Starting phenix.real_space_refine on Sat Aug 23 12:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnh_27572/08_2025/8dnh_27572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnh_27572/08_2025/8dnh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnh_27572/08_2025/8dnh_27572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnh_27572/08_2025/8dnh_27572.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnh_27572/08_2025/8dnh_27572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnh_27572/08_2025/8dnh_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.25, per 1000 atoms: 0.28 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: 1.07 Conformation dependent library (CDL) restraints added in 601.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.59 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: 2.08 Time building geometry restraints manager: 1.41 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.230 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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= 0.338 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 aren 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 covalent geometry : bond 0.00589 (12052) covalent geometry : angle 0.87513 (16352) hydrogen bonds : bond 0.29847 ( 531) hydrogen bonds : angle 6.10769 ( 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 : 0.412 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: 0.7365 (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: 0.5510 time to fit residues: 158.2432 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 : 0.321 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.152342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141776 restraints weight = 16392.482| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.80 r_work: 0.3795 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12052 Z= 0.125 Angle : 0.618 6.327 16352 Z= 0.312 Chirality : 0.045 0.127 1812 Planarity : 0.004 0.056 2096 Dihedral : 13.459 179.157 1686 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.29 % Allowed : 17.41 % 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 aren not related in a simple way. whole: 0.35 (0.22), residues: 1476 helix: 0.60 (0.22), 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 0.005 0.000 ARG D 209 TYR 0.012 0.001 TYR C 142 PHE 0.010 0.001 PHE A 222 TRP 0.007 0.001 TRP C 85 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00264 (12052) covalent geometry : angle 0.61782 (16352) hydrogen bonds : bond 0.03994 ( 531) hydrogen bonds : angle 4.53443 ( 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 209 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.418 Fit side-chains REVERT: A 43 MET cc_start: 0.4335 (mmp) cc_final: 0.3263 (mtm) REVERT: A 83 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8333 (mppt) REVERT: A 190 LYS cc_start: 0.7713 (ttmt) cc_final: 0.7200 (mttt) REVERT: A 271 CYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7031 (p) REVERT: A 275 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6960 (mm-30) REVERT: A 291 ASP cc_start: 0.7661 (m-30) cc_final: 0.7444 (m-30) REVERT: A 369 VAL cc_start: 0.7772 (t) cc_final: 0.7528 (p) REVERT: B 40 GLN cc_start: 0.6590 (pm20) cc_final: 0.5953 (mt0) REVERT: B 46 MET cc_start: 0.2848 (mmm) cc_final: 0.2464 (tmm) REVERT: B 49 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7629 (mppt) REVERT: B 67 LYS cc_start: 0.7832 (mttm) cc_final: 0.7602 (mtmm) REVERT: B 90 TYR cc_start: 0.8243 (m-80) cc_final: 0.7909 (m-80) REVERT: B 116 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7084 (mt-10) REVERT: B 271 CYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7623 (m) REVERT: B 304 MET cc_start: 0.8425 (tpt) cc_final: 0.8077 (tpt) REVERT: B 327 LYS cc_start: 0.8091 (mttp) cc_final: 0.7865 (mttt) REVERT: C 237 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6327 (mttt) REVERT: C 327 LYS cc_start: 0.7255 (mttp) cc_final: 0.7005 (mppt) REVERT: C 358 LYS cc_start: 0.7857 (tmtt) cc_final: 0.7548 (tttt) REVERT: C 362 ASP cc_start: 0.7180 (t0) cc_final: 0.6347 (m-30) REVERT: D 49 LYS cc_start: 0.6946 (mtpp) cc_final: 0.6650 (mmtm) REVERT: D 59 SER cc_start: 0.8209 (t) cc_final: 0.7901 (t) REVERT: D 82 GLU cc_start: 0.7271 (pp20) cc_final: 0.7004 (pp20) REVERT: D 92 GLU cc_start: 0.6502 (tp30) cc_final: 0.6192 (mt-10) REVERT: D 98 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: D 124 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7280 (pt0) REVERT: D 132 TYR cc_start: 0.8259 (t80) cc_final: 0.8045 (t80) REVERT: D 152 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6641 (tpt) REVERT: D 271 CYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7760 (p) REVERT: D 362 ASP cc_start: 0.6283 (t0) cc_final: 0.6044 (p0) outliers start: 29 outliers final: 6 residues processed: 197 average time/residue: 0.5422 time to fit residues: 115.3114 Evaluate side-chains 152 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 52 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 33 optimal weight: 0.0000 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3777 r_free = 0.3777 target = 0.137056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126237 restraints weight = 16449.994| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.79 r_work: 0.3568 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 12052 Z= 0.294 Angle : 0.757 8.240 16352 Z= 0.390 Chirality : 0.051 0.170 1812 Planarity : 0.006 0.062 2096 Dihedral : 12.343 172.027 1684 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.11 % Allowed : 18.67 % Favored : 77.22 % 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 aren not related in a simple way. whole: -0.19 (0.21), residues: 1476 helix: 0.20 (0.21), residues: 620 sheet: 0.31 (0.31), residues: 284 loop : -0.55 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 209 TYR 0.024 0.003 TYR C 239 PHE 0.017 0.002 PHE D 222 TRP 0.013 0.002 TRP A 78 HIS 0.007 0.002 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00679 (12052) covalent geometry : angle 0.75735 (16352) hydrogen bonds : bond 0.06982 ( 531) hydrogen bonds : angle 4.63545 ( 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 199 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4283 (mmp) cc_final: 0.3082 (mtm) REVERT: A 83 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8074 (mtpt) REVERT: A 147 THR cc_start: 0.8432 (p) cc_final: 0.8226 (m) REVERT: A 190 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7396 (mttt) REVERT: A 271 CYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7469 (p) REVERT: A 275 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 327 LYS cc_start: 0.7360 (pttt) cc_final: 0.6833 (ptpp) REVERT: A 363 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5752 (mp0) REVERT: A 369 VAL cc_start: 0.7751 (t) cc_final: 0.7477 (p) REVERT: B 46 MET cc_start: 0.3030 (mmm) cc_final: 0.2562 (tmm) REVERT: B 49 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7539 (mppt) REVERT: B 67 LYS cc_start: 0.7833 (mttm) cc_final: 0.7600 (mtmm) REVERT: B 90 TYR cc_start: 0.8542 (m-80) cc_final: 0.8184 (m-80) REVERT: B 116 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7450 (mt-10) REVERT: B 271 CYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7920 (p) REVERT: B 282 MET cc_start: 0.8602 (tpp) cc_final: 0.8343 (mmp) REVERT: B 290 LYS cc_start: 0.8326 (tttm) cc_final: 0.8075 (tptt) REVERT: B 327 LYS cc_start: 0.8035 (mttp) cc_final: 0.7763 (mttt) REVERT: B 366 PRO cc_start: 0.7964 (Cg_endo) cc_final: 0.7676 (Cg_exo) REVERT: C 191 ILE cc_start: 0.8906 (tt) cc_final: 0.8685 (tp) REVERT: C 237 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6595 (mttt) REVERT: C 327 LYS cc_start: 0.7517 (mttp) cc_final: 0.7210 (mtmt) REVERT: C 362 ASP cc_start: 0.7750 (t0) cc_final: 0.6847 (m-30) REVERT: D 49 LYS cc_start: 0.7244 (mtpp) cc_final: 0.7021 (mmtm) REVERT: D 82 GLU cc_start: 0.7500 (pp20) cc_final: 0.7137 (pp20) REVERT: D 92 GLU cc_start: 0.7183 (tp30) cc_final: 0.6773 (mm-30) REVERT: D 98 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: D 124 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7120 (pt0) REVERT: D 131 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7976 (ttt) REVERT: D 152 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7443 (tpt) REVERT: D 268 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8500 (ptp) REVERT: D 271 CYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7959 (p) REVERT: D 362 ASP cc_start: 0.6397 (t0) cc_final: 0.6080 (p0) outliers start: 52 outliers final: 21 residues processed: 183 average time/residue: 0.6195 time to fit residues: 122.1031 Evaluate side-chains 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 357 SER 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 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: 0.9980 chunk 139 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN 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 = 0.3799 r_free = 0.3799 target = 0.139354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128575 restraints weight = 16294.623| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.76 r_work: 0.3589 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12052 Z= 0.147 Angle : 0.605 8.337 16352 Z= 0.300 Chirality : 0.045 0.147 1812 Planarity : 0.005 0.061 2096 Dihedral : 11.668 162.172 1684 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.48 % Allowed : 21.44 % 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 aren not related in a simple way. whole: -0.04 (0.21), residues: 1476 helix: 0.45 (0.21), residues: 620 sheet: 0.32 (0.31), residues: 284 loop : -0.60 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 209 TYR 0.012 0.001 TYR A 142 PHE 0.010 0.001 PHE B 222 TRP 0.012 0.002 TRP C 78 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00338 (12052) covalent geometry : angle 0.60502 (16352) hydrogen bonds : bond 0.04440 ( 531) hydrogen bonds : angle 4.33138 ( 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 190 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4308 (mmp) cc_final: 0.2973 (mtm) REVERT: A 190 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7345 (mttt) REVERT: A 243 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5993 (t70) REVERT: A 271 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7555 (p) REVERT: A 275 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 359 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6506 (pm20) REVERT: A 363 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5791 (mp0) REVERT: A 369 VAL cc_start: 0.7722 (t) cc_final: 0.7442 (p) REVERT: B 46 MET cc_start: 0.2919 (mmm) cc_final: 0.2468 (tmm) REVERT: B 49 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7605 (mppt) REVERT: B 67 LYS cc_start: 0.7862 (mttm) cc_final: 0.7632 (mtmm) REVERT: B 90 TYR cc_start: 0.8424 (m-80) cc_final: 0.8084 (m-80) REVERT: B 116 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7372 (mt-10) REVERT: B 271 CYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7984 (p) REVERT: B 282 MET cc_start: 0.8535 (tpp) cc_final: 0.8224 (mmp) REVERT: B 290 LYS cc_start: 0.8265 (tttm) cc_final: 0.8028 (tptt) REVERT: B 327 LYS cc_start: 0.7959 (mttp) cc_final: 0.7716 (mttt) REVERT: B 366 PRO cc_start: 0.7914 (Cg_endo) cc_final: 0.7699 (Cg_exo) REVERT: C 237 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6606 (mttt) REVERT: C 327 LYS cc_start: 0.7518 (mttp) cc_final: 0.7211 (mppt) REVERT: C 362 ASP cc_start: 0.7719 (t0) cc_final: 0.6816 (m-30) REVERT: D 49 LYS cc_start: 0.7266 (mtpp) cc_final: 0.7052 (mmtm) REVERT: D 82 GLU cc_start: 0.7463 (pp20) cc_final: 0.7164 (pp20) REVERT: D 92 GLU cc_start: 0.7199 (tp30) cc_final: 0.6838 (mm-30) REVERT: D 98 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: D 124 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7001 (pt0) REVERT: D 131 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7968 (ttt) REVERT: D 152 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7380 (tpt) REVERT: D 362 ASP cc_start: 0.6552 (t0) cc_final: 0.6160 (p0) outliers start: 44 outliers final: 18 residues processed: 175 average time/residue: 0.5637 time to fit residues: 106.9982 Evaluate side-chains 160 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 151 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 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 357 SER 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN C 160 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131153 restraints weight = 16180.826| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.75 r_work: 0.3627 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12052 Z= 0.103 Angle : 0.566 8.759 16352 Z= 0.273 Chirality : 0.043 0.133 1812 Planarity : 0.004 0.062 2096 Dihedral : 11.130 162.380 1684 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.32 % Allowed : 21.99 % Favored : 74.68 % 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 aren not related in a simple way. whole: 0.41 (0.22), residues: 1476 helix: 0.91 (0.22), residues: 600 sheet: 0.45 (0.32), residues: 284 loop : -0.37 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 94 TYR 0.011 0.001 TYR A 239 PHE 0.010 0.001 PHE B 222 TRP 0.008 0.001 TRP B 355 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00230 (12052) covalent geometry : angle 0.56582 (16352) hydrogen bonds : bond 0.03390 ( 531) hydrogen bonds : angle 4.12702 ( 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 185 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4337 (mmp) cc_final: 0.2942 (mtm) REVERT: A 190 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7326 (mttt) REVERT: A 271 CYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7576 (p) REVERT: A 275 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 359 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6435 (pm20) REVERT: A 363 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5724 (mp0) REVERT: A 369 VAL cc_start: 0.7565 (t) cc_final: 0.7298 (p) REVERT: B 46 MET cc_start: 0.2641 (mmm) cc_final: 0.2257 (tmm) REVERT: B 49 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7600 (mppt) REVERT: B 67 LYS cc_start: 0.7928 (mttm) cc_final: 0.7661 (mtmm) REVERT: B 90 TYR cc_start: 0.8397 (m-80) cc_final: 0.8024 (m-80) REVERT: B 116 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 271 CYS cc_start: 0.8168 (m) cc_final: 0.7967 (p) REVERT: B 282 MET cc_start: 0.8444 (tpp) cc_final: 0.8161 (mmp) REVERT: B 290 LYS cc_start: 0.8218 (tttm) cc_final: 0.7965 (tptt) REVERT: B 327 LYS cc_start: 0.7948 (mttp) cc_final: 0.7717 (mttt) REVERT: B 362 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6790 (t0) REVERT: C 237 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6382 (mttt) REVERT: C 327 LYS cc_start: 0.7580 (mttp) cc_final: 0.7245 (mppt) REVERT: C 362 ASP cc_start: 0.7712 (t0) cc_final: 0.6807 (m-30) REVERT: D 49 LYS cc_start: 0.7189 (mtpp) cc_final: 0.6974 (mmtm) REVERT: D 82 GLU cc_start: 0.7434 (pp20) cc_final: 0.7168 (pp20) REVERT: D 92 GLU cc_start: 0.7164 (tp30) cc_final: 0.6772 (mm-30) REVERT: D 98 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: D 124 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6965 (pt0) REVERT: D 152 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7214 (tpt) REVERT: D 162 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7796 (p) REVERT: D 166 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6486 (pt0) REVERT: D 362 ASP cc_start: 0.6650 (t0) cc_final: 0.6210 (p0) outliers start: 42 outliers final: 18 residues processed: 171 average time/residue: 0.5316 time to fit residues: 98.8928 Evaluate side-chains 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 271 CYS 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 24 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 237 LYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 0.0020 chunk 141 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN D 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126867 restraints weight = 16205.445| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.74 r_work: 0.3570 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12052 Z= 0.181 Angle : 0.628 9.958 16352 Z= 0.311 Chirality : 0.046 0.145 1812 Planarity : 0.005 0.065 2096 Dihedral : 11.234 160.446 1684 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.40 % Allowed : 22.94 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), residues: 1476 helix: 0.79 (0.22), residues: 600 sheet: 0.42 (0.31), residues: 284 loop : -0.54 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 176 TYR 0.015 0.002 TYR A 239 PHE 0.011 0.001 PHE D 30 TRP 0.010 0.002 TRP B 355 HIS 0.005 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00424 (12052) covalent geometry : angle 0.62766 (16352) hydrogen bonds : bond 0.05044 ( 531) hydrogen bonds : angle 4.20235 ( 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 181 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.518 Fit side-chains REVERT: A 43 MET cc_start: 0.4579 (mmp) cc_final: 0.2935 (mtm) REVERT: A 81 MET cc_start: 0.8392 (tpt) cc_final: 0.8120 (tpt) REVERT: A 190 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7372 (mttt) REVERT: A 275 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7196 (mm-30) REVERT: A 359 GLN cc_start: 0.7315 (mm-40) cc_final: 0.6506 (pm20) REVERT: A 363 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5789 (mp0) REVERT: A 369 VAL cc_start: 0.7766 (t) cc_final: 0.7444 (p) REVERT: B 46 MET cc_start: 0.2881 (mmm) cc_final: 0.2365 (tmm) REVERT: B 49 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7566 (mppt) REVERT: B 67 LYS cc_start: 0.7911 (mttm) cc_final: 0.7646 (mtmm) REVERT: B 90 TYR cc_start: 0.8438 (m-80) cc_final: 0.8063 (m-80) REVERT: B 116 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7330 (mt-10) REVERT: B 271 CYS cc_start: 0.8156 (m) cc_final: 0.7899 (p) REVERT: B 290 LYS cc_start: 0.8232 (tttm) cc_final: 0.7985 (tptt) REVERT: B 327 LYS cc_start: 0.7913 (mttp) cc_final: 0.7682 (mttt) REVERT: B 362 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6790 (t0) REVERT: C 313 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7960 (tp40) REVERT: C 327 LYS cc_start: 0.7562 (mttp) cc_final: 0.7354 (mtmp) REVERT: C 362 ASP cc_start: 0.7811 (t0) cc_final: 0.6870 (m-30) REVERT: D 49 LYS cc_start: 0.7181 (mtpp) cc_final: 0.6971 (mmtm) REVERT: D 82 GLU cc_start: 0.7577 (pp20) cc_final: 0.7270 (pp20) REVERT: D 92 GLU cc_start: 0.7309 (tp30) cc_final: 0.6926 (mm-30) REVERT: D 98 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: D 124 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6936 (pt0) REVERT: D 162 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7866 (p) REVERT: D 271 CYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8001 (p) REVERT: D 362 ASP cc_start: 0.6726 (t0) cc_final: 0.6254 (p0) outliers start: 43 outliers final: 21 residues processed: 166 average time/residue: 0.6058 time to fit residues: 108.9368 Evaluate side-chains 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE 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 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 B residue 357 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 369 VAL Chi-restraints excluded: chain D residue 29 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 271 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 104 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127482 restraints weight = 16020.096| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.73 r_work: 0.3575 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12052 Z= 0.163 Angle : 0.618 10.842 16352 Z= 0.305 Chirality : 0.045 0.139 1812 Planarity : 0.005 0.067 2096 Dihedral : 11.107 157.816 1684 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.40 % Allowed : 23.26 % Favored : 73.34 % 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 aren not related in a simple way. whole: 0.17 (0.22), residues: 1476 helix: 0.80 (0.22), residues: 600 sheet: 0.43 (0.31), residues: 284 loop : -0.67 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 94 TYR 0.015 0.001 TYR A 239 PHE 0.009 0.001 PHE A 278 TRP 0.011 0.002 TRP B 355 HIS 0.005 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00382 (12052) covalent geometry : angle 0.61764 (16352) hydrogen bonds : bond 0.04560 ( 531) hydrogen bonds : angle 4.17453 ( 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 186 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.4816 (mmp) cc_final: 0.3053 (mtm) REVERT: A 81 MET cc_start: 0.8400 (tpt) cc_final: 0.8102 (tpt) REVERT: A 190 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7406 (mttt) REVERT: A 275 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7227 (mm-30) REVERT: A 324 MET cc_start: 0.7894 (mmp) cc_final: 0.7649 (mmm) REVERT: A 359 GLN cc_start: 0.7357 (mm-40) cc_final: 0.7143 (mm-40) REVERT: A 363 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5781 (mp0) REVERT: A 368 ILE cc_start: 0.7144 (tt) cc_final: 0.6832 (tp) REVERT: A 369 VAL cc_start: 0.7692 (t) cc_final: 0.7382 (p) REVERT: B 46 MET cc_start: 0.3014 (mmm) cc_final: 0.2453 (tmm) REVERT: B 49 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7577 (mppt) REVERT: B 67 LYS cc_start: 0.7949 (mttm) cc_final: 0.7654 (mtmm) REVERT: B 90 TYR cc_start: 0.8453 (m-80) cc_final: 0.8078 (m-80) REVERT: B 116 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7309 (mt-10) REVERT: B 271 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7910 (p) REVERT: B 290 LYS cc_start: 0.8208 (tttm) cc_final: 0.7950 (tptt) REVERT: B 327 LYS cc_start: 0.7864 (mttp) cc_final: 0.7654 (mttt) REVERT: B 362 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6804 (t0) REVERT: C 313 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7960 (tp40) REVERT: C 327 LYS cc_start: 0.7559 (mttp) cc_final: 0.7278 (mttp) REVERT: C 362 ASP cc_start: 0.7889 (t0) cc_final: 0.6979 (m-30) REVERT: D 49 LYS cc_start: 0.7192 (mtpp) cc_final: 0.6951 (mmtt) REVERT: D 82 GLU cc_start: 0.7562 (pp20) cc_final: 0.7262 (pp20) REVERT: D 92 GLU cc_start: 0.7325 (tp30) cc_final: 0.6956 (mm-30) REVERT: D 98 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: D 124 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6967 (pt0) REVERT: D 166 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6492 (pt0) REVERT: D 271 CYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8066 (p) REVERT: D 324 MET cc_start: 0.6814 (mmp) cc_final: 0.6547 (mmt) REVERT: D 362 ASP cc_start: 0.6751 (t0) cc_final: 0.6159 (p0) outliers start: 43 outliers final: 25 residues processed: 174 average time/residue: 0.6078 time to fit residues: 114.5445 Evaluate side-chains 170 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 270 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 327 LYS 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 357 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 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 243 ASP Chi-restraints excluded: chain D residue 271 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 0.0040 chunk 31 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.140208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129682 restraints weight = 16054.390| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.74 r_work: 0.3605 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12052 Z= 0.105 Angle : 0.564 11.109 16352 Z= 0.273 Chirality : 0.043 0.147 1812 Planarity : 0.005 0.069 2096 Dihedral : 10.842 153.985 1684 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.61 % Allowed : 24.37 % Favored : 73.02 % 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 aren not related in a simple way. whole: 0.43 (0.22), residues: 1476 helix: 1.04 (0.22), residues: 596 sheet: 0.57 (0.31), residues: 284 loop : -0.54 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 94 TYR 0.013 0.001 TYR A 239 PHE 0.008 0.001 PHE A 278 TRP 0.009 0.001 TRP B 355 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00237 (12052) covalent geometry : angle 0.56378 (16352) hydrogen bonds : bond 0.03466 ( 531) hydrogen bonds : angle 4.05555 ( 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: 33 poor density : 144 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4681 (mmp) cc_final: 0.3066 (mtm) REVERT: A 81 MET cc_start: 0.8338 (tpt) cc_final: 0.8042 (tpt) REVERT: A 190 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7356 (mttt) REVERT: A 275 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 313 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: A 359 GLN cc_start: 0.7288 (mm-40) cc_final: 0.7058 (mm-40) REVERT: A 363 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5742 (mp0) REVERT: A 369 VAL cc_start: 0.7627 (t) cc_final: 0.7348 (p) REVERT: B 46 MET cc_start: 0.3097 (mmm) cc_final: 0.2525 (tmm) REVERT: B 49 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7542 (mppt) REVERT: B 67 LYS cc_start: 0.7964 (mttm) cc_final: 0.7658 (mtmm) REVERT: B 90 TYR cc_start: 0.8407 (m-80) cc_final: 0.8042 (m-80) REVERT: B 116 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7239 (mt-10) REVERT: B 271 CYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7917 (p) REVERT: B 290 LYS cc_start: 0.8208 (tttm) cc_final: 0.7946 (tptt) REVERT: B 327 LYS cc_start: 0.7882 (mttp) cc_final: 0.7662 (mttt) REVERT: B 362 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6798 (t0) REVERT: C 124 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6759 (tt0) REVERT: C 313 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7822 (tp40) REVERT: C 327 LYS cc_start: 0.7528 (mttp) cc_final: 0.7320 (mtmp) REVERT: D 82 GLU cc_start: 0.7507 (pp20) cc_final: 0.7227 (pt0) REVERT: D 92 GLU cc_start: 0.7248 (tp30) cc_final: 0.6893 (mm-30) REVERT: D 98 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: D 124 GLU cc_start: 0.7651 (mt-10) cc_final: 0.6957 (pt0) REVERT: D 162 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7797 (p) REVERT: D 166 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6363 (pt0) REVERT: D 170 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7507 (mp) REVERT: D 271 CYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8068 (p) REVERT: D 324 MET cc_start: 0.6832 (mmp) cc_final: 0.6562 (mmt) REVERT: D 362 ASP cc_start: 0.6647 (t0) cc_final: 0.6068 (p0) outliers start: 33 outliers final: 21 residues processed: 169 average time/residue: 0.5325 time to fit residues: 97.2710 Evaluate side-chains 168 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 270 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 327 LYS 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 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 SER 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 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 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 271 CYS 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: 3.9990 chunk 120 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3777 r_free = 0.3777 target = 0.137196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126299 restraints weight = 16031.155| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.79 r_work: 0.3554 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12052 Z= 0.181 Angle : 0.630 12.003 16352 Z= 0.312 Chirality : 0.046 0.148 1812 Planarity : 0.005 0.072 2096 Dihedral : 10.976 156.934 1684 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.93 % Allowed : 24.92 % Favored : 72.15 % 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 aren not related in a simple way. whole: 0.20 (0.22), residues: 1476 helix: 0.84 (0.22), residues: 600 sheet: 0.46 (0.30), residues: 284 loop : -0.68 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 94 TYR 0.017 0.002 TYR A 239 PHE 0.009 0.001 PHE C 265 TRP 0.010 0.002 TRP B 355 HIS 0.005 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00424 (12052) covalent geometry : angle 0.62952 (16352) hydrogen bonds : bond 0.04971 ( 531) hydrogen bonds : angle 4.14179 ( 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 177 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.357 Fit side-chains REVERT: A 43 MET cc_start: 0.4638 (mmp) cc_final: 0.2961 (mtm) REVERT: A 81 MET cc_start: 0.8376 (tpt) cc_final: 0.8060 (tpt) REVERT: A 190 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7347 (mttt) REVERT: A 275 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7200 (mm-30) REVERT: A 313 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: A 324 MET cc_start: 0.7842 (mmp) cc_final: 0.7560 (mmm) REVERT: A 359 GLN cc_start: 0.7273 (mm-40) cc_final: 0.7072 (mm-40) REVERT: A 363 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5671 (mp0) REVERT: B 46 MET cc_start: 0.3142 (mmm) cc_final: 0.2754 (tmm) REVERT: B 49 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7550 (mppt) REVERT: B 67 LYS cc_start: 0.7982 (mttm) cc_final: 0.7667 (mtmm) REVERT: B 90 TYR cc_start: 0.8504 (m-80) cc_final: 0.8125 (m-80) REVERT: B 116 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7374 (mt-10) REVERT: B 271 CYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7911 (p) REVERT: B 290 LYS cc_start: 0.8298 (tttm) cc_final: 0.7962 (tptt) REVERT: B 327 LYS cc_start: 0.7872 (mttp) cc_final: 0.7652 (mttt) REVERT: B 362 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6840 (t0) REVERT: C 124 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6756 (tt0) REVERT: C 313 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: C 327 LYS cc_start: 0.7635 (mttp) cc_final: 0.7424 (mtmp) REVERT: C 362 ASP cc_start: 0.7959 (t0) cc_final: 0.6984 (m-30) REVERT: D 82 GLU cc_start: 0.7589 (pp20) cc_final: 0.7271 (pt0) REVERT: D 92 GLU cc_start: 0.7305 (tp30) cc_final: 0.6902 (mm-30) REVERT: D 98 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: D 124 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7037 (pt0) REVERT: D 166 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6343 (pt0) REVERT: D 271 CYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8069 (p) REVERT: D 324 MET cc_start: 0.6912 (mmp) cc_final: 0.6657 (mmt) REVERT: D 362 ASP cc_start: 0.6737 (t0) cc_final: 0.6076 (p0) outliers start: 37 outliers final: 27 residues processed: 167 average time/residue: 0.6084 time to fit residues: 109.4186 Evaluate side-chains 172 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 65 THR 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 357 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 15 MET 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 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 50 ASP 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 271 CYS 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: 0.0670 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.128529 restraints weight = 16074.809| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.81 r_work: 0.3584 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12052 Z= 0.109 Angle : 0.579 12.237 16352 Z= 0.281 Chirality : 0.044 0.145 1812 Planarity : 0.005 0.073 2096 Dihedral : 10.734 161.003 1684 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.85 % Allowed : 25.16 % Favored : 71.99 % 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 aren not related in a simple way. whole: 0.39 (0.22), residues: 1476 helix: 1.03 (0.22), residues: 596 sheet: 0.54 (0.30), residues: 284 loop : -0.58 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 94 TYR 0.014 0.001 TYR A 239 PHE 0.011 0.001 PHE A 278 TRP 0.010 0.001 TRP B 355 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00244 (12052) covalent geometry : angle 0.57923 (16352) hydrogen bonds : bond 0.03662 ( 531) hydrogen bonds : angle 4.05068 ( 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 176 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.430 Fit side-chains REVERT: A 43 MET cc_start: 0.4619 (mmp) cc_final: 0.2931 (mtm) REVERT: A 81 MET cc_start: 0.8319 (tpt) cc_final: 0.8005 (tpt) REVERT: A 190 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7314 (mttt) REVERT: A 275 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7172 (mm-30) REVERT: A 313 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: A 324 MET cc_start: 0.7834 (mmp) cc_final: 0.7563 (mmm) REVERT: A 359 GLN cc_start: 0.7259 (mm-40) cc_final: 0.7035 (mm-40) REVERT: A 363 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: B 46 MET cc_start: 0.3110 (mmm) cc_final: 0.2731 (tmm) REVERT: B 49 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7481 (mppt) REVERT: B 67 LYS cc_start: 0.7994 (mttm) cc_final: 0.7662 (mtmm) REVERT: B 90 TYR cc_start: 0.8449 (m-80) cc_final: 0.8081 (m-80) REVERT: B 116 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7307 (mt-10) REVERT: B 271 CYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7898 (p) REVERT: B 282 MET cc_start: 0.8425 (tpp) cc_final: 0.8056 (mmp) REVERT: B 290 LYS cc_start: 0.8242 (tttm) cc_final: 0.7930 (tptt) REVERT: B 327 LYS cc_start: 0.7856 (mttp) cc_final: 0.7638 (mttt) REVERT: B 362 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6896 (t0) REVERT: C 124 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6783 (tt0) REVERT: C 313 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7768 (tp40) REVERT: C 327 LYS cc_start: 0.7605 (mttp) cc_final: 0.7396 (mtmp) REVERT: D 82 GLU cc_start: 0.7539 (pp20) cc_final: 0.7245 (pt0) REVERT: D 92 GLU cc_start: 0.7268 (tp30) cc_final: 0.6895 (mm-30) REVERT: D 124 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6982 (pt0) REVERT: D 166 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6299 (pt0) REVERT: D 170 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7491 (mp) REVERT: D 271 CYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8075 (p) REVERT: D 324 MET cc_start: 0.6920 (mmp) cc_final: 0.6661 (mmt) REVERT: D 362 ASP cc_start: 0.6708 (t0) cc_final: 0.6058 (p0) outliers start: 36 outliers final: 22 residues processed: 167 average time/residue: 0.5803 time to fit residues: 104.7046 Evaluate side-chains 167 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 65 THR 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 357 SER 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 C residue 369 VAL Chi-restraints excluded: chain D residue 29 VAL 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 271 CYS 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: 5.9990 chunk 43 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 4 optimal weight: 0.0020 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127243 restraints weight = 16026.840| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.79 r_work: 0.3567 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4904 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= 0.145 Angle : 0.603 12.027 16352 Z= 0.295 Chirality : 0.045 0.143 1812 Planarity : 0.005 0.072 2096 Dihedral : 10.658 167.536 1684 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.69 % Allowed : 25.55 % 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 aren not related in a simple way. whole: 0.34 (0.22), residues: 1476 helix: 0.98 (0.22), residues: 596 sheet: 0.56 (0.30), residues: 284 loop : -0.64 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 94 TYR 0.016 0.001 TYR A 239 PHE 0.009 0.001 PHE A 278 TRP 0.010 0.001 TRP B 355 HIS 0.004 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00336 (12052) covalent geometry : angle 0.60303 (16352) hydrogen bonds : bond 0.04298 ( 531) hydrogen bonds : angle 4.08360 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3590.57 seconds wall clock time: 61 minutes 59.28 seconds (3719.28 seconds total)