Starting phenix.real_space_refine on Wed Jul 30 03:38:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnh_27572/07_2025/8dnh_27572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnh_27572/07_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_27572/07_2025/8dnh_27572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2025/8dnh_27572.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2025/8dnh_27572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnh_27572/07_2025/8dnh_27572.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.03, per 1000 atoms: 0.68 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: 3.07 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.92 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: 4.05 Time building geometry restraints manager: 3.56 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: 0.03 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: 0.660 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.890 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (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 TRP 0.018 0.003 TRP A 78 HIS 0.004 0.001 HIS A 172 PHE 0.013 0.001 PHE A 89 TYR 0.012 0.001 TYR B 336 ARG 0.004 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.29847 ( 531) hydrogen bonds : angle 6.10769 ( 1416) covalent geometry : bond 0.00589 (12052) covalent geometry : angle 0.87513 (16352) *********************** 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 : 1.330 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: 1.2384 time to fit residues: 356.4422 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 : 1.224 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN C 100 HIS D 11 ASN D 100 HIS D 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140413 restraints weight = 16266.246| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.80 r_work: 0.3769 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2268 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= 0.131 Angle : 0.620 6.392 16352 Z= 0.315 Chirality : 0.045 0.140 1812 Planarity : 0.004 0.055 2096 Dihedral : 13.502 179.591 1686 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.61 % Allowed : 16.61 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1476 helix: 0.62 (0.22), residues: 616 sheet: 0.75 (0.33), residues: 260 loop : -0.19 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 85 HIS 0.005 0.001 HIS D 100 PHE 0.012 0.001 PHE A 222 TYR 0.012 0.001 TYR C 142 ARG 0.005 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 531) hydrogen bonds : angle 4.53633 ( 1416) covalent geometry : bond 0.00281 (12052) covalent geometry : angle 0.61988 (16352) *********************** 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 213 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.393 Fit side-chains REVERT: A 43 MET cc_start: 0.4354 (mmp) cc_final: 0.3241 (mtm) REVERT: A 83 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8336 (mppt) REVERT: A 190 LYS cc_start: 0.7746 (ttmt) cc_final: 0.7225 (mttt) REVERT: A 271 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7048 (p) REVERT: A 275 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 291 ASP cc_start: 0.7675 (m-30) cc_final: 0.7453 (m-30) REVERT: A 369 VAL cc_start: 0.7773 (t) cc_final: 0.7523 (p) REVERT: B 40 GLN cc_start: 0.6557 (pm20) cc_final: 0.5937 (mt0) REVERT: B 46 MET cc_start: 0.2856 (mmm) cc_final: 0.2458 (tmm) REVERT: B 49 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7597 (mppt) REVERT: B 67 LYS cc_start: 0.7820 (mttm) cc_final: 0.7597 (mtmm) REVERT: B 90 TYR cc_start: 0.8266 (m-80) cc_final: 0.7922 (m-80) REVERT: B 116 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7098 (mt-10) REVERT: B 271 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7625 (m) REVERT: B 304 MET cc_start: 0.8426 (tpt) cc_final: 0.8082 (tpt) REVERT: B 327 LYS cc_start: 0.8083 (mttp) cc_final: 0.7866 (mttt) REVERT: B 357 SER cc_start: 0.8249 (m) cc_final: 0.8046 (p) REVERT: C 237 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6365 (mttt) REVERT: C 282 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7665 (mmm) REVERT: C 327 LYS cc_start: 0.7280 (mttp) cc_final: 0.7032 (mppt) REVERT: C 358 LYS cc_start: 0.7867 (tmtt) cc_final: 0.7590 (tttt) REVERT: C 362 ASP cc_start: 0.7203 (t0) cc_final: 0.6378 (m-30) REVERT: D 49 LYS cc_start: 0.6963 (mtpp) cc_final: 0.6645 (mmtm) REVERT: D 59 SER cc_start: 0.8208 (t) cc_final: 0.8007 (m) REVERT: D 82 GLU cc_start: 0.7296 (pp20) cc_final: 0.7011 (pp20) REVERT: D 92 GLU cc_start: 0.6557 (tp30) cc_final: 0.6243 (mt-10) REVERT: D 98 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: D 124 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7274 (pt0) REVERT: D 132 TYR cc_start: 0.8294 (t80) cc_final: 0.8074 (t80) REVERT: D 152 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6654 (tpt) REVERT: D 271 CYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7784 (p) outliers start: 33 outliers final: 9 residues processed: 199 average time/residue: 1.2948 time to fit residues: 278.8856 Evaluate side-chains 153 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 131 MET 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 241 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 369 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 0.0980 chunk 132 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 144 optimal weight: 0.0370 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 106 optimal weight: 0.0010 overall best weight: 1.6268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN B 262 GLN C 100 HIS D 11 ASN D 100 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132877 restraints weight = 16278.904| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.77 r_work: 0.3669 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12052 Z= 0.150 Angle : 0.620 12.104 16352 Z= 0.305 Chirality : 0.046 0.140 1812 Planarity : 0.004 0.061 2096 Dihedral : 11.902 167.304 1686 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.56 % Allowed : 18.91 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1476 helix: 0.66 (0.21), residues: 620 sheet: 0.76 (0.32), residues: 272 loop : -0.14 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 78 HIS 0.007 0.001 HIS D 100 PHE 0.016 0.001 PHE B 222 TYR 0.013 0.002 TYR A 239 ARG 0.005 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 531) hydrogen bonds : angle 4.26689 ( 1416) covalent geometry : bond 0.00344 (12052) covalent geometry : angle 0.61993 (16352) *********************** 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 193 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4221 (mmp) cc_final: 0.3081 (mtm) REVERT: A 190 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7503 (mttt) REVERT: A 243 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5985 (t70) REVERT: A 271 CYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7331 (p) REVERT: A 275 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 327 LYS cc_start: 0.7243 (pttt) cc_final: 0.6819 (ptpp) REVERT: A 369 VAL cc_start: 0.7816 (t) cc_final: 0.7556 (p) REVERT: B 46 MET cc_start: 0.2888 (mmm) cc_final: 0.2486 (tmm) REVERT: B 49 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7529 (mppt) REVERT: B 67 LYS cc_start: 0.7835 (mttm) cc_final: 0.7576 (mtmm) REVERT: B 90 TYR cc_start: 0.8418 (m-80) cc_final: 0.8073 (m-80) REVERT: B 116 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7317 (mt-10) REVERT: B 282 MET cc_start: 0.8524 (tpp) cc_final: 0.8300 (mmp) REVERT: B 290 LYS cc_start: 0.8209 (tttm) cc_final: 0.7966 (tptt) REVERT: B 304 MET cc_start: 0.8442 (tpt) cc_final: 0.8159 (tpt) REVERT: B 327 LYS cc_start: 0.8112 (mttp) cc_final: 0.7852 (mttt) REVERT: B 357 SER cc_start: 0.8636 (m) cc_final: 0.8433 (t) REVERT: B 366 PRO cc_start: 0.7804 (Cg_endo) cc_final: 0.7440 (Cg_exo) REVERT: C 124 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6696 (mm-30) REVERT: C 191 ILE cc_start: 0.8858 (tt) cc_final: 0.8595 (tp) REVERT: C 237 LYS cc_start: 0.6586 (OUTLIER) cc_final: 0.6148 (mttt) REVERT: C 327 LYS cc_start: 0.7373 (mttp) cc_final: 0.7067 (mppt) REVERT: C 362 ASP cc_start: 0.7618 (t0) cc_final: 0.6748 (m-30) REVERT: D 49 LYS cc_start: 0.7199 (mtpp) cc_final: 0.6955 (mmtm) REVERT: D 82 GLU cc_start: 0.7406 (pp20) cc_final: 0.7145 (pp20) REVERT: D 92 GLU cc_start: 0.7055 (tp30) cc_final: 0.6626 (mm-30) REVERT: D 98 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: D 124 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7150 (pt0) REVERT: D 131 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7922 (ttt) REVERT: D 152 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7005 (tpt) REVERT: D 271 CYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7797 (p) REVERT: D 362 ASP cc_start: 0.6365 (t0) cc_final: 0.6022 (p0) outliers start: 45 outliers final: 21 residues processed: 175 average time/residue: 1.2173 time to fit residues: 231.2529 Evaluate side-chains 159 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 131 MET 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 347 SER 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 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 241 LEU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 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 243 ASP Chi-restraints excluded: chain D residue 271 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 16 optimal weight: 6.9990 chunk 147 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 1.0238 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.144790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133929 restraints weight = 16106.565| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.75 r_work: 0.3684 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12052 Z= 0.109 Angle : 0.560 7.758 16352 Z= 0.272 Chirality : 0.043 0.135 1812 Planarity : 0.004 0.062 2096 Dihedral : 11.514 162.941 1686 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.32 % Allowed : 20.09 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1476 helix: 0.81 (0.22), residues: 620 sheet: 0.59 (0.32), residues: 284 loop : -0.17 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 78 HIS 0.007 0.001 HIS D 100 PHE 0.006 0.001 PHE D 30 TYR 0.009 0.001 TYR B 165 ARG 0.006 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 531) hydrogen bonds : angle 4.13251 ( 1416) covalent geometry : bond 0.00239 (12052) covalent geometry : angle 0.56001 (16352) *********************** 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 185 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4227 (mmp) cc_final: 0.3072 (mtm) REVERT: A 65 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7421 (p) REVERT: A 120 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6612 (tt0) REVERT: A 190 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7407 (mttt) REVERT: A 275 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7009 (mm-30) REVERT: A 313 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6949 (tp40) REVERT: A 327 LYS cc_start: 0.7357 (pttt) cc_final: 0.6857 (ptpp) REVERT: A 369 VAL cc_start: 0.7758 (t) cc_final: 0.7494 (p) REVERT: B 46 MET cc_start: 0.2844 (mmm) cc_final: 0.2459 (tmm) REVERT: B 49 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7564 (mppt) REVERT: B 67 LYS cc_start: 0.7938 (mttm) cc_final: 0.7687 (mtmm) REVERT: B 90 TYR cc_start: 0.8358 (m-80) cc_final: 0.8035 (m-80) REVERT: B 116 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 282 MET cc_start: 0.8501 (tpp) cc_final: 0.8231 (mmp) REVERT: B 290 LYS cc_start: 0.8225 (tttm) cc_final: 0.7997 (tptt) REVERT: B 327 LYS cc_start: 0.8061 (mttp) cc_final: 0.7815 (mttt) REVERT: B 366 PRO cc_start: 0.7845 (Cg_endo) cc_final: 0.7539 (Cg_exo) REVERT: C 81 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7623 (mmm) REVERT: C 124 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6638 (mt-10) REVERT: C 191 ILE cc_start: 0.8830 (tt) cc_final: 0.8598 (tp) REVERT: C 237 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6290 (mttt) REVERT: C 327 LYS cc_start: 0.7449 (mttp) cc_final: 0.7124 (mtmt) REVERT: C 362 ASP cc_start: 0.7617 (t0) cc_final: 0.6726 (m-30) REVERT: D 82 GLU cc_start: 0.7335 (pp20) cc_final: 0.7089 (pp20) REVERT: D 92 GLU cc_start: 0.7049 (tp30) cc_final: 0.6637 (mm-30) REVERT: D 98 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: D 124 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7172 (pt0) REVERT: D 131 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7968 (ttt) REVERT: D 152 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6895 (tpt) REVERT: D 271 CYS cc_start: 0.8300 (m) cc_final: 0.7917 (p) REVERT: D 310 ASP cc_start: 0.7228 (m-30) cc_final: 0.7008 (t0) REVERT: D 362 ASP cc_start: 0.6453 (t0) cc_final: 0.6072 (p0) outliers start: 42 outliers final: 13 residues processed: 169 average time/residue: 1.1821 time to fit residues: 217.7691 Evaluate side-chains 156 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 120 GLN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 77 ASN 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 90 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN D 11 ASN D 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123201 restraints weight = 16146.789| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.79 r_work: 0.3524 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 12052 Z= 0.328 Angle : 0.793 8.351 16352 Z= 0.408 Chirality : 0.053 0.208 1812 Planarity : 0.006 0.066 2096 Dihedral : 11.882 165.649 1684 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.19 % Allowed : 20.81 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1476 helix: 0.17 (0.21), residues: 616 sheet: 0.12 (0.30), residues: 288 loop : -0.85 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 339 HIS 0.008 0.002 HIS B 100 PHE 0.021 0.002 PHE C 265 TYR 0.026 0.003 TYR B 336 ARG 0.006 0.001 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.07561 ( 531) hydrogen bonds : angle 4.60658 ( 1416) covalent geometry : bond 0.00766 (12052) covalent geometry : angle 0.79264 (16352) *********************** 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 195 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 1.321 Fit side-chains REVERT: A 43 MET cc_start: 0.4580 (mmp) cc_final: 0.2836 (mtm) REVERT: A 81 MET cc_start: 0.8377 (tpt) cc_final: 0.8126 (tpt) REVERT: A 190 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7364 (mttt) REVERT: A 275 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 363 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5779 (mp0) REVERT: A 369 VAL cc_start: 0.7794 (t) cc_final: 0.7478 (p) REVERT: B 46 MET cc_start: 0.2950 (mmm) cc_final: 0.2405 (tmm) REVERT: B 49 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7559 (mppt) REVERT: B 67 LYS cc_start: 0.7855 (mttm) cc_final: 0.7589 (mtmm) REVERT: B 81 MET cc_start: 0.7757 (tpt) cc_final: 0.7555 (tpp) REVERT: B 90 TYR cc_start: 0.8548 (m-80) cc_final: 0.8182 (m-80) REVERT: B 116 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 290 LYS cc_start: 0.8411 (tttm) cc_final: 0.8119 (tptt) REVERT: B 312 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8321 (ttp) REVERT: B 327 LYS cc_start: 0.7900 (mttp) cc_final: 0.7672 (mttt) REVERT: B 362 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6675 (t0) REVERT: C 46 MET cc_start: 0.4760 (mmt) cc_final: 0.4437 (mmt) REVERT: C 124 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6651 (mt-10) REVERT: C 191 ILE cc_start: 0.8845 (tt) cc_final: 0.8639 (tp) REVERT: C 275 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: C 313 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7994 (tp40) REVERT: C 327 LYS cc_start: 0.7522 (mttp) cc_final: 0.7181 (mppt) REVERT: C 362 ASP cc_start: 0.7928 (t0) cc_final: 0.6996 (m-30) REVERT: D 82 GLU cc_start: 0.7515 (pp20) cc_final: 0.7117 (pp20) REVERT: D 92 GLU cc_start: 0.7297 (tp30) cc_final: 0.6863 (mm-30) REVERT: D 98 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: D 124 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6936 (pt0) REVERT: D 271 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7955 (p) REVERT: D 362 ASP cc_start: 0.6719 (t0) cc_final: 0.6164 (p0) outliers start: 53 outliers final: 25 residues processed: 179 average time/residue: 1.3247 time to fit residues: 255.8848 Evaluate side-chains 163 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 151 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 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 312 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 282 MET 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 77 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 151 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 Chi-restraints excluded: chain D residue 344 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 C 160 HIS D 11 ASN D 100 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.139119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128499 restraints weight = 16114.239| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.75 r_work: 0.3591 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12052 Z= 0.117 Angle : 0.585 6.843 16352 Z= 0.289 Chirality : 0.044 0.139 1812 Planarity : 0.005 0.063 2096 Dihedral : 11.312 162.169 1684 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.09 % Allowed : 23.18 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1476 helix: 0.74 (0.22), residues: 596 sheet: 0.52 (0.31), residues: 276 loop : -0.71 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 78 HIS 0.005 0.001 HIS D 100 PHE 0.009 0.001 PHE B 123 TYR 0.013 0.001 TYR A 239 ARG 0.010 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 531) hydrogen bonds : angle 4.20835 ( 1416) covalent geometry : bond 0.00264 (12052) covalent geometry : angle 0.58461 (16352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4622 (mmp) cc_final: 0.2919 (mtm) REVERT: A 81 MET cc_start: 0.8328 (tpt) cc_final: 0.8039 (tpt) REVERT: A 190 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7337 (mttt) REVERT: A 275 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7202 (mm-30) REVERT: A 327 LYS cc_start: 0.7504 (pttm) cc_final: 0.7263 (pptt) REVERT: A 363 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: A 368 ILE cc_start: 0.7137 (tt) cc_final: 0.6828 (tp) REVERT: A 369 VAL cc_start: 0.7745 (t) cc_final: 0.7430 (p) REVERT: B 46 MET cc_start: 0.2832 (mmm) cc_final: 0.2336 (tmm) REVERT: B 49 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7574 (mppt) REVERT: B 67 LYS cc_start: 0.7896 (mttm) cc_final: 0.7621 (mtmm) REVERT: B 90 TYR cc_start: 0.8438 (m-80) cc_final: 0.8072 (m-80) REVERT: B 116 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 290 LYS cc_start: 0.8192 (tttm) cc_final: 0.7933 (tptt) REVERT: B 327 LYS cc_start: 0.7894 (mttp) cc_final: 0.7665 (mttt) REVERT: C 94 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7517 (mtm110) REVERT: C 124 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6706 (mt-10) REVERT: C 362 ASP cc_start: 0.7884 (t0) cc_final: 0.6962 (m-30) REVERT: D 82 GLU cc_start: 0.7537 (pp20) cc_final: 0.7253 (pp20) REVERT: D 92 GLU cc_start: 0.7275 (tp30) cc_final: 0.6909 (mm-30) REVERT: D 98 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: D 124 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6929 (pt0) REVERT: D 166 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6555 (pt0) REVERT: D 362 ASP cc_start: 0.6653 (t0) cc_final: 0.6136 (p0) outliers start: 39 outliers final: 20 residues processed: 167 average time/residue: 1.3046 time to fit residues: 237.1892 Evaluate side-chains 153 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 151 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 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 170 LEU Chi-restraints excluded: chain D residue 236 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 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 = 0.3809 r_free = 0.3809 target = 0.140108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129544 restraints weight = 16198.501| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.74 r_work: 0.3600 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12052 Z= 0.116 Angle : 0.569 9.383 16352 Z= 0.276 Chirality : 0.044 0.130 1812 Planarity : 0.005 0.065 2096 Dihedral : 10.995 160.105 1684 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.01 % Allowed : 23.81 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1476 helix: 0.97 (0.22), residues: 596 sheet: 0.68 (0.31), residues: 276 loop : -0.57 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 355 HIS 0.003 0.001 HIS A 160 PHE 0.009 0.001 PHE A 278 TYR 0.013 0.001 TYR A 239 ARG 0.008 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 531) hydrogen bonds : angle 4.05143 ( 1416) covalent geometry : bond 0.00265 (12052) covalent geometry : angle 0.56899 (16352) *********************** 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 178 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4586 (mmp) cc_final: 0.2994 (mtm) REVERT: A 65 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7411 (p) REVERT: A 81 MET cc_start: 0.8314 (tpt) cc_final: 0.8017 (tpt) REVERT: A 190 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7366 (mttt) REVERT: A 275 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 313 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: A 327 LYS cc_start: 0.7449 (pttm) cc_final: 0.7228 (pptt) REVERT: A 359 GLN cc_start: 0.7311 (mm-40) cc_final: 0.6558 (pm20) REVERT: A 363 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5753 (mp0) REVERT: A 368 ILE cc_start: 0.7114 (tt) cc_final: 0.6805 (tp) REVERT: A 369 VAL cc_start: 0.7661 (t) cc_final: 0.7384 (p) REVERT: B 46 MET cc_start: 0.2879 (mmm) cc_final: 0.2374 (tmm) REVERT: B 49 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7595 (mppt) REVERT: B 67 LYS cc_start: 0.7970 (mttm) cc_final: 0.7695 (mtmm) REVERT: B 90 TYR cc_start: 0.8430 (m-80) cc_final: 0.8092 (m-80) REVERT: B 116 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7293 (mt-10) REVERT: B 290 LYS cc_start: 0.8237 (tttm) cc_final: 0.7987 (tptt) REVERT: B 327 LYS cc_start: 0.7898 (mttp) cc_final: 0.7677 (mttt) REVERT: C 94 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7532 (mtm110) REVERT: C 124 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6844 (mt-10) REVERT: C 313 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7891 (tp40) REVERT: C 362 ASP cc_start: 0.7875 (t0) cc_final: 0.6979 (m-30) REVERT: D 82 GLU cc_start: 0.7543 (pp20) cc_final: 0.7250 (pp20) REVERT: D 92 GLU cc_start: 0.7257 (tp30) cc_final: 0.6909 (mm-30) REVERT: D 98 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: D 124 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6998 (pt0) REVERT: D 166 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6400 (pt0) REVERT: D 362 ASP cc_start: 0.6689 (t0) cc_final: 0.6147 (p0) outliers start: 38 outliers final: 20 residues processed: 168 average time/residue: 1.2942 time to fit residues: 235.4500 Evaluate side-chains 159 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 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 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 81 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 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 170 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN D 11 ASN D 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130307 restraints weight = 16010.287| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.74 r_work: 0.3612 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12052 Z= 0.108 Angle : 0.563 10.876 16352 Z= 0.272 Chirality : 0.043 0.138 1812 Planarity : 0.005 0.069 2096 Dihedral : 10.735 154.670 1684 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.53 % Allowed : 24.68 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1476 helix: 1.10 (0.22), residues: 600 sheet: 0.64 (0.31), residues: 284 loop : -0.42 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 355 HIS 0.003 0.001 HIS B 100 PHE 0.008 0.001 PHE A 278 TYR 0.012 0.001 TYR A 239 ARG 0.007 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 531) hydrogen bonds : angle 3.96646 ( 1416) covalent geometry : bond 0.00249 (12052) covalent geometry : angle 0.56282 (16352) *********************** 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 172 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4539 (mmp) cc_final: 0.2963 (mtm) REVERT: A 81 MET cc_start: 0.8324 (tpt) cc_final: 0.7983 (tpt) REVERT: A 190 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7373 (mttt) REVERT: A 275 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 313 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: A 327 LYS cc_start: 0.7422 (pttm) cc_final: 0.7211 (pptt) REVERT: A 359 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6530 (pm20) REVERT: A 363 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5769 (mp0) REVERT: A 369 VAL cc_start: 0.7644 (t) cc_final: 0.7355 (p) REVERT: B 46 MET cc_start: 0.2987 (mmm) cc_final: 0.2464 (tmm) REVERT: B 49 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7567 (mppt) REVERT: B 67 LYS cc_start: 0.8011 (mttm) cc_final: 0.7720 (mtmm) REVERT: B 90 TYR cc_start: 0.8395 (m-80) cc_final: 0.8018 (m-80) REVERT: B 116 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 147 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8592 (t) REVERT: B 290 LYS cc_start: 0.8204 (tttm) cc_final: 0.7940 (tptt) REVERT: B 327 LYS cc_start: 0.7910 (mttp) cc_final: 0.7696 (mttt) REVERT: C 46 MET cc_start: 0.4686 (mtt) cc_final: 0.4297 (mtt) REVERT: C 94 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7536 (mtm110) REVERT: C 313 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7842 (tp40) REVERT: C 368 ILE cc_start: 0.8101 (tt) cc_final: 0.7857 (tp) REVERT: D 82 GLU cc_start: 0.7513 (pp20) cc_final: 0.7289 (pt0) REVERT: D 92 GLU cc_start: 0.7259 (tp30) cc_final: 0.6905 (mm-30) REVERT: D 124 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6972 (pt0) REVERT: D 166 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6345 (pt0) REVERT: D 170 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7544 (mp) REVERT: D 324 MET cc_start: 0.6951 (mmp) cc_final: 0.6730 (mmt) REVERT: D 362 ASP cc_start: 0.6703 (t0) cc_final: 0.6212 (p0) outliers start: 32 outliers final: 21 residues processed: 164 average time/residue: 1.2882 time to fit residues: 228.3097 Evaluate side-chains 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 MET 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 271 CYS Chi-restraints excluded: chain B residue 319 LEU 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 50 ASP 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 170 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 243 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN D 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126209 restraints weight = 16081.523| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.80 r_work: 0.3552 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12052 Z= 0.213 Angle : 0.648 12.236 16352 Z= 0.322 Chirality : 0.047 0.146 1812 Planarity : 0.005 0.071 2096 Dihedral : 10.945 155.896 1684 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.01 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1476 helix: 0.85 (0.22), residues: 600 sheet: 0.61 (0.31), residues: 276 loop : -0.66 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 355 HIS 0.005 0.001 HIS B 100 PHE 0.011 0.002 PHE A 278 TYR 0.016 0.002 TYR A 239 ARG 0.007 0.001 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 531) hydrogen bonds : angle 4.10291 ( 1416) covalent geometry : bond 0.00501 (12052) covalent geometry : angle 0.64811 (16352) *********************** 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 176 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4595 (mmp) cc_final: 0.2901 (mtm) REVERT: A 81 MET cc_start: 0.8369 (tpt) cc_final: 0.8041 (tpt) REVERT: A 131 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7973 (ttp) REVERT: A 190 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7343 (mttt) REVERT: A 275 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7208 (mm-30) REVERT: A 313 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: A 324 MET cc_start: 0.7757 (mmp) cc_final: 0.7524 (mmm) REVERT: A 359 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6523 (pm20) REVERT: A 363 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.5743 (mp0) REVERT: B 46 MET cc_start: 0.3157 (mmm) cc_final: 0.2763 (tmm) REVERT: B 49 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7512 (mppt) REVERT: B 67 LYS cc_start: 0.8027 (mttm) cc_final: 0.7703 (mtmm) REVERT: B 90 TYR cc_start: 0.8499 (m-80) cc_final: 0.8147 (m-80) REVERT: B 116 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7392 (mt-10) REVERT: B 152 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7929 (ttm) REVERT: B 290 LYS cc_start: 0.8365 (tttm) cc_final: 0.8066 (tptt) REVERT: B 327 LYS cc_start: 0.7852 (mttp) cc_final: 0.7641 (mttt) REVERT: B 362 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6851 (t0) REVERT: C 46 MET cc_start: 0.4867 (mtt) cc_final: 0.4453 (mtt) REVERT: C 313 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7864 (tp40) REVERT: C 362 ASP cc_start: 0.7913 (t0) cc_final: 0.6984 (m-30) REVERT: D 82 GLU cc_start: 0.7590 (pp20) cc_final: 0.7286 (pt0) REVERT: D 92 GLU cc_start: 0.7278 (tp30) cc_final: 0.6877 (mm-30) REVERT: D 98 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: D 124 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7037 (pt0) REVERT: D 166 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6330 (pt0) REVERT: D 271 CYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8103 (p) REVERT: D 324 MET cc_start: 0.7002 (mmp) cc_final: 0.6784 (mmt) REVERT: D 362 ASP cc_start: 0.6750 (t0) cc_final: 0.6082 (p0) outliers start: 38 outliers final: 22 residues processed: 160 average time/residue: 1.3500 time to fit residues: 233.3333 Evaluate side-chains 166 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 131 MET 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 152 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 81 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 369 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 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 3 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN D 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127504 restraints weight = 15881.138| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.79 r_work: 0.3571 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12052 Z= 0.148 Angle : 0.609 12.323 16352 Z= 0.298 Chirality : 0.045 0.146 1812 Planarity : 0.005 0.072 2096 Dihedral : 10.792 161.821 1684 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.37 % Allowed : 25.95 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1476 helix: 0.88 (0.22), residues: 600 sheet: 0.60 (0.30), residues: 276 loop : -0.65 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 355 HIS 0.004 0.001 HIS B 100 PHE 0.011 0.001 PHE A 278 TYR 0.015 0.001 TYR A 239 ARG 0.006 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 531) hydrogen bonds : angle 4.07916 ( 1416) covalent geometry : bond 0.00347 (12052) covalent geometry : angle 0.60947 (16352) ********************** 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 165 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.269 Fit side-chains REVERT: A 43 MET cc_start: 0.4712 (mmp) cc_final: 0.3027 (mtm) REVERT: A 65 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7373 (p) REVERT: A 81 MET cc_start: 0.8333 (tpt) cc_final: 0.7992 (tpt) REVERT: A 116 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7137 (mp0) REVERT: A 190 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7286 (mttt) REVERT: A 275 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 313 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: A 359 GLN cc_start: 0.7291 (mm-40) cc_final: 0.6628 (pm20) REVERT: A 363 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5788 (mt-10) REVERT: B 46 MET cc_start: 0.3175 (mmm) cc_final: 0.2808 (tmm) REVERT: B 49 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7437 (mppt) REVERT: B 67 LYS cc_start: 0.8002 (mttm) cc_final: 0.7666 (mtmm) REVERT: B 90 TYR cc_start: 0.8486 (m-80) cc_final: 0.8139 (m-80) REVERT: B 116 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 152 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7896 (ttm) REVERT: B 290 LYS cc_start: 0.8331 (tttm) cc_final: 0.8015 (tptt) REVERT: B 327 LYS cc_start: 0.7845 (mttp) cc_final: 0.7625 (mttt) REVERT: B 362 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6843 (t0) REVERT: C 46 MET cc_start: 0.4884 (mtt) cc_final: 0.4469 (mtt) REVERT: C 124 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6781 (mt-10) REVERT: C 313 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7923 (tp40) REVERT: D 82 GLU cc_start: 0.7557 (pp20) cc_final: 0.7247 (pt0) REVERT: D 92 GLU cc_start: 0.7274 (tp30) cc_final: 0.6880 (mm-30) REVERT: D 98 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: D 124 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6982 (pt0) REVERT: D 166 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6287 (pt0) REVERT: D 170 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7522 (mp) REVERT: D 271 CYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8120 (p) REVERT: D 362 ASP cc_start: 0.6718 (t0) cc_final: 0.6036 (p0) outliers start: 30 outliers final: 20 residues processed: 157 average time/residue: 1.3139 time to fit residues: 222.7823 Evaluate side-chains 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 152 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 81 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 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 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 99 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.137664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126790 restraints weight = 15908.408| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.78 r_work: 0.3558 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12052 Z= 0.166 Angle : 0.631 12.312 16352 Z= 0.309 Chirality : 0.045 0.143 1812 Planarity : 0.005 0.071 2096 Dihedral : 10.762 168.770 1684 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.53 % Allowed : 25.79 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1476 helix: 0.80 (0.22), residues: 600 sheet: 0.61 (0.30), residues: 276 loop : -0.72 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 355 HIS 0.005 0.001 HIS B 100 PHE 0.009 0.001 PHE A 278 TYR 0.016 0.001 TYR A 239 ARG 0.007 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 531) hydrogen bonds : angle 4.11420 ( 1416) covalent geometry : bond 0.00388 (12052) covalent geometry : angle 0.63143 (16352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7908.22 seconds wall clock time: 135 minutes 31.85 seconds (8131.85 seconds total)