERT: B 282 MET cc_start: 0.8177 (mmt) cc_final: 0.7935 (mmm) REVERT: B 304 MET cc_start: 0.8336 (tpt) cc_final: 0.7958 (tpt) REVERT: B 327 LYS cc_start: 0.7823 (mttp) cc_final: 0.7366 (mttt) REVERT: B 357 SER cc_start: 0.7630 (m) cc_final: 0.7155 (p) REVERT: C 49 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7307 (mttm) REVERT: C 81 MET cc_start: 0.7446 (tpp) cc_final: 0.7211 (mmm) REVERT: C 210 ASP cc_start: 0.6871 (m-30) cc_final: 0.6446 (t0) REVERT: C 273 ILE cc_start: 0.8037 (mm) cc_final: 0.7557 (pt) REVERT: C 275 GLU cc_start: 0.6836 (tp30) cc_final: 0.6399 (tt0) REVERT: C 285 ASP cc_start: 0.6803 (m-30) cc_final: 0.6599 (m-30) REVERT: C 290 LYS cc_start: 0.7464 (tttm) cc_final: 0.7167 (ttpt) REVERT: C 327 LYS cc_start: 0.6742 (mttp) cc_final: 0.6215 (mppt) REVERT: C 358 LYS cc_start: 0.7353 (tmtt) cc_final: 0.6818 (tppt) REVERT: C 362 ASP cc_start: 0.6510 (t0) cc_final: 0.5635 (m-30) REVERT: D 46 MET cc_start: 0.3668 (mmm) cc_final: 0.3443 (ttm) REVERT: D 49 LYS cc_start: 0.6576 (mtpp) cc_final: 0.5763 (tppt) REVERT: D 50 ASP cc_start: 0.5947 (m-30) cc_final: 0.5337 (p0) REVERT: D 59 SER cc_start: 0.7534 (t) cc_final: 0.7316 (m) REVERT: D 90 TYR cc_start: 0.8162 (m-80) cc_final: 0.7935 (m-80) REVERT: D 124 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6458 (pt0) REVERT: D 132 TYR cc_start: 0.8351 (t80) cc_final: 0.7911 (t80) REVERT: D 166 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6274 (mt-10) REVERT: D 191 ILE cc_start: 0.7295 (tt) cc_final: 0.6969 (pt) REVERT: D 206 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7468 (mm-30) REVERT: D 210 ASP cc_start: 0.7139 (m-30) cc_final: 0.6645 (m-30) REVERT: D 237 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7528 (mttt) REVERT: D 315 GLU cc_start: 0.6454 (mm-30) cc_final: 0.6165 (mt-10) REVERT: D 352 GLN cc_start: 0.7141 (mm110) cc_final: 0.6779 (mm110) outliers start: 2 outliers final: 2 residues processed: 266 average time/residue: 0.5854 time to fit residues: 168.0435 Evaluate side-chains 161 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 100 HIS D 11 ASN D 100 HIS D 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141779 restraints weight = 16386.505| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.80 r_work: 0.3764 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12052 Z= 0.125 Angle : 0.619 6.407 16352 Z= 0.313 Chirality : 0.044 0.136 1812 Planarity : 0.004 0.055 2096 Dihedral : 13.450 179.194 1686 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.53 % Allowed : 17.17 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.22), residues: 1476 helix: 0.59 (0.21), residues: 616 sheet: 0.52 (0.33), residues: 252 loop : -0.11 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 209 TYR 0.013 0.001 TYR B 165 PHE 0.011 0.001 PHE A 222 TRP 0.009 0.001 TRP D 339 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (12052) covalent geometry : angle 0.61919 / 0.31 (16352) hydrogen bonds : bond 0.03839 / 2.64 ( 531) hydrogen bonds : angle 4.53360 / 3.16 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.450 Fit side-chains REVERT: A 43 MET cc_start: 0.4291 (mmp) cc_final: 0.3182 (mtm) REVERT: A 83 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8287 (mppt) REVERT: A 190 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7149 (mttt) REVERT: A 271 CYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6984 (p) REVERT: A 275 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6911 (mm-30) REVERT: A 291 ASP cc_start: 0.7636 (m-30) cc_final: 0.7403 (m-30) REVERT: A 369 VAL cc_start: 0.7747 (t) cc_final: 0.7499 (p) REVERT: B 40 GLN cc_start: 0.6575 (pm20) cc_final: 0.5914 (mt0) REVERT: B 46 MET cc_start: 0.2825 (mmm) cc_final: 0.2430 (tmm) REVERT: B 49 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7578 (mppt) REVERT: B 67 LYS cc_start: 0.7801 (mttm) cc_final: 0.7539 (mtmm) REVERT: B 90 TYR cc_start: 0.8244 (m-80) cc_final: 0.7896 (m-80) REVERT: B 116 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7053 (mt-10) REVERT: B 271 CYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7575 (m) REVERT: B 304 MET cc_start: 0.8443 (tpt) cc_final: 0.8063 (tpt) REVERT: B 327 LYS cc_start: 0.8095 (mttp) cc_final: 0.7846 (mttt) REVERT: B 357 SER cc_start: 0.8246 (m) cc_final: 0.8037 (p) REVERT: C 237 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.6315 (mttt) REVERT: C 282 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7700 (mmm) REVERT: C 327 LYS cc_start: 0.7264 (mttp) cc_final: 0.6987 (mppt) REVERT: C 358 LYS cc_start: 0.7834 (tmtt) cc_final: 0.7508 (tttt) REVERT: C 362 ASP cc_start: 0.7147 (t0) cc_final: 0.6302 (m-30) REVERT: D 49 LYS cc_start: 0.6916 (mtpp) cc_final: 0.6585 (mmtm) REVERT: D 59 SER cc_start: 0.8141 (t) cc_final: 0.7825 (t) REVERT: D 82 GLU cc_start: 0.7262 (pp20) cc_final: 0.6943 (pp20) REVERT: D 92 GLU cc_start: 0.6478 (tp30) cc_final: 0.6145 (mt-10) REVERT: D 98 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: D 124 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7224 (pt0) REVERT: D 132 TYR cc_start: 0.8271 (t80) cc_final: 0.8020 (t80) REVERT: D 152 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6654 (tpt) REVERT: D 271 CYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7708 (p) REVERT: D 352 GLN cc_start: 0.7418 (mm110) cc_final: 0.7202 (mm110) outliers start: 32 outliers final: 6 residues processed: 197 average time/residue: 0.5705 time to fit residues: 121.7092 Evaluate side-chains 153 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 134 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 120 GLN B 262 GLN C 100 HIS D 11 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126803 restraints weight = 16432.241| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.79 r_work: 0.3590 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12052 Z= 0.255 Angle : 0.733 9.241 16352 Z= 0.374 Chirality : 0.050 0.165 1812 Planarity : 0.005 0.062 2096 Dihedral : 12.209 170.339 1684 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.11 % Allowed : 18.51 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.21), residues: 1476 helix: 0.29 (0.21), residues: 620 sheet: 0.35 (0.31), residues: 284 loop : -0.48 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 209 TYR 0.022 0.002 TYR C 239 PHE 0.015 0.002 PHE D 222 TRP 0.014 0.002 TRP A 78 HIS 0.009 0.002 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (12052) covalent geometry : angle 0.73332 / 0.37 (16352) hydrogen bonds : bond 0.06919 / 4.68 ( 531) hydrogen bonds : angle 4.58200 / 3.21 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4272 (mmp) cc_final: 0.3081 (mtm) REVERT: A 83 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8128 (mtpt) REVERT: A 190 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7464 (mttt) REVERT: A 271 CYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7469 (p) REVERT: A 275 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7096 (mm-30) REVERT: A 327 LYS cc_start: 0.7286 (pttt) cc_final: 0.6762 (ptpp) REVERT: A 363 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5753 (mp0) REVERT: A 369 VAL cc_start: 0.7727 (t) cc_final: 0.7465 (p) REVERT: B 46 MET cc_start: 0.2886 (mmm) cc_final: 0.2532 (tmm) REVERT: B 49 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7542 (mppt) REVERT: B 67 LYS cc_start: 0.7862 (mttm) cc_final: 0.7632 (mtmm) REVERT: B 90 TYR cc_start: 0.8528 (m-80) cc_final: 0.8169 (m-80) REVERT: B 116 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7445 (mt-10) REVERT: B 271 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7943 (p) REVERT: B 282 MET cc_start: 0.8551 (tpp) cc_final: 0.8307 (mmp) REVERT: B 290 LYS cc_start: 0.8337 (tttm) cc_final: 0.8103 (tptt) REVERT: B 327 LYS cc_start: 0.8045 (mttp) cc_final: 0.7773 (mttt) REVERT: B 366 PRO cc_start: 0.7952 (Cg_endo) cc_final: 0.7672 (Cg_exo) REVERT: C 191 ILE cc_start: 0.8885 (tt) cc_final: 0.8658 (tp) REVERT: C 237 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6577 (mttt) REVERT: C 327 LYS cc_start: 0.7532 (mttp) cc_final: 0.7210 (mtmt) REVERT: C 362 ASP cc_start: 0.7748 (t0) cc_final: 0.6851 (m-30) REVERT: D 49 LYS cc_start: 0.7245 (mtpp) cc_final: 0.7027 (mmtm) REVERT: D 82 GLU cc_start: 0.7482 (pp20) cc_final: 0.7055 (pp20) REVERT: D 92 GLU cc_start: 0.7164 (tp30) cc_final: 0.6746 (mm-30) REVERT: D 98 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: D 124 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7159 (pt0) REVERT: D 131 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7981 (ttt) REVERT: D 152 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7378 (tpt) REVERT: D 268 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8494 (ptp) REVERT: D 271 CYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7968 (p) REVERT: D 352 GLN cc_start: 0.7395 (mm110) cc_final: 0.7167 (mm110) REVERT: D 362 ASP cc_start: 0.6407 (t0) cc_final: 0.6081 (p0) outliers start: 52 outliers final: 22 residues processed: 183 average time/residue: 0.6185 time to fit residues: 122.2660 Evaluate side-chains 165 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 369 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 5 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN D 11 ASN D 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125303 restraints weight = 16273.710| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.74 r_work: 0.3544 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12052 Z= 0.238 Angle : 0.688 8.170 16352 Z= 0.350 Chirality : 0.048 0.165 1812 Planarity : 0.006 0.063 2096 Dihedral : 11.766 164.493 1684 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.83 % Allowed : 20.09 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1476 helix: 0.16 (0.21), residues: 624 sheet: 0.03 (0.30), residues: 292 loop : -0.87 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 94 TYR 0.017 0.002 TYR B 336 PHE 0.015 0.002 PHE C 265 TRP 0.014 0.002 TRP B 355 HIS 0.007 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (12052) covalent geometry : angle 0.68781 / 0.35 (16352) hydrogen bonds : bond 0.05753 / 3.91 ( 531) hydrogen bonds : angle 4.48015 / 3.14 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 0.473 Fit side-chains REVERT: A 43 MET cc_start: 0.4382 (mmp) cc_final: 0.2921 (mtm) REVERT: A 83 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7986 (mtpt) REVERT: A 190 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7394 (mttt) REVERT: A 243 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6000 (t70) REVERT: A 275 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7200 (mm-30) REVERT: A 313 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.6910 (tp40) REVERT: A 327 LYS cc_start: 0.7415 (pttt) cc_final: 0.7122 (pttm) REVERT: A 359 GLN cc_start: 0.7384 (mm-40) cc_final: 0.6647 (pm20) REVERT: A 363 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: A 369 VAL cc_start: 0.7826 (t) cc_final: 0.7512 (p) REVERT: B 46 MET cc_start: 0.2907 (mmm) cc_final: 0.2374 (tmm) REVERT: B 49 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7591 (mppt) REVERT: B 67 LYS cc_start: 0.7849 (mttm) cc_final: 0.7626 (mtmm) REVERT: B 90 TYR cc_start: 0.8472 (m-80) cc_final: 0.8130 (m-80) REVERT: B 116 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 271 CYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7888 (p) REVERT: B 290 LYS cc_start: 0.8354 (tttm) cc_final: 0.8117 (tptt) REVERT: B 327 LYS cc_start: 0.7902 (mttp) cc_final: 0.7672 (mttt) REVERT: B 362 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6673 (t0) REVERT: C 191 ILE cc_start: 0.8860 (tt) cc_final: 0.8652 (tp) REVERT: C 327 LYS cc_start: 0.7620 (mttp) cc_final: 0.7292 (mppt) REVERT: C 362 ASP cc_start: 0.7903 (t0) cc_final: 0.7024 (m-30) REVERT: D 49 LYS cc_start: 0.7202 (mtpp) cc_final: 0.6960 (mmtm) REVERT: D 82 GLU cc_start: 0.7552 (pp20) cc_final: 0.7242 (pp20) REVERT: D 92 GLU cc_start: 0.7325 (tp30) cc_final: 0.6922 (mm-30) REVERT: D 98 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: D 124 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6932 (pt0) REVERT: D 152 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7436 (tpt) REVERT: D 271 CYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7991 (p) REVERT: D 352 GLN cc_start: 0.7511 (mm110) cc_final: 0.7264 (mm110) REVERT: D 362 ASP cc_start: 0.6641 (t0) cc_final: 0.6180 (p0) outliers start: 61 outliers final: 25 residues processed: 188 average time/residue: 0.5525 time to fit residues: 112.5408 Evaluate side-chains 168 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 369 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 114 ASN C 160 HIS D 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129669 restraints weight = 16217.415| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.75 r_work: 0.3599 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12052 Z= 0.104 Angle : 0.569 9.448 16352 Z= 0.278 Chirality : 0.043 0.133 1812 Planarity : 0.005 0.060 2096 Dihedral : 11.189 162.089 1684 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.61 % Allowed : 23.42 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1476 helix: 0.79 (0.22), residues: 596 sheet: 0.35 (0.31), residues: 284 loop : -0.61 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 182 TYR 0.011 0.001 TYR A 239 PHE 0.009 0.001 PHE B 222 TRP 0.009 0.001 TRP C 78 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (12052) covalent geometry : angle 0.56863 / 0.28 (16352) hydrogen bonds : bond 0.03548 / 2.44 ( 531) hydrogen bonds : angle 4.19366 / 2.93 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4561 (mmp) cc_final: 0.2804 (mtm) REVERT: A 190 LYS cc_start: 0.8033 (ttmt) cc_final: 0.7336 (mttt) REVERT: A 275 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7166 (mm-30) REVERT: A 359 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6443 (pm20) REVERT: A 363 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5759 (mp0) REVERT: A 369 VAL cc_start: 0.7636 (t) cc_final: 0.7375 (p) REVERT: B 46 MET cc_start: 0.2805 (mmm) cc_final: 0.2317 (tmm) REVERT: B 49 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7597 (mppt) REVERT: B 67 LYS cc_start: 0.7923 (mttm) cc_final: 0.7647 (mtmm) REVERT: B 90 TYR cc_start: 0.8408 (m-80) cc_final: 0.8024 (m-80) REVERT: B 116 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7291 (mt-10) REVERT: B 271 CYS cc_start: 0.8175 (m) cc_final: 0.7940 (p) REVERT: B 290 LYS cc_start: 0.8215 (tttm) cc_final: 0.7993 (tptt) REVERT: B 327 LYS cc_start: 0.7894 (mttp) cc_final: 0.7661 (mttt) REVERT: C 327 LYS cc_start: 0.7547 (mttp) cc_final: 0.7202 (mppt) REVERT: C 362 ASP cc_start: 0.7860 (t0) cc_final: 0.6980 (m-30) REVERT: D 82 GLU cc_start: 0.7503 (pp20) cc_final: 0.7223 (pp20) REVERT: D 92 GLU cc_start: 0.7239 (tp30) cc_final: 0.6887 (mm-30) REVERT: D 98 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: D 124 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6884 (pt0) REVERT: D 152 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7352 (tpt) REVERT: D 162 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7827 (p) REVERT: D 166 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6535 (pt0) REVERT: D 352 GLN cc_start: 0.7531 (mm110) cc_final: 0.7272 (mm110) REVERT: D 362 ASP cc_start: 0.6610 (t0) cc_final: 0.6137 (p0) outliers start: 33 outliers final: 16 residues processed: 165 average time/residue: 0.6075 time to fit residues: 108.4718 Evaluate side-chains 155 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 243 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 4.9990 chunk 4 optimal weight: 0.0030 chunk 141 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 120 GLN C 58 GLN D 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127637 restraints weight = 16191.950| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.75 r_work: 0.3575 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12052 Z= 0.146 Angle : 0.593 10.016 16352 Z= 0.291 Chirality : 0.045 0.135 1812 Planarity : 0.005 0.064 2096 Dihedral : 11.131 161.077 1684 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.77 % Allowed : 24.29 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.22), residues: 1476 helix: 0.79 (0.22), residues: 600 sheet: 0.38 (0.31), residues: 284 loop : -0.59 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 94 TYR 0.013 0.001 TYR A 239 PHE 0.009 0.001 PHE D 30 TRP 0.010 0.002 TRP B 355 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (12052) covalent geometry : angle 0.59253 / 0.29 (16352) hydrogen bonds : bond 0.04403 / 3.01 ( 531) hydrogen bonds : angle 4.15915 / 2.90 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.361 Fit side-chains REVERT: A 43 MET cc_start: 0.4786 (mmp) cc_final: 0.3069 (mtm) REVERT: A 190 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7374 (mttt) REVERT: A 275 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 359 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6481 (pm20) REVERT: A 363 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5768 (mp0) REVERT: A 369 VAL cc_start: 0.7690 (t) cc_final: 0.7394 (p) REVERT: B 46 MET cc_start: 0.2959 (mmm) cc_final: 0.2390 (tmm) REVERT: B 49 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7580 (mppt) REVERT: B 67 LYS cc_start: 0.7906 (mttm) cc_final: 0.7645 (mtmm) REVERT: B 90 TYR cc_start: 0.8441 (m-80) cc_final: 0.8050 (m-80) REVERT: B 116 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7338 (mt-10) REVERT: B 271 CYS cc_start: 0.8195 (m) cc_final: 0.7942 (p) REVERT: B 290 LYS cc_start: 0.8209 (tttm) cc_final: 0.7949 (tptt) REVERT: B 327 LYS cc_start: 0.7898 (mttp) cc_final: 0.7679 (mttt) REVERT: C 46 MET cc_start: 0.4745 (mmt) cc_final: 0.4510 (mtt) REVERT: C 313 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7975 (tp40) REVERT: C 327 LYS cc_start: 0.7583 (mttp) cc_final: 0.7373 (mtmp) REVERT: C 362 ASP cc_start: 0.7917 (t0) cc_final: 0.6978 (m-30) REVERT: D 82 GLU cc_start: 0.7552 (pp20) cc_final: 0.7245 (pp20) REVERT: D 92 GLU cc_start: 0.7318 (tp30) cc_final: 0.6946 (mm-30) REVERT: D 98 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: D 124 GLU cc_start: 0.7628 (mt-10) cc_final: 0.6920 (pt0) REVERT: D 152 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7335 (tpt) REVERT: D 166 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6488 (pt0) REVERT: D 352 GLN cc_start: 0.7604 (mm110) cc_final: 0.7358 (mm110) REVERT: D 362 ASP cc_start: 0.6671 (t0) cc_final: 0.6084 (p0) outliers start: 35 outliers final: 17 residues processed: 166 average time/residue: 0.5639 time to fit residues: 101.4542 Evaluate side-chains 163 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 236 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 104 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN D 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125170 restraints weight = 16082.365| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.79 r_work: 0.3539 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12052 Z= 0.205 Angle : 0.647 10.920 16352 Z= 0.324 Chirality : 0.047 0.149 1812 Planarity : 0.005 0.066 2096 Dihedral : 11.239 159.143 1684 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.64 % Allowed : 24.05 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1476 helix: 0.61 (0.22), residues: 600 sheet: 0.23 (0.30), residues: 292 loop : -0.77 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 94 TYR 0.018 0.002 TYR A 239 PHE 0.011 0.001 PHE C 265 TRP 0.012 0.002 TRP B 355 HIS 0.005 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (12052) covalent geometry : angle 0.64742 / 0.32 (16352) hydrogen bonds : bond 0.05412 / 3.68 ( 531) hydrogen bonds : angle 4.27843 / 2.98 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.371 Fit side-chains REVERT: A 43 MET cc_start: 0.4775 (mmp) cc_final: 0.3027 (mtm) REVERT: A 190 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7348 (mttt) REVERT: A 275 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 363 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5746 (mp0) REVERT: A 368 ILE cc_start: 0.7101 (tt) cc_final: 0.6779 (tp) REVERT: B 46 MET cc_start: 0.3048 (mmm) cc_final: 0.2601 (tmm) REVERT: B 49 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7502 (mppt) REVERT: B 67 LYS cc_start: 0.7945 (mttm) cc_final: 0.7622 (mtmm) REVERT: B 90 TYR cc_start: 0.8504 (m-80) cc_final: 0.8155 (m-80) REVERT: B 116 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 271 CYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7913 (p) REVERT: B 290 LYS cc_start: 0.8347 (tttm) cc_final: 0.8056 (tptt) REVERT: B 327 LYS cc_start: 0.7867 (mttp) cc_final: 0.7650 (mttt) REVERT: B 362 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6804 (t0) REVERT: C 313 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: C 323 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7344 (p) REVERT: C 327 LYS cc_start: 0.7613 (mttp) cc_final: 0.7407 (mtmp) REVERT: C 362 ASP cc_start: 0.7886 (t0) cc_final: 0.6936 (m-30) REVERT: D 46 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.3083 (ttt) REVERT: D 82 GLU cc_start: 0.7563 (pp20) cc_final: 0.7261 (pt0) REVERT: D 92 GLU cc_start: 0.7325 (tp30) cc_final: 0.6913 (mm-30) REVERT: D 98 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: D 124 GLU cc_start: 0.7656 (mt-10) cc_final: 0.6978 (pt0) REVERT: D 162 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7940 (p) REVERT: D 166 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6478 (pt0) REVERT: D 324 MET cc_start: 0.6926 (mmp) cc_final: 0.6672 (mmt) REVERT: D 352 GLN cc_start: 0.7628 (mm110) cc_final: 0.7360 (mm110) REVERT: D 362 ASP cc_start: 0.6724 (t0) cc_final: 0.6063 (p0) outliers start: 46 outliers final: 24 residues processed: 175 average time/residue: 0.6058 time to fit residues: 114.4084 Evaluate side-chains 170 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 236 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.0170 chunk 31 optimal weight: 5.9990 chunk 139 optimal weight: 0.0000 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 120 GLN D 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129125 restraints weight = 15973.729| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.72 r_work: 0.3602 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12052 Z= 0.104 Angle : 0.577 11.288 16352 Z= 0.279 Chirality : 0.043 0.136 1812 Planarity : 0.005 0.069 2096 Dihedral : 10.860 155.673 1684 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.45 % Allowed : 25.79 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.22), residues: 1476 helix: 0.90 (0.22), residues: 596 sheet: 0.52 (0.30), residues: 284 loop : -0.61 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 94 TYR 0.013 0.001 TYR A 239 PHE 0.009 0.001 PHE A 278 TRP 0.010 0.001 TRP C 78 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (12052) covalent geometry : angle 0.57675 / 0.28 (16352) hydrogen bonds : bond 0.03372 / 2.32 ( 531) hydrogen bonds : angle 4.08381 / 2.84 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4720 (mmp) cc_final: 0.2935 (mtm) REVERT: A 190 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7362 (mttt) REVERT: A 275 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 313 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: B 46 MET cc_start: 0.3184 (mmm) cc_final: 0.2769 (tmm) REVERT: B 49 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7508 (mppt) REVERT: B 67 LYS cc_start: 0.7920 (mttm) cc_final: 0.7645 (mtmm) REVERT: B 90 TYR cc_start: 0.8439 (m-80) cc_final: 0.8106 (m-80) REVERT: B 116 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7320 (mt-10) REVERT: B 147 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8564 (t) REVERT: B 271 CYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7872 (p) REVERT: B 290 LYS cc_start: 0.8204 (tttm) cc_final: 0.7922 (tptt) REVERT: B 362 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6816 (t0) REVERT: C 124 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6768 (tt0) REVERT: C 269 GLU cc_start: 0.7939 (tp30) cc_final: 0.6364 (tt0) REVERT: C 313 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7819 (tp40) REVERT: D 82 GLU cc_start: 0.7511 (pp20) cc_final: 0.7248 (pt0) REVERT: D 92 GLU cc_start: 0.7276 (tp30) cc_final: 0.6926 (mm-30) REVERT: D 124 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6955 (pt0) REVERT: D 162 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7842 (p) REVERT: D 166 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6387 (pt0) REVERT: D 170 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7509 (mp) REVERT: D 324 MET cc_start: 0.7011 (mmp) cc_final: 0.6774 (mmt) REVERT: D 352 GLN cc_start: 0.7622 (mm110) cc_final: 0.7378 (mm110) REVERT: D 362 ASP cc_start: 0.6708 (t0) cc_final: 0.6087 (p0) outliers start: 31 outliers final: 15 residues processed: 164 average time/residue: 0.5795 time to fit residues: 102.5146 Evaluate side-chains 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 285 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN D 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124833 restraints weight = 16001.067| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.78 r_work: 0.3534 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12052 Z= 0.219 Angle : 0.666 11.766 16352 Z= 0.332 Chirality : 0.047 0.154 1812 Planarity : 0.005 0.072 2096 Dihedral : 11.108 161.287 1684 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.85 % Allowed : 25.79 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1476 helix: 0.63 (0.22), residues: 600 sheet: 0.32 (0.30), residues: 292 loop : -0.80 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 94 TYR 0.018 0.002 TYR A 239 PHE 0.010 0.001 PHE C 265 TRP 0.011 0.002 TRP B 339 HIS 0.006 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (12052) covalent geometry : angle 0.66597 / 0.33 (16352) hydrogen bonds : bond 0.05539 / 3.76 ( 531) hydrogen bonds : angle 4.24595 / 2.96 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.491 Fit side-chains REVERT: A 15 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8791 (mtm) REVERT: A 43 MET cc_start: 0.4709 (mmp) cc_final: 0.3045 (mtm) REVERT: A 190 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7338 (mttt) REVERT: A 275 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 313 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: A 363 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: B 46 MET cc_start: 0.3243 (mmm) cc_final: 0.2788 (tmm) REVERT: B 49 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7442 (mppt) REVERT: B 67 LYS cc_start: 0.7934 (mttm) cc_final: 0.7617 (mtmm) REVERT: B 90 TYR cc_start: 0.8502 (m-80) cc_final: 0.8163 (m-80) REVERT: B 116 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 271 CYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7952 (p) REVERT: B 290 LYS cc_start: 0.8363 (tttm) cc_final: 0.8049 (tptt) REVERT: B 362 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6831 (t0) REVERT: C 124 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6772 (tt0) REVERT: C 313 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7856 (tp40) REVERT: C 323 THR cc_start: 0.7735 (m) cc_final: 0.7341 (p) REVERT: C 362 ASP cc_start: 0.8026 (t0) cc_final: 0.7016 (m-30) REVERT: D 82 GLU cc_start: 0.7594 (pp20) cc_final: 0.7275 (pt0) REVERT: D 92 GLU cc_start: 0.7334 (tp30) cc_final: 0.6981 (mm-30) REVERT: D 98 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: D 124 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6971 (pt0) REVERT: D 162 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7953 (p) REVERT: D 166 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6417 (pt0) REVERT: D 324 MET cc_start: 0.7129 (mmp) cc_final: 0.6882 (mmt) REVERT: D 352 GLN cc_start: 0.7653 (mm110) cc_final: 0.7399 (mm110) REVERT: D 362 ASP cc_start: 0.6725 (t0) cc_final: 0.6048 (p0) outliers start: 36 outliers final: 23 residues processed: 164 average time/residue: 0.5944 time to fit residues: 105.4158 Evaluate side-chains 166 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 120 GLN D 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128222 restraints weight = 16004.656| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.78 r_work: 0.3593 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12052 Z= 0.115 Angle : 0.589 12.098 16352 Z= 0.285 Chirality : 0.044 0.146 1812 Planarity : 0.005 0.072 2096 Dihedral : 10.728 166.974 1684 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 26.34 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.22), residues: 1476 helix: 0.88 (0.22), residues: 596 sheet: 0.56 (0.30), residues: 284 loop : -0.70 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 94 TYR 0.014 0.001 TYR A 239 PHE 0.009 0.001 PHE A 278 TRP 0.011 0.001 TRP A 355 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12052) covalent geometry : angle 0.58869 / 0.29 (16352) hydrogen bonds : bond 0.03615 / 2.48 ( 531) hydrogen bonds : angle 4.08568 / 2.85 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.441 Fit side-chains REVERT: A 43 MET cc_start: 0.4728 (mmp) cc_final: 0.3088 (mtm) REVERT: A 190 LYS cc_start: 0.8019 (ttmt) cc_final: 0.7290 (mttt) REVERT: A 275 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7194 (mm-30) REVERT: A 313 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: A 363 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5702 (mp0) REVERT: B 46 MET cc_start: 0.3292 (mmm) cc_final: 0.2849 (tmm) REVERT: B 49 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7383 (mppt) REVERT: B 67 LYS cc_start: 0.7968 (mttm) cc_final: 0.7630 (mtmm) REVERT: B 90 TYR cc_start: 0.8479 (m-80) cc_final: 0.8139 (m-80) REVERT: B 116 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7300 (mt-10) REVERT: B 147 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8587 (t) REVERT: B 271 CYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7918 (p) REVERT: B 290 LYS cc_start: 0.8288 (tttm) cc_final: 0.7962 (tptt) REVERT: B 353 GLN cc_start: 0.8104 (mm110) cc_final: 0.7740 (mt0) REVERT: B 362 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6894 (t0) REVERT: C 46 MET cc_start: 0.4907 (mtt) cc_final: 0.4470 (mtt) REVERT: C 124 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6800 (tt0) REVERT: C 313 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7817 (tp40) REVERT: D 82 GLU cc_start: 0.7545 (pp20) cc_final: 0.7237 (pt0) REVERT: D 92 GLU cc_start: 0.7279 (tp30) cc_final: 0.6898 (mm-30) REVERT: D 98 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: D 124 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6882 (pt0) REVERT: D 166 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6249 (pt0) REVERT: D 170 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7488 (mp) REVERT: D 324 MET cc_start: 0.7035 (mmp) cc_final: 0.6830 (mmp) REVERT: D 352 GLN cc_start: 0.7650 (mm110) cc_final: 0.7402 (mm110) REVERT: D 362 ASP cc_start: 0.6702 (t0) cc_final: 0.5991 (p0) outliers start: 31 outliers final: 19 residues processed: 163 average time/residue: 0.5384 time to fit residues: 94.6621 Evaluate side-chains 165 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 137 optimal weight: 0.0670 chunk 99 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 120 GLN D 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125113 restraints weight = 15984.074| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.77 r_work: 0.3543 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12052 Z= 0.231 Angle : 0.667 12.705 16352 Z= 0.332 Chirality : 0.047 0.147 1812 Planarity : 0.005 0.071 2096 Dihedral : 10.872 169.533 1684 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.85 % Allowed : 26.03 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1476 helix: 0.66 (0.22), residues: 596 sheet: 0.44 (0.30), residues: 284 loop : -0.88 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 94 TYR 0.018 0.002 TYR A 239 PHE 0.012 0.002 PHE C 265 TRP 0.011 0.002 TRP B 355 HIS 0.006 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (12052) covalent geometry : angle 0.66695 / 0.33 (16352) hydrogen bonds : bond 0.05322 / 3.62 ( 531) hydrogen bonds : angle 4.21574 / 2.94 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3586.39 seconds wall clock time: 61 minutes 54.61 seconds (3714.61 seconds total)