Starting phenix.real_space_refine on Fri Sep 11 22:23:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6djn_7937/09_2026/6djn_7937.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djn_7937/09_2026/6djn_7937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6djn_7937/09_2026/6djn_7937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djn_7937/09_2026/6djn_7937.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6djn_7937/09_2026/6djn_7937.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6djn_7937/09_2026/6djn_7937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6djn_7937/09_2026/6djn_7937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djn_7937/09_2026/6djn_7937.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.17, per 1000 atoms: 0.27 Number of scatterers: 11768 At special positions: 0 Unit cell: (100.32, 76.285, 165.11, 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 84 16.00 P 12 15.00 Mg 4 11.99 O 2280 8.00 N 1980 7.00 C 7408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 577.4 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 24 sheets defined 44.2% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.902A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.785A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.879A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.996A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.813A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.514A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.266A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.862A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.944A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.901A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.785A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.879A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.996A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.813A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.513A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.266A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.863A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.944A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 371' Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.901A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.837A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.785A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.879A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.995A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.813A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.514A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 351 through 355 removed outlier: 4.266A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.862A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.945A pdb=" N SER C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 371' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.901A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.785A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.880A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.996A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.814A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.513A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.266A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.863A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.945A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 371' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.557A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.534A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.185A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.556A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.535A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.185A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.557A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.535A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.185A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.557A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.534A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.184A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 450 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3420 1.33 - 1.45: 1833 1.45 - 1.57: 6607 1.57 - 1.68: 12 1.68 - 1.80: 148 Bond restraints: 12020 Sorted by residual: bond pdb=" O3 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.569 1.494 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3 PO4 D 803 " pdb=" P PO4 D 803 " ideal model delta sigma weight residual 1.569 1.496 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O2 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.567 1.496 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3 PO4 C 803 " pdb=" P PO4 C 803 " ideal model delta sigma weight residual 1.569 1.498 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.569 1.501 0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 12015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 15421 1.92 - 3.83: 775 3.83 - 5.75: 88 5.75 - 7.66: 24 7.66 - 9.58: 8 Bond angle restraints: 16316 Sorted by residual: angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 122.08 127.89 -5.81 1.47e+00 4.63e-01 1.56e+01 angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 122.08 127.85 -5.77 1.47e+00 4.63e-01 1.54e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 122.08 127.84 -5.76 1.47e+00 4.63e-01 1.54e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 122.08 127.84 -5.76 1.47e+00 4.63e-01 1.53e+01 angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.45 -5.95 1.70e+00 3.46e-01 1.23e+01 ... (remaining 16311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 7035 23.63 - 47.26: 177 47.26 - 70.89: 0 70.89 - 94.53: 4 94.53 - 118.16: 4 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" C5' ADP B 802 " pdb=" O5' ADP B 802 " pdb=" PA ADP B 802 " pdb=" O2A ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 58.16 -118.16 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 53.64 -113.63 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" C5' ADP C 802 " pdb=" O5' ADP C 802 " pdb=" PA ADP C 802 " pdb=" O2A ADP C 802 " ideal model delta sinusoidal sigma weight residual -60.00 48.00 -108.00 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1193 0.057 - 0.114: 530 0.114 - 0.171: 61 0.171 - 0.228: 12 0.228 - 0.285: 12 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 332 " 0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO A 333 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 332 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO D 333 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 332 " 0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO C 333 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.048 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 240 2.66 - 3.22: 10485 3.22 - 3.78: 18286 3.78 - 4.34: 26213 4.34 - 4.90: 43418 Nonbonded interactions: 98642 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.117 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.131 2.170 nonbonded pdb="MG MG A 801 " pdb=" O4 PO4 A 803 " model vdw 2.146 2.170 ... (remaining 98637 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: 0.04 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.011 0.075 12020 Z= 0.458 Angle : 0.950 9.577 16316 Z= 0.495 Chirality : 0.062 0.285 1808 Planarity : 0.008 0.087 2084 Dihedral : 10.671 118.157 4468 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.61 (0.16), residues: 1468 helix: -4.20 (0.10), residues: 600 sheet: -2.19 (0.29), residues: 244 loop : -1.95 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 147 TYR 0.015 0.002 TYR B 169 PHE 0.019 0.003 PHE A 31 TRP 0.036 0.005 TRP C 340 HIS 0.011 0.003 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.46 (12020) covalent geometry : angle 0.95015 / 0.49 (16316) hydrogen bonds : bond 0.28869 / 19.48 ( 442) hydrogen bonds : angle 10.03799 / 6.92 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.445 Fit side-chains REVERT: A 157 ASP cc_start: 0.7962 (t0) cc_final: 0.7663 (t0) REVERT: A 202 THR cc_start: 0.9037 (p) cc_final: 0.8632 (p) REVERT: A 205 GLU cc_start: 0.8141 (mp0) cc_final: 0.7772 (mp0) REVERT: B 51 ASP cc_start: 0.7591 (t70) cc_final: 0.7314 (p0) REVERT: B 82 MET cc_start: 0.9160 (tpt) cc_final: 0.8745 (tpt) REVERT: B 184 ASP cc_start: 0.8012 (m-30) cc_final: 0.7804 (m-30) REVERT: B 191 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7877 (tttm) REVERT: B 194 THR cc_start: 0.8884 (m) cc_final: 0.8616 (p) REVERT: B 314 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8049 (tt0) REVERT: C 92 ASN cc_start: 0.8420 (m110) cc_final: 0.8161 (m-40) REVERT: C 191 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7972 (tttm) REVERT: D 92 ASN cc_start: 0.8298 (m110) cc_final: 0.8061 (m-40) REVERT: D 191 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8121 (ttmm) REVERT: D 225 ASN cc_start: 0.8181 (m-40) cc_final: 0.7795 (m-40) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1310 time to fit residues: 43.8159 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 78 ASN A 137 GLN A 161 HIS A 162 ASN A 263 GLN B 12 ASN B 59 GLN B 78 ASN B 161 HIS B 162 ASN C 121 GLN C 161 HIS C 162 ASN C 246 GLN D 12 ASN D 161 HIS D 162 ASN D 173 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.080782 restraints weight = 19248.374| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.03 r_work: 0.2881 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12020 Z= 0.144 Angle : 0.625 6.689 16316 Z= 0.309 Chirality : 0.046 0.150 1808 Planarity : 0.006 0.065 2084 Dihedral : 7.811 97.676 1672 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.88 % Allowed : 7.64 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.19), residues: 1468 helix: -2.72 (0.16), residues: 624 sheet: -1.65 (0.29), residues: 236 loop : -1.07 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 95 TYR 0.010 0.001 TYR C 143 PHE 0.009 0.001 PHE D 262 TRP 0.020 0.002 TRP A 340 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (12020) covalent geometry : angle 0.62535 / 0.31 (16316) hydrogen bonds : bond 0.03255 / 2.14 ( 442) hydrogen bonds : angle 5.07897 / 3.49 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8536 (p0) cc_final: 0.8268 (p0) REVERT: A 191 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8528 (ttmt) REVERT: A 291 LYS cc_start: 0.9145 (tmtt) cc_final: 0.8824 (tptt) REVERT: A 305 MET cc_start: 0.9103 (mmm) cc_final: 0.8854 (mmt) REVERT: B 51 ASP cc_start: 0.8046 (t70) cc_final: 0.7716 (p0) REVERT: B 82 MET cc_start: 0.9401 (tpt) cc_final: 0.9008 (tpt) REVERT: B 191 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8287 (tttm) REVERT: B 227 MET cc_start: 0.8837 (tpt) cc_final: 0.8636 (tpt) REVERT: B 305 MET cc_start: 0.8853 (mmt) cc_final: 0.8515 (mmt) REVERT: C 225 ASN cc_start: 0.8729 (m-40) cc_final: 0.8384 (m110) REVERT: D 176 MET cc_start: 0.9195 (mmm) cc_final: 0.8919 (mmm) REVERT: D 283 MET cc_start: 0.8815 (mmm) cc_final: 0.8544 (mmt) REVERT: D 325 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7338 (ptp) outliers start: 11 outliers final: 6 residues processed: 144 average time/residue: 0.1052 time to fit residues: 22.2822 Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 GLN D 12 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080626 restraints weight = 19259.033| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.03 r_work: 0.2874 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12020 Z= 0.123 Angle : 0.570 6.754 16316 Z= 0.276 Chirality : 0.045 0.180 1808 Planarity : 0.005 0.058 2084 Dihedral : 7.012 89.204 1672 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.80 % Allowed : 9.08 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.20), residues: 1468 helix: -1.71 (0.19), residues: 640 sheet: -1.15 (0.31), residues: 236 loop : -0.60 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 206 TYR 0.009 0.001 TYR C 91 PHE 0.007 0.001 PHE A 127 TRP 0.015 0.002 TRP A 340 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (12020) covalent geometry : angle 0.57049 / 0.28 (16316) hydrogen bonds : bond 0.02838 / 1.89 ( 442) hydrogen bonds : angle 4.42526 / 3.03 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.331 Fit side-chains REVERT: A 12 ASN cc_start: 0.8566 (p0) cc_final: 0.8284 (p0) REVERT: A 305 MET cc_start: 0.9119 (mmm) cc_final: 0.8883 (mmt) REVERT: A 325 MET cc_start: 0.8084 (ppp) cc_final: 0.7326 (ppp) REVERT: B 276 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8174 (mt-10) REVERT: B 305 MET cc_start: 0.8788 (mmt) cc_final: 0.8491 (mmt) REVERT: B 325 MET cc_start: 0.7998 (ppp) cc_final: 0.7043 (ppp) REVERT: C 132 MET cc_start: 0.8866 (ppp) cc_final: 0.8587 (ptm) REVERT: C 355 MET cc_start: 0.8761 (mtm) cc_final: 0.8462 (mtm) REVERT: D 176 MET cc_start: 0.9289 (mmm) cc_final: 0.9001 (mmm) outliers start: 10 outliers final: 7 residues processed: 127 average time/residue: 0.0885 time to fit residues: 17.4330 Evaluate side-chains 102 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.078424 restraints weight = 19372.767| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.01 r_work: 0.2839 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12020 Z= 0.189 Angle : 0.609 7.108 16316 Z= 0.295 Chirality : 0.047 0.185 1808 Planarity : 0.005 0.055 2084 Dihedral : 7.229 93.525 1672 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.75 % Allowed : 8.92 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.21), residues: 1468 helix: -1.22 (0.20), residues: 632 sheet: -0.93 (0.31), residues: 236 loop : -0.30 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 206 TYR 0.008 0.001 TYR C 53 PHE 0.010 0.001 PHE D 262 TRP 0.015 0.002 TRP C 340 HIS 0.006 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (12020) covalent geometry : angle 0.60942 / 0.30 (16316) hydrogen bonds : bond 0.02977 / 1.98 ( 442) hydrogen bonds : angle 4.35123 / 2.97 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.521 Fit side-chains REVERT: A 12 ASN cc_start: 0.8597 (p0) cc_final: 0.8382 (p0) REVERT: A 291 LYS cc_start: 0.9239 (tmtt) cc_final: 0.8876 (tptt) REVERT: A 325 MET cc_start: 0.8264 (ppp) cc_final: 0.7513 (ppp) REVERT: B 276 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 325 MET cc_start: 0.8038 (ppp) cc_final: 0.7148 (ppp) REVERT: C 84 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8817 (mttt) REVERT: D 176 MET cc_start: 0.9292 (mmm) cc_final: 0.8969 (mmm) outliers start: 22 outliers final: 14 residues processed: 119 average time/residue: 0.0997 time to fit residues: 18.1155 Evaluate side-chains 109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 78 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 137 optimal weight: 0.0570 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 12 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.094779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080626 restraints weight = 19186.401| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.03 r_work: 0.2879 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12020 Z= 0.108 Angle : 0.552 6.503 16316 Z= 0.262 Chirality : 0.044 0.162 1808 Planarity : 0.004 0.052 2084 Dihedral : 6.578 83.474 1672 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.11 % Allowed : 9.39 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.22), residues: 1468 helix: -0.75 (0.21), residues: 632 sheet: -0.82 (0.31), residues: 256 loop : -0.21 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 335 TYR 0.007 0.001 TYR C 91 PHE 0.006 0.001 PHE D 31 TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (12020) covalent geometry : angle 0.55185 / 0.26 (16316) hydrogen bonds : bond 0.02424 / 1.62 ( 442) hydrogen bonds : angle 4.13520 / 2.80 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.517 Fit side-chains REVERT: A 157 ASP cc_start: 0.8204 (t70) cc_final: 0.7882 (m-30) REVERT: A 325 MET cc_start: 0.8158 (ppp) cc_final: 0.7644 (ppp) REVERT: B 227 MET cc_start: 0.8856 (tpt) cc_final: 0.8636 (mmt) REVERT: B 276 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8228 (mt-10) REVERT: B 325 MET cc_start: 0.7996 (ppp) cc_final: 0.7097 (ppp) REVERT: C 84 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8790 (mtmt) REVERT: D 176 MET cc_start: 0.9308 (mmm) cc_final: 0.8994 (mmm) outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 0.0895 time to fit residues: 16.9709 Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.080055 restraints weight = 19306.965| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.02 r_work: 0.2865 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12020 Z= 0.133 Angle : 0.567 6.609 16316 Z= 0.271 Chirality : 0.045 0.167 1808 Planarity : 0.004 0.051 2084 Dihedral : 6.595 84.014 1672 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.27 % Allowed : 10.03 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.22), residues: 1468 helix: -0.36 (0.22), residues: 612 sheet: -0.58 (0.32), residues: 236 loop : -0.07 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 335 TYR 0.006 0.001 TYR C 91 PHE 0.006 0.001 PHE A 127 TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (12020) covalent geometry : angle 0.56665 / 0.27 (16316) hydrogen bonds : bond 0.02537 / 1.69 ( 442) hydrogen bonds : angle 4.10710 / 2.78 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.472 Fit side-chains REVERT: A 12 ASN cc_start: 0.8439 (p0) cc_final: 0.8202 (p0) REVERT: A 157 ASP cc_start: 0.8352 (t70) cc_final: 0.7927 (m-30) REVERT: A 325 MET cc_start: 0.8256 (ppp) cc_final: 0.7767 (ppp) REVERT: B 276 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8255 (mt-10) REVERT: B 325 MET cc_start: 0.8171 (ppp) cc_final: 0.7262 (ppp) REVERT: C 84 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8766 (mtmt) outliers start: 16 outliers final: 13 residues processed: 123 average time/residue: 0.0873 time to fit residues: 16.8945 Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.079276 restraints weight = 19181.269| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.96 r_work: 0.2851 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12020 Z= 0.172 Angle : 0.591 6.929 16316 Z= 0.283 Chirality : 0.046 0.175 1808 Planarity : 0.004 0.051 2084 Dihedral : 6.838 87.248 1672 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.59 % Allowed : 10.11 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.22), residues: 1468 helix: -0.32 (0.22), residues: 612 sheet: -0.55 (0.33), residues: 236 loop : -0.03 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 335 TYR 0.008 0.001 TYR B 69 PHE 0.007 0.001 PHE A 127 TRP 0.014 0.002 TRP D 79 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (12020) covalent geometry : angle 0.59061 / 0.28 (16316) hydrogen bonds : bond 0.02711 / 1.81 ( 442) hydrogen bonds : angle 4.17241 / 2.83 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.546 Fit side-chains REVERT: A 12 ASN cc_start: 0.8459 (p0) cc_final: 0.8137 (p0) REVERT: A 157 ASP cc_start: 0.8305 (t70) cc_final: 0.7834 (m-30) REVERT: A 325 MET cc_start: 0.8311 (ppp) cc_final: 0.7814 (ppp) REVERT: B 276 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 325 MET cc_start: 0.8242 (ppp) cc_final: 0.7326 (ppp) REVERT: C 84 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8829 (mtmt) outliers start: 20 outliers final: 15 residues processed: 127 average time/residue: 0.0895 time to fit residues: 17.7089 Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 121 GLN B 115 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.081730 restraints weight = 19066.061| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.92 r_work: 0.2891 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12020 Z= 0.111 Angle : 0.558 7.137 16316 Z= 0.264 Chirality : 0.044 0.157 1808 Planarity : 0.004 0.050 2084 Dihedral : 6.363 76.398 1672 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.35 % Allowed : 10.59 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1468 helix: -0.25 (0.22), residues: 632 sheet: -0.71 (0.32), residues: 260 loop : 0.16 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 335 TYR 0.007 0.001 TYR C 91 PHE 0.006 0.001 PHE A 127 TRP 0.010 0.001 TRP C 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12020) covalent geometry : angle 0.55821 / 0.26 (16316) hydrogen bonds : bond 0.02361 / 1.58 ( 442) hydrogen bonds : angle 4.06451 / 2.75 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.475 Fit side-chains REVERT: A 12 ASN cc_start: 0.8449 (p0) cc_final: 0.8112 (p0) REVERT: A 157 ASP cc_start: 0.8194 (t70) cc_final: 0.7722 (m-30) REVERT: A 325 MET cc_start: 0.8220 (ppp) cc_final: 0.7795 (ppp) REVERT: B 325 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7365 (ppp) REVERT: C 84 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8767 (mtmt) REVERT: D 269 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8630 (mtp) outliers start: 17 outliers final: 12 residues processed: 124 average time/residue: 0.0871 time to fit residues: 17.2601 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 121 GLN A 360 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080253 restraints weight = 18803.034| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.03 r_work: 0.2873 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12020 Z= 0.170 Angle : 0.596 6.919 16316 Z= 0.285 Chirality : 0.046 0.173 1808 Planarity : 0.004 0.049 2084 Dihedral : 6.754 84.710 1672 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.67 % Allowed : 10.75 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1468 helix: -0.15 (0.22), residues: 612 sheet: -0.46 (0.33), residues: 236 loop : 0.10 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 335 TYR 0.008 0.001 TYR B 69 PHE 0.007 0.001 PHE A 127 TRP 0.016 0.002 TRP D 79 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (12020) covalent geometry : angle 0.59557 / 0.29 (16316) hydrogen bonds : bond 0.02677 / 1.79 ( 442) hydrogen bonds : angle 4.15282 / 2.82 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.504 Fit side-chains REVERT: A 12 ASN cc_start: 0.8476 (p0) cc_final: 0.8120 (p0) REVERT: A 103 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9147 (p) REVERT: A 157 ASP cc_start: 0.8238 (t70) cc_final: 0.7804 (m-30) REVERT: A 325 MET cc_start: 0.8229 (ppp) cc_final: 0.7752 (ppp) REVERT: B 325 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7320 (ppp) REVERT: C 84 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8825 (mtmt) REVERT: C 328 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8639 (tptp) REVERT: C 355 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8698 (ptp) outliers start: 21 outliers final: 12 residues processed: 121 average time/residue: 0.0893 time to fit residues: 16.9484 Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 137 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080352 restraints weight = 19214.865| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.00 r_work: 0.2872 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12020 Z= 0.125 Angle : 0.568 6.446 16316 Z= 0.271 Chirality : 0.045 0.160 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.435 77.758 1672 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.43 % Allowed : 11.23 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1468 helix: -0.18 (0.22), residues: 632 sheet: -0.68 (0.32), residues: 260 loop : 0.25 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 335 TYR 0.007 0.001 TYR C 294 PHE 0.007 0.001 PHE A 127 TRP 0.013 0.002 TRP D 79 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12020) covalent geometry : angle 0.56806 / 0.27 (16316) hydrogen bonds : bond 0.02450 / 1.64 ( 442) hydrogen bonds : angle 4.08991 / 2.77 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.543 Fit side-chains REVERT: A 12 ASN cc_start: 0.8495 (p0) cc_final: 0.8121 (p0) REVERT: A 103 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9178 (p) REVERT: A 157 ASP cc_start: 0.8214 (t70) cc_final: 0.7726 (m-30) REVERT: A 325 MET cc_start: 0.8250 (ppp) cc_final: 0.7798 (ppp) REVERT: B 276 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: B 325 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7370 (ppp) REVERT: C 84 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8787 (mtmt) REVERT: C 328 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8559 (tptp) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.0782 time to fit residues: 15.1244 Evaluate side-chains 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.0030 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.080801 restraints weight = 19133.463| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.04 r_work: 0.2881 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12020 Z= 0.149 Angle : 0.585 6.709 16316 Z= 0.280 Chirality : 0.046 0.165 1808 Planarity : 0.004 0.032 2084 Dihedral : 6.577 80.854 1672 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.43 % Allowed : 11.23 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1468 helix: -0.00 (0.22), residues: 608 sheet: -0.57 (0.32), residues: 256 loop : 0.26 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 335 TYR 0.008 0.001 TYR C 294 PHE 0.007 0.001 PHE A 127 TRP 0.016 0.002 TRP D 79 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12020) covalent geometry : angle 0.58509 / 0.28 (16316) hydrogen bonds : bond 0.02569 / 1.71 ( 442) hydrogen bonds : angle 4.10870 / 2.78 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.31 seconds wall clock time: 43 minutes 15.56 seconds (2595.56 seconds total)