Starting phenix.real_space_refine on Wed Mar 4 19:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tu4_10587/03_2026/6tu4_10587.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tu4_10587/03_2026/6tu4_10587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tu4_10587/03_2026/6tu4_10587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tu4_10587/03_2026/6tu4_10587.map" model { file = "/net/cci-nas-00/data/ceres_data/6tu4_10587/03_2026/6tu4_10587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tu4_10587/03_2026/6tu4_10587.cif" } resolution = 2.6 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= 0.010 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: 7 Type Number sf(0) Gaussians Br 5 7.06 5 P 10 5.49 5 Mg 5 5.21 5 S 90 5.16 5 C 9935 2.51 5 N 2570 2.21 5 O 3075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15690 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3035 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2824 Chain: "B" Number of atoms: 3039 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2819 Chain: "C" Number of atoms: 3035 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2824 Chain: "D" Number of atoms: 3039 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2819 Chain: "F" Number of atoms: 3027 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2834 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Time building chain proxies: 6.06, per 1000 atoms: 0.39 Number of scatterers: 15690 At special positions: 0 Unit cell: (99.19, 83.93, 198.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 5 34.99 S 90 16.00 P 10 15.00 Mg 5 11.99 O 3075 8.00 N 2570 7.00 C 9935 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: 1.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3642 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 30 sheets defined 48.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.533A pdb=" N GLN A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.149A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 173 through 176 removed outlier: 3.648A pdb=" N ILE A 176 " --> pdb=" O PRO A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.585A pdb=" N GLU A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.711A pdb=" N LYS A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.596A pdb=" N ARG A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 349 through 354 removed outlier: 6.326A pdb=" N THR A 352 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 354 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 367 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.797A pdb=" N VAL A 371 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.596A pdb=" N GLN B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.642A pdb=" N HIS B 102 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 removed outlier: 4.049A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.519A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 removed outlier: 3.738A pdb=" N ILE B 176 " --> pdb=" O PRO B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.660A pdb=" N GLU B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.774A pdb=" N GLU B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.517A pdb=" N THR B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.638A pdb=" N ARG B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 349 through 356 removed outlier: 6.350A pdb=" N THR B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 354 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 113 through 127 removed outlier: 4.247A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 147 Processing helix chain 'C' and resid 173 through 176 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 203 through 218 removed outlier: 3.732A pdb=" N GLU C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.636A pdb=" N GLU C 232 " --> pdb=" O MET C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.625A pdb=" N GLY C 296 " --> pdb=" O LYS C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.644A pdb=" N ARG C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 352 through 356 removed outlier: 4.216A pdb=" N GLN C 355 " --> pdb=" O THR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.568A pdb=" N GLN D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 113 through 127 removed outlier: 4.124A pdb=" N ARG D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 147 Processing helix chain 'D' and resid 173 through 176 removed outlier: 3.588A pdb=" N ILE D 176 " --> pdb=" O PRO D 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 234 removed outlier: 3.621A pdb=" N LYS D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.708A pdb=" N GLY D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 removed outlier: 4.279A pdb=" N TYR D 307 " --> pdb=" O THR D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.599A pdb=" N ARG D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 349 through 354 removed outlier: 6.353A pdb=" N THR D 352 " --> pdb=" O SER D 349 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 354 " --> pdb=" O SER D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 367 Processing helix chain 'D' and resid 370 through 375 Processing helix chain 'F' and resid 56 through 62 removed outlier: 3.574A pdb=" N GLN F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 113 through 127 removed outlier: 4.227A pdb=" N ARG F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'F' and resid 173 through 176 Processing helix chain 'F' and resid 182 through 194 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 203 through 218 removed outlier: 3.542A pdb=" N ILE F 209 " --> pdb=" O ALA F 205 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 231 removed outlier: 3.796A pdb=" N LYS F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 234 No H-bonds generated for 'chain 'F' and resid 232 through 234' Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 264 through 269 Processing helix chain 'F' and resid 274 through 285 Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 309 through 322 removed outlier: 3.607A pdb=" N ARG F 313 " --> pdb=" O GLY F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 360 through 367 Processing helix chain 'F' and resid 370 through 375 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.680A pdb=" N LEU A 9 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR A 107 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL A 11 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 171 removed outlier: 6.571A pdb=" N ILE A 298 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.677A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N VAL B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.517A pdb=" N ILE B 298 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.726A pdb=" N LEU C 9 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR C 107 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N VAL C 11 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 73 Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 171 removed outlier: 6.242A pdb=" N ILE C 298 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 242 Processing sheet with id=AC1, first strand: chain 'D' and resid 30 through 33 removed outlier: 6.646A pdb=" N LEU D 9 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR D 107 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL D 11 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AC3, first strand: chain 'D' and resid 72 through 73 Processing sheet with id=AC4, first strand: chain 'D' and resid 170 through 171 Processing sheet with id=AC5, first strand: chain 'D' and resid 170 through 171 removed outlier: 6.198A pdb=" N ILE D 298 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 239 through 242 Processing sheet with id=AC7, first strand: chain 'F' and resid 30 through 33 removed outlier: 6.764A pdb=" N LEU F 9 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR F 107 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL F 11 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AC9, first strand: chain 'F' and resid 72 through 73 Processing sheet with id=AD1, first strand: chain 'F' and resid 170 through 171 Processing sheet with id=AD2, first strand: chain 'F' and resid 170 through 171 removed outlier: 6.511A pdb=" N ILE F 298 " --> pdb=" O VAL F 331 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 239 through 242 700 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4955 1.35 - 1.49: 4054 1.49 - 1.62: 6831 1.62 - 1.76: 0 1.76 - 1.90: 165 Bond restraints: 16005 Sorted by residual: bond pdb=" C9 9UE A 402 " pdb=" N1 9UE A 402 " ideal model delta sigma weight residual 1.353 1.402 -0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" C9 9UE D 402 " pdb=" N1 9UE D 402 " ideal model delta sigma weight residual 1.353 1.402 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C9 9UE C 402 " pdb=" N1 9UE C 402 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C9 9UE B 402 " pdb=" N1 9UE B 402 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C9 9UE F 402 " pdb=" N1 9UE F 402 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 16000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 21612 2.76 - 5.51: 231 5.51 - 8.27: 41 8.27 - 11.02: 7 11.02 - 13.78: 7 Bond angle restraints: 21898 Sorted by residual: angle pdb=" C6 9UE C 402 " pdb=" N 9UE C 402 " pdb=" C7 9UE C 402 " ideal model delta sigma weight residual 128.90 115.12 13.78 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C6 9UE B 402 " pdb=" N 9UE B 402 " pdb=" C7 9UE B 402 " ideal model delta sigma weight residual 128.90 115.18 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" C6 9UE D 402 " pdb=" N 9UE D 402 " pdb=" C7 9UE D 402 " ideal model delta sigma weight residual 128.90 115.61 13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C20 9UE B 402 " pdb=" C8 9UE B 402 " pdb=" C7 9UE B 402 " ideal model delta sigma weight residual 118.25 105.83 12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C20 9UE D 402 " pdb=" C8 9UE D 402 " pdb=" C7 9UE D 402 " ideal model delta sigma weight residual 118.25 106.35 11.90 3.00e+00 1.11e-01 1.57e+01 ... (remaining 21893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9657 35.97 - 71.94: 166 71.94 - 107.91: 56 107.91 - 143.89: 70 143.89 - 179.86: 35 Dihedral angle restraints: 9984 sinusoidal: 4204 harmonic: 5780 Sorted by residual: dihedral pdb=" O1B ADP D 403 " pdb=" O3A ADP D 403 " pdb=" PB ADP D 403 " pdb=" PA ADP D 403 " ideal model delta sinusoidal sigma weight residual 300.00 129.09 170.90 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PB ADP F 403 " pdb=" PA ADP F 403 " ideal model delta sinusoidal sigma weight residual -60.00 104.19 -164.19 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O1B ADP B 403 " pdb=" O3A ADP B 403 " pdb=" PB ADP B 403 " pdb=" PA ADP B 403 " ideal model delta sinusoidal sigma weight residual 300.00 137.55 162.45 1 2.00e+01 2.50e-03 4.69e+01 ... (remaining 9981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2361 0.108 - 0.216: 71 0.216 - 0.325: 0 0.325 - 0.433: 11 0.433 - 0.541: 5 Chirality restraints: 2448 Sorted by residual: chirality pdb=" C8 9UE B 402 " pdb=" C20 9UE B 402 " pdb=" C7 9UE B 402 " pdb=" N1 9UE B 402 " both_signs ideal model delta sigma weight residual False 2.15 2.69 -0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" C6 9UE A 402 " pdb=" N 9UE A 402 " pdb=" C29 9UE A 402 " pdb=" C5 9UE A 402 " both_signs ideal model delta sigma weight residual False -1.97 -2.51 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" C8 9UE C 402 " pdb=" C20 9UE C 402 " pdb=" C7 9UE C 402 " pdb=" N1 9UE C 402 " both_signs ideal model delta sigma weight residual False 2.15 2.67 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 2445 not shown) Planarity restraints: 2805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 9UE F 402 " 0.021 2.00e-02 2.50e+03 1.71e-02 3.66e+00 pdb=" C6 9UE F 402 " -0.020 2.00e-02 2.50e+03 pdb=" C7 9UE F 402 " 0.017 2.00e-02 2.50e+03 pdb=" C8 9UE F 402 " -0.018 2.00e-02 2.50e+03 pdb=" O2 9UE F 402 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 9UE D 402 " -0.016 2.00e-02 2.50e+03 1.55e-02 3.02e+00 pdb=" C6 9UE D 402 " 0.017 2.00e-02 2.50e+03 pdb=" C7 9UE D 402 " -0.019 2.00e-02 2.50e+03 pdb=" C8 9UE D 402 " 0.017 2.00e-02 2.50e+03 pdb=" O2 9UE D 402 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 322 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO F 323 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO F 323 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 323 " -0.024 5.00e-02 4.00e+02 ... (remaining 2802 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 127 2.59 - 3.16: 11988 3.16 - 3.74: 22780 3.74 - 4.32: 35675 4.32 - 4.90: 58447 Nonbonded interactions: 129017 Sorted by model distance: nonbonded pdb="MG MG A 401 " pdb=" O HOH A 513 " model vdw 2.007 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 514 " model vdw 2.018 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 515 " model vdw 2.026 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 520 " model vdw 2.035 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 514 " model vdw 2.035 2.170 ... (remaining 129012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) selection = (chain 'B' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) selection = (chain 'C' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) selection = (chain 'D' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) selection = (chain 'F' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) } 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=0.50 max=1.00 mean=0.96 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: 3.580 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.500 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.004 0.049 16005 Z= 0.191 Angle : 0.778 13.781 21898 Z= 0.389 Chirality : 0.058 0.541 2448 Planarity : 0.005 0.043 2805 Dihedral : 23.328 179.856 6342 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.10 % Allowed : 4.44 % Favored : 92.46 % 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: -1.72 (0.17), residues: 1962 helix: -1.76 (0.15), residues: 805 sheet: -0.09 (0.23), residues: 352 loop : -0.71 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 336 TYR 0.010 0.001 TYR A 144 PHE 0.009 0.001 PHE A 256 TRP 0.014 0.002 TRP D 341 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00395 (16005) covalent geometry : angle 0.77832 (21898) hydrogen bonds : bond 0.21465 ( 690) hydrogen bonds : angle 7.02079 ( 1752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8527 (tt0) cc_final: 0.8303 (tt0) REVERT: A 177 MET cc_start: 0.9222 (mmm) cc_final: 0.9017 (mmt) REVERT: A 287 ASP cc_start: 0.7444 (m-30) cc_final: 0.7223 (m-30) REVERT: A 316 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.7399 (ttp-170) REVERT: A 326 MET cc_start: 0.8839 (mmp) cc_final: 0.8141 (mmp) REVERT: B 122 GLN cc_start: 0.8484 (tt0) cc_final: 0.8270 (tt0) REVERT: C 83 MET cc_start: 0.8764 (tpt) cc_final: 0.8438 (tpt) REVERT: C 122 GLN cc_start: 0.8343 (tt0) cc_final: 0.8100 (tt0) REVERT: C 355 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7643 (tp40) REVERT: D 7 GLN cc_start: 0.8288 (mt0) cc_final: 0.8041 (mt0) REVERT: D 45 MET cc_start: 0.7913 (mmm) cc_final: 0.6772 (mmt) REVERT: D 60 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8743 (tp40) REVERT: D 65 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8389 (pp) REVERT: D 124 MET cc_start: 0.8956 (mmt) cc_final: 0.8110 (mmt) REVERT: D 365 GLU cc_start: 0.7583 (tt0) cc_final: 0.7344 (tt0) REVERT: F 83 MET cc_start: 0.8602 (tpt) cc_final: 0.8376 (tpt) REVERT: F 94 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8109 (mm-30) REVERT: F 228 MET cc_start: 0.8814 (mmm) cc_final: 0.8499 (mmm) REVERT: F 233 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: F 316 ARG cc_start: 0.7970 (ttt-90) cc_final: 0.7725 (ttp-170) REVERT: F 326 MET cc_start: 0.8767 (mmp) cc_final: 0.8415 (mmp) outliers start: 22 outliers final: 12 residues processed: 204 average time/residue: 0.7917 time to fit residues: 173.5533 Evaluate side-chains 166 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN B 13 ASN B 281 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 281 ASN C 297 ASN D 102 HIS B D 223 ASN B D 281 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN F 281 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.106924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.082150 restraints weight = 105836.455| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 4.10 r_work: 0.2548 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16005 Z= 0.109 Angle : 0.642 7.643 21898 Z= 0.304 Chirality : 0.048 0.358 2448 Planarity : 0.005 0.039 2805 Dihedral : 29.305 177.463 2556 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.27 % Allowed : 8.12 % Favored : 88.60 % 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: -0.28 (0.18), residues: 1962 helix: -0.32 (0.18), residues: 795 sheet: 0.35 (0.25), residues: 382 loop : -0.08 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 257 TYR 0.011 0.001 TYR A 144 PHE 0.008 0.001 PHE A 256 TRP 0.010 0.002 TRP D 341 HIS 0.003 0.001 HIS F 162 Details of bonding type rmsd covalent geometry : bond 0.00236 (16005) covalent geometry : angle 0.64222 (21898) hydrogen bonds : bond 0.04209 ( 690) hydrogen bonds : angle 4.90893 ( 1752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7830 (tp30) REVERT: A 122 GLN cc_start: 0.8974 (tt0) cc_final: 0.8756 (tt0) REVERT: A 177 MET cc_start: 0.9188 (mmm) cc_final: 0.8969 (mmt) REVERT: A 316 ARG cc_start: 0.8295 (ttt-90) cc_final: 0.7965 (ttp-170) REVERT: A 324 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 326 MET cc_start: 0.8883 (mmp) cc_final: 0.8186 (mmp) REVERT: B 51 LYS cc_start: 0.8415 (mttt) cc_final: 0.8141 (mttm) REVERT: C 50 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7422 (tm-30) REVERT: C 73 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: C 83 MET cc_start: 0.9149 (tpt) cc_final: 0.8791 (tpt) REVERT: C 122 GLN cc_start: 0.8792 (tt0) cc_final: 0.8576 (tt0) REVERT: D 7 GLN cc_start: 0.8463 (mt0) cc_final: 0.8226 (mt0) REVERT: D 60 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8914 (tp40) REVERT: D 124 MET cc_start: 0.9211 (mmt) cc_final: 0.8521 (mmt) REVERT: F 73 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7997 (tp30) REVERT: F 228 MET cc_start: 0.8966 (mmm) cc_final: 0.8683 (mmm) REVERT: F 233 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: F 316 ARG cc_start: 0.8470 (ttt-90) cc_final: 0.8261 (ttp-170) REVERT: F 326 MET cc_start: 0.8857 (mmp) cc_final: 0.8589 (mmp) REVERT: F 361 GLU cc_start: 0.7946 (mp0) cc_final: 0.7737 (mp0) outliers start: 24 outliers final: 12 residues processed: 181 average time/residue: 0.7672 time to fit residues: 149.6414 Evaluate side-chains 168 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 167 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS A C 253 ASN C 354 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.077565 restraints weight = 107454.475| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.83 r_work: 0.2466 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16005 Z= 0.200 Angle : 0.755 9.216 21898 Z= 0.363 Chirality : 0.056 0.537 2448 Planarity : 0.006 0.043 2805 Dihedral : 29.209 179.885 2549 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.74 % Allowed : 8.94 % Favored : 87.32 % 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: -0.16 (0.18), residues: 1962 helix: -0.26 (0.18), residues: 830 sheet: 0.51 (0.25), residues: 387 loop : -0.01 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 184 TYR 0.011 0.002 TYR F 144 PHE 0.010 0.002 PHE A 256 TRP 0.017 0.003 TRP D 341 HIS 0.005 0.001 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00484 (16005) covalent geometry : angle 0.75500 (21898) hydrogen bonds : bond 0.05950 ( 690) hydrogen bonds : angle 4.83389 ( 1752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7138 (tm-30) REVERT: A 73 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: A 177 MET cc_start: 0.9236 (mmm) cc_final: 0.9014 (mmt) REVERT: A 316 ARG cc_start: 0.8353 (ttt-90) cc_final: 0.8045 (ttp-170) REVERT: A 324 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8415 (p) REVERT: A 326 MET cc_start: 0.8909 (mmp) cc_final: 0.8284 (mmp) REVERT: B 51 LYS cc_start: 0.8427 (mttt) cc_final: 0.8158 (mttm) REVERT: B 73 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7966 (tp30) REVERT: B 328 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.9009 (mp) REVERT: C 50 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7305 (tm-30) REVERT: C 73 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: C 83 MET cc_start: 0.9162 (tpt) cc_final: 0.8852 (tpt) REVERT: C 324 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8546 (p) REVERT: D 7 GLN cc_start: 0.8444 (mt0) cc_final: 0.8221 (mt0) REVERT: D 60 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8842 (tp40) REVERT: D 65 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8313 (pp) REVERT: D 73 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: D 124 MET cc_start: 0.9247 (mmt) cc_final: 0.8604 (mmt) REVERT: F 73 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: F 94 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8491 (mm-30) REVERT: F 233 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: F 316 ARG cc_start: 0.8491 (ttt-90) cc_final: 0.8270 (ttp-170) REVERT: F 326 MET cc_start: 0.8923 (mmp) cc_final: 0.8611 (mmp) REVERT: F 361 GLU cc_start: 0.7965 (mp0) cc_final: 0.7760 (mp0) outliers start: 31 outliers final: 10 residues processed: 176 average time/residue: 0.7850 time to fit residues: 149.0166 Evaluate side-chains 168 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 111 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 158 optimal weight: 0.0980 chunk 173 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN F 102 HIS A Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.081605 restraints weight = 113819.156| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.94 r_work: 0.2532 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16005 Z= 0.115 Angle : 0.628 7.366 21898 Z= 0.298 Chirality : 0.049 0.447 2448 Planarity : 0.004 0.042 2805 Dihedral : 27.423 179.912 2549 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.33 % Allowed : 9.64 % Favored : 87.03 % 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: 0.48 (0.18), residues: 1962 helix: 0.36 (0.19), residues: 800 sheet: 0.70 (0.25), residues: 382 loop : 0.32 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 178 TYR 0.009 0.001 TYR A 144 PHE 0.009 0.001 PHE A 256 TRP 0.011 0.002 TRP D 341 HIS 0.004 0.001 HIS F 162 Details of bonding type rmsd covalent geometry : bond 0.00258 (16005) covalent geometry : angle 0.62824 (21898) hydrogen bonds : bond 0.03989 ( 690) hydrogen bonds : angle 4.59290 ( 1752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7201 (tm-30) REVERT: A 73 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: A 177 MET cc_start: 0.9202 (mmm) cc_final: 0.8977 (mmt) REVERT: A 306 MET cc_start: 0.8913 (mmt) cc_final: 0.8568 (mmt) REVERT: A 308 GLU cc_start: 0.8763 (tp30) cc_final: 0.8562 (tp30) REVERT: A 316 ARG cc_start: 0.8271 (ttt-90) cc_final: 0.7952 (ttp-170) REVERT: A 324 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 326 MET cc_start: 0.8891 (mmp) cc_final: 0.8267 (mmp) REVERT: B 51 LYS cc_start: 0.8397 (mttt) cc_final: 0.8109 (mttm) REVERT: B 73 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: C 65 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8370 (pp) REVERT: C 73 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7685 (tp30) REVERT: C 83 MET cc_start: 0.9147 (tpt) cc_final: 0.8803 (tpt) REVERT: C 324 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8471 (p) REVERT: D 7 GLN cc_start: 0.8426 (mt0) cc_final: 0.8212 (mt0) REVERT: D 50 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6949 (tm-30) REVERT: D 60 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8834 (tp40) REVERT: D 65 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8234 (pp) REVERT: D 124 MET cc_start: 0.9184 (mmt) cc_final: 0.8541 (mmt) REVERT: F 73 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7961 (tp30) REVERT: F 94 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8462 (mm-30) REVERT: F 233 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: F 326 MET cc_start: 0.8872 (mmp) cc_final: 0.8566 (mmp) REVERT: F 361 GLU cc_start: 0.7933 (mp0) cc_final: 0.7722 (mp0) outliers start: 24 outliers final: 9 residues processed: 172 average time/residue: 0.7297 time to fit residues: 135.7412 Evaluate side-chains 166 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 113 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 354 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.082036 restraints weight = 116979.665| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.77 r_work: 0.2579 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16005 Z= 0.134 Angle : 0.652 7.235 21898 Z= 0.311 Chirality : 0.050 0.344 2448 Planarity : 0.004 0.038 2805 Dihedral : 26.720 174.771 2547 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.21 % Allowed : 10.11 % Favored : 86.67 % 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 (0.19), residues: 1962 helix: 0.50 (0.19), residues: 795 sheet: 0.56 (0.24), residues: 422 loop : 0.38 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 178 TYR 0.011 0.001 TYR A 144 PHE 0.010 0.001 PHE A 256 TRP 0.014 0.002 TRP D 341 HIS 0.004 0.001 HIS F 162 Details of bonding type rmsd covalent geometry : bond 0.00309 (16005) covalent geometry : angle 0.65193 (21898) hydrogen bonds : bond 0.04581 ( 690) hydrogen bonds : angle 4.57048 ( 1752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 73 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: A 177 MET cc_start: 0.9240 (mmm) cc_final: 0.9019 (mmt) REVERT: A 316 ARG cc_start: 0.8320 (ttt-90) cc_final: 0.8017 (ttp-170) REVERT: A 324 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8340 (p) REVERT: A 326 MET cc_start: 0.8942 (mmp) cc_final: 0.8246 (mmp) REVERT: B 51 LYS cc_start: 0.8361 (mttt) cc_final: 0.8107 (mttm) REVERT: B 73 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: B 328 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.9006 (mp) REVERT: C 65 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8423 (pp) REVERT: C 73 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: C 83 MET cc_start: 0.9168 (tpt) cc_final: 0.8833 (tpt) REVERT: C 324 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8479 (p) REVERT: D 7 GLN cc_start: 0.8455 (mt0) cc_final: 0.8237 (mt0) REVERT: D 50 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6919 (tm-30) REVERT: D 60 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8811 (tp40) REVERT: D 65 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8288 (pp) REVERT: D 124 MET cc_start: 0.9175 (mmt) cc_final: 0.8451 (mmt) REVERT: F 73 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: F 94 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8474 (mm-30) REVERT: F 233 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7494 (mt0) outliers start: 21 outliers final: 9 residues processed: 168 average time/residue: 0.7217 time to fit residues: 131.4029 Evaluate side-chains 170 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** F 297 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 = 0.3127 r_free = 0.3127 target = 0.104675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.081480 restraints weight = 122185.163| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.76 r_work: 0.2537 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16005 Z= 0.158 Angle : 0.686 7.414 21898 Z= 0.330 Chirality : 0.052 0.382 2448 Planarity : 0.005 0.038 2805 Dihedral : 26.725 175.227 2545 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.57 % Allowed : 9.94 % Favored : 86.50 % 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 (0.19), residues: 1962 helix: 0.29 (0.18), residues: 825 sheet: 0.72 (0.25), residues: 387 loop : 0.33 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 178 TYR 0.010 0.001 TYR F 144 PHE 0.010 0.002 PHE A 256 TRP 0.015 0.003 TRP D 341 HIS 0.004 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00374 (16005) covalent geometry : angle 0.68585 (21898) hydrogen bonds : bond 0.05012 ( 690) hydrogen bonds : angle 4.62272 ( 1752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 73 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: A 177 MET cc_start: 0.9248 (mmm) cc_final: 0.9014 (mmt) REVERT: A 316 ARG cc_start: 0.8295 (ttt-90) cc_final: 0.7964 (ttp-170) REVERT: A 324 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8366 (p) REVERT: A 326 MET cc_start: 0.8945 (mmp) cc_final: 0.8262 (mmp) REVERT: B 51 LYS cc_start: 0.8384 (mttt) cc_final: 0.8129 (mttm) REVERT: B 73 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: B 328 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8992 (mp) REVERT: C 65 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8431 (pp) REVERT: C 73 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: C 83 MET cc_start: 0.9178 (tpt) cc_final: 0.8858 (tpt) REVERT: C 324 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8513 (p) REVERT: D 7 GLN cc_start: 0.8470 (mt0) cc_final: 0.8249 (mt0) REVERT: D 50 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6925 (tm-30) REVERT: D 60 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8813 (tp40) REVERT: D 65 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8303 (pp) REVERT: D 73 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: D 124 MET cc_start: 0.9201 (mmt) cc_final: 0.8526 (mmt) REVERT: F 73 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8000 (tp30) outliers start: 26 outliers final: 11 residues processed: 168 average time/residue: 0.7270 time to fit residues: 132.1143 Evaluate side-chains 168 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 119 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 354 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.105834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.082645 restraints weight = 117812.296| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.76 r_work: 0.2587 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16005 Z= 0.126 Angle : 0.641 7.165 21898 Z= 0.306 Chirality : 0.050 0.329 2448 Planarity : 0.004 0.038 2805 Dihedral : 26.372 174.713 2542 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.57 % Allowed : 9.88 % Favored : 86.56 % 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: 0.77 (0.19), residues: 1962 helix: 0.57 (0.19), residues: 800 sheet: 0.86 (0.26), residues: 377 loop : 0.51 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 178 TYR 0.009 0.001 TYR A 144 PHE 0.009 0.001 PHE A 256 TRP 0.013 0.002 TRP D 341 HIS 0.004 0.001 HIS F 162 Details of bonding type rmsd covalent geometry : bond 0.00289 (16005) covalent geometry : angle 0.64123 (21898) hydrogen bonds : bond 0.04281 ( 690) hydrogen bonds : angle 4.54286 ( 1752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7165 (tm-30) REVERT: A 73 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: A 177 MET cc_start: 0.9231 (mmm) cc_final: 0.9007 (mmt) REVERT: A 316 ARG cc_start: 0.8316 (ttt-90) cc_final: 0.8015 (ttp-170) REVERT: A 326 MET cc_start: 0.8948 (mmp) cc_final: 0.8260 (mmp) REVERT: B 51 LYS cc_start: 0.8359 (mttt) cc_final: 0.8117 (mttm) REVERT: B 73 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: B 328 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.9001 (mp) REVERT: C 65 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8404 (pp) REVERT: C 73 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7709 (tp30) REVERT: C 83 MET cc_start: 0.9165 (tpt) cc_final: 0.8833 (tpt) REVERT: D 7 GLN cc_start: 0.8458 (mt0) cc_final: 0.8236 (mt0) REVERT: D 50 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6972 (tm-30) REVERT: D 60 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8812 (tp40) REVERT: D 65 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8286 (pp) REVERT: D 73 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: D 124 MET cc_start: 0.9170 (mmt) cc_final: 0.8497 (mmt) REVERT: F 73 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: F 233 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7483 (mt0) outliers start: 25 outliers final: 10 residues processed: 167 average time/residue: 0.7142 time to fit residues: 129.3586 Evaluate side-chains 165 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 116 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** F 297 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 = 0.3075 r_free = 0.3075 target = 0.101171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.077980 restraints weight = 117448.304| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.72 r_work: 0.2498 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2475 r_free = 0.2475 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16005 Z= 0.288 Angle : 0.829 8.564 21898 Z= 0.407 Chirality : 0.060 0.514 2448 Planarity : 0.006 0.055 2805 Dihedral : 27.488 177.631 2542 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.68 % Allowed : 9.99 % Favored : 86.32 % 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: 0.12 (0.18), residues: 1962 helix: -0.06 (0.18), residues: 830 sheet: 0.65 (0.25), residues: 387 loop : 0.20 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 184 TYR 0.012 0.002 TYR B 363 PHE 0.012 0.003 PHE D 32 TRP 0.023 0.004 TRP F 341 HIS 0.006 0.002 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00712 (16005) covalent geometry : angle 0.82875 (21898) hydrogen bonds : bond 0.06868 ( 690) hydrogen bonds : angle 4.86749 ( 1752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 73 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: A 177 MET cc_start: 0.9278 (mmm) cc_final: 0.9054 (mmt) REVERT: A 316 ARG cc_start: 0.8382 (ttt-90) cc_final: 0.8069 (ttp-170) REVERT: A 326 MET cc_start: 0.8954 (mmp) cc_final: 0.8324 (mmp) REVERT: B 51 LYS cc_start: 0.8362 (mttt) cc_final: 0.8065 (mttm) REVERT: B 73 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: B 83 MET cc_start: 0.9118 (tpt) cc_final: 0.8694 (tpt) REVERT: B 328 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.9020 (mp) REVERT: C 65 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8463 (pp) REVERT: C 73 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7684 (tp30) REVERT: C 83 MET cc_start: 0.9192 (tpt) cc_final: 0.8891 (tpt) REVERT: C 355 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: D 7 GLN cc_start: 0.8554 (mt0) cc_final: 0.8311 (mt0) REVERT: D 50 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6997 (tm-30) REVERT: D 60 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8808 (tp40) REVERT: D 65 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8347 (pp) REVERT: D 73 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: F 73 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: F 233 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7504 (mt0) outliers start: 28 outliers final: 15 residues processed: 168 average time/residue: 0.7572 time to fit residues: 137.3173 Evaluate side-chains 172 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 152 optimal weight: 0.0020 chunk 102 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN D 122 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 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 = 0.3138 r_free = 0.3138 target = 0.105427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.082215 restraints weight = 126958.499| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.72 r_work: 0.2560 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16005 Z= 0.122 Angle : 0.655 7.378 21898 Z= 0.315 Chirality : 0.050 0.332 2448 Planarity : 0.004 0.040 2805 Dihedral : 26.881 176.869 2542 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.45 % Allowed : 10.46 % Favored : 86.09 % 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: 0.68 (0.19), residues: 1962 helix: 0.50 (0.19), residues: 800 sheet: 0.83 (0.26), residues: 377 loop : 0.44 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 178 TYR 0.009 0.001 TYR A 144 PHE 0.010 0.001 PHE A 256 TRP 0.013 0.002 TRP D 341 HIS 0.004 0.001 HIS F 162 Details of bonding type rmsd covalent geometry : bond 0.00272 (16005) covalent geometry : angle 0.65473 (21898) hydrogen bonds : bond 0.04365 ( 690) hydrogen bonds : angle 4.60560 ( 1752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 73 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: A 177 MET cc_start: 0.9230 (mmm) cc_final: 0.8989 (mmt) REVERT: A 316 ARG cc_start: 0.8295 (ttt-90) cc_final: 0.7937 (ttp-170) REVERT: A 326 MET cc_start: 0.8949 (mmp) cc_final: 0.8364 (mmp) REVERT: B 51 LYS cc_start: 0.8355 (mttt) cc_final: 0.8108 (mttm) REVERT: B 73 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: B 328 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8993 (mp) REVERT: C 65 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 73 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: C 83 MET cc_start: 0.9172 (tpt) cc_final: 0.8844 (tpt) REVERT: D 7 GLN cc_start: 0.8463 (mt0) cc_final: 0.8245 (mt0) REVERT: D 50 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6994 (tm-30) REVERT: D 60 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8786 (tp40) REVERT: D 65 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8267 (pp) REVERT: D 73 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7941 (tp30) REVERT: D 124 MET cc_start: 0.9161 (mmt) cc_final: 0.8515 (mmt) REVERT: F 73 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: F 233 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7466 (mt0) outliers start: 23 outliers final: 14 residues processed: 161 average time/residue: 0.7296 time to fit residues: 126.9014 Evaluate side-chains 169 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 144 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN D 122 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 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 = 0.3088 r_free = 0.3088 target = 0.102022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.078831 restraints weight = 113225.857| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.66 r_work: 0.2513 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16005 Z= 0.243 Angle : 0.779 7.854 21898 Z= 0.380 Chirality : 0.057 0.435 2448 Planarity : 0.006 0.050 2805 Dihedral : 27.308 177.126 2542 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.45 % Allowed : 10.64 % Favored : 85.91 % 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: 0.25 (0.18), residues: 1962 helix: 0.07 (0.18), residues: 830 sheet: 0.67 (0.25), residues: 387 loop : 0.26 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 184 TYR 0.011 0.002 TYR F 144 PHE 0.012 0.002 PHE A 256 TRP 0.021 0.003 TRP F 341 HIS 0.005 0.002 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00594 (16005) covalent geometry : angle 0.77891 (21898) hydrogen bonds : bond 0.06277 ( 690) hydrogen bonds : angle 4.79505 ( 1752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7163 (tm-30) REVERT: A 73 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: A 177 MET cc_start: 0.9261 (mmm) cc_final: 0.9017 (mmt) REVERT: A 316 ARG cc_start: 0.8344 (ttt-90) cc_final: 0.8031 (ttp-170) REVERT: A 326 MET cc_start: 0.8950 (mmp) cc_final: 0.8333 (mmp) REVERT: B 51 LYS cc_start: 0.8371 (mttt) cc_final: 0.8113 (mttm) REVERT: B 73 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: B 83 MET cc_start: 0.9101 (tpt) cc_final: 0.8663 (tpt) REVERT: B 328 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9017 (mp) REVERT: C 65 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8439 (pp) REVERT: C 73 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: C 83 MET cc_start: 0.9187 (tpt) cc_final: 0.8868 (tpt) REVERT: D 7 GLN cc_start: 0.8524 (mt0) cc_final: 0.8277 (mt0) REVERT: D 50 GLU cc_start: 0.7293 (tm-30) cc_final: 0.7000 (tm-30) REVERT: D 60 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8790 (tp40) REVERT: D 65 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8337 (pp) REVERT: D 73 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7932 (tp30) REVERT: F 73 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: F 233 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7471 (mt0) outliers start: 23 outliers final: 14 residues processed: 161 average time/residue: 0.7664 time to fit residues: 133.0125 Evaluate side-chains 169 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN D 122 GLN ** F 13 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 = 0.3159 r_free = 0.3159 target = 0.106956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.083660 restraints weight = 111828.344| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.69 r_work: 0.2586 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16005 Z= 0.109 Angle : 0.625 7.108 21898 Z= 0.298 Chirality : 0.048 0.305 2448 Planarity : 0.004 0.039 2805 Dihedral : 26.589 175.880 2542 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.27 % Allowed : 10.87 % Favored : 85.86 % 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: 0.81 (0.19), residues: 1962 helix: 0.62 (0.19), residues: 800 sheet: 0.86 (0.26), residues: 377 loop : 0.51 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 336 TYR 0.009 0.001 TYR A 144 PHE 0.010 0.001 PHE A 256 TRP 0.012 0.002 TRP C 80 HIS 0.004 0.001 HIS F 162 Details of bonding type rmsd covalent geometry : bond 0.00239 (16005) covalent geometry : angle 0.62484 (21898) hydrogen bonds : bond 0.03914 ( 690) hydrogen bonds : angle 4.56670 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5171.69 seconds wall clock time: 88 minutes 48.78 seconds (5328.78 seconds total)