Starting phenix.real_space_refine on Tue Mar 3 17:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cgy_30366/03_2026/7cgy_30366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cgy_30366/03_2026/7cgy_30366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cgy_30366/03_2026/7cgy_30366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cgy_30366/03_2026/7cgy_30366.map" model { file = "/net/cci-nas-00/data/ceres_data/7cgy_30366/03_2026/7cgy_30366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cgy_30366/03_2026/7cgy_30366.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 9 5.49 5 S 36 5.16 5 C 4533 2.51 5 N 1263 2.21 5 O 1368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 7212 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.79, per 1000 atoms: 0.25 Number of scatterers: 7212 At special positions: 0 Unit cell: (94.92, 90.72, 116.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 36 16.00 P 9 15.00 O 1368 8.00 N 1263 7.00 C 4533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 273.5 milliseconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 47.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.705A pdb=" N ILE A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.760A pdb=" N GLU A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.602A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.594A pdb=" N CYS A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.134A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 177 removed outlier: 4.318A pdb=" N ASP A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.656A pdb=" N VAL A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 201 Processing helix chain 'A' and resid 201 through 213 removed outlier: 4.469A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.674A pdb=" N ASP A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 233' Processing helix chain 'A' and resid 238 through 260 removed outlier: 4.042A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'B' and resid 27 through 31 removed outlier: 3.827A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 44 removed outlier: 3.562A pdb=" N LEU B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 42 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.513A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.794A pdb=" N ASP B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.603A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.593A pdb=" N CYS B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.134A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 177 removed outlier: 4.319A pdb=" N ASP B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.656A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 Processing helix chain 'B' and resid 201 through 213 removed outlier: 4.468A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.905A pdb=" N ASP B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 233' Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.912A pdb=" N GLN B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 260 removed outlier: 3.785A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'C' and resid 27 through 31 removed outlier: 3.828A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 44 removed outlier: 3.562A pdb=" N LEU C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.514A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.794A pdb=" N ASP C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.603A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.593A pdb=" N CYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 4.134A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 177 removed outlier: 4.318A pdb=" N ASP C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.656A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 Processing helix chain 'C' and resid 201 through 213 removed outlier: 4.468A pdb=" N TYR C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 238 removed outlier: 3.846A pdb=" N GLU C 238 " --> pdb=" O GLY C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 238' Processing helix chain 'C' and resid 239 through 260 removed outlier: 3.965A pdb=" N GLN C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 297 Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 336 removed outlier: 3.840A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR A 122 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN A 268 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA A 124 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 218 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N PHE A 265 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 220 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR A 267 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE A 222 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS A 155 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 219 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 156 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ALA A 191 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 158 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.532A pdb=" N LYS A 286 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 334 through 336 removed outlier: 5.980A pdb=" N THR B 122 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN B 268 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA B 124 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS B 218 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE B 265 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 220 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N THR B 267 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 222 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS B 155 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 219 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ALA B 191 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE B 158 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.532A pdb=" N LYS B 286 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.753A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ALA C 191 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE C 158 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS C 155 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU C 219 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS C 218 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE C 265 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 220 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N THR C 267 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE C 222 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR C 122 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN C 268 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA C 124 " --> pdb=" O ASN C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.532A pdb=" N LYS C 286 " --> pdb=" O THR C 271 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2357 1.34 - 1.46: 1134 1.46 - 1.57: 3762 1.57 - 1.69: 7 1.69 - 1.81: 63 Bond restraints: 7323 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 7318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 9725 4.12 - 8.24: 122 8.24 - 12.36: 8 12.36 - 16.49: 0 16.49 - 20.61: 3 Bond angle restraints: 9858 Sorted by residual: angle pdb=" N VAL B 231 " pdb=" CA VAL B 231 " pdb=" C VAL B 231 " ideal model delta sigma weight residual 110.62 118.33 -7.71 1.02e+00 9.61e-01 5.71e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 106.34 20.61 3.00e+00 1.11e-01 4.72e+01 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 111.36 118.01 -6.65 1.17e+00 7.31e-01 3.23e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 110.29 16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 110.30 16.65 3.00e+00 1.11e-01 3.08e+01 ... (remaining 9853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 4189 25.74 - 51.47: 230 51.47 - 77.20: 59 77.20 - 102.94: 14 102.94 - 128.67: 2 Dihedral angle restraints: 4494 sinusoidal: 1890 harmonic: 2604 Sorted by residual: dihedral pdb=" CA SER B 66 " pdb=" C SER B 66 " pdb=" N GLU B 67 " pdb=" CA GLU B 67 " ideal model delta harmonic sigma weight residual -180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA SER C 66 " pdb=" C SER C 66 " pdb=" N GLU C 67 " pdb=" CA GLU C 67 " ideal model delta harmonic sigma weight residual 180.00 -148.68 -31.32 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA ILE C 24 " pdb=" C ILE C 24 " pdb=" N ASP C 25 " pdb=" CA ASP C 25 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 4491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 896 0.069 - 0.139: 184 0.139 - 0.208: 28 0.208 - 0.277: 0 0.277 - 0.346: 5 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CA GLU B 241 " pdb=" N GLU B 241 " pdb=" C GLU B 241 " pdb=" CB GLU B 241 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA GLU C 241 " pdb=" N GLU C 241 " pdb=" C GLU C 241 " pdb=" CB GLU C 241 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1110 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 165 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C PHE A 165 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE A 165 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 166 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 165 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C PHE C 165 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE C 165 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 166 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 165 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C PHE B 165 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE B 165 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG B 166 " 0.013 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 13 2.22 - 2.89: 2683 2.89 - 3.56: 8834 3.56 - 4.23: 16163 4.23 - 4.90: 27660 Nonbonded interactions: 55353 Sorted by model distance: nonbonded pdb=" OE1 GLU B 238 " pdb=" OE2 GLU B 241 " model vdw 1.554 3.040 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.069 2.510 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.070 2.510 nonbonded pdb=" OG1 THR B 133 " pdb="CA CA B 401 " model vdw 2.074 2.510 nonbonded pdb=" OG1 THR A 133 " pdb="CA CA A 401 " model vdw 2.089 2.510 ... (remaining 55348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 337) selection = (chain 'B' and resid 22 through 337) selection = (chain 'C' and resid 22 through 337) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.008 0.154 7323 Z= 0.360 Angle : 1.151 20.608 9858 Z= 0.628 Chirality : 0.060 0.346 1113 Planarity : 0.005 0.034 1251 Dihedral : 18.085 128.673 2820 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.87 % Favored : 94.91 % Rotamer: Outliers : 0.27 % Allowed : 10.76 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.82 (0.21), residues: 903 helix: -4.64 (0.10), residues: 375 sheet: -0.79 (0.37), residues: 162 loop : -2.50 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.009 0.002 TYR A 194 PHE 0.025 0.003 PHE C 128 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00757 ( 7323) covalent geometry : angle 1.15087 ( 9858) hydrogen bonds : bond 0.30550 ( 222) hydrogen bonds : angle 10.54914 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.6469 (m-30) cc_final: 0.6136 (t0) REVERT: A 79 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6450 (ptmm) REVERT: A 106 GLN cc_start: 0.7679 (mp10) cc_final: 0.7087 (mt0) REVERT: A 178 ASN cc_start: 0.6998 (m-40) cc_final: 0.6781 (m-40) REVERT: A 182 ASP cc_start: 0.6985 (p0) cc_final: 0.6543 (m-30) REVERT: A 205 TYR cc_start: 0.8337 (m-80) cc_final: 0.7920 (m-80) REVERT: A 254 GLN cc_start: 0.8231 (tp40) cc_final: 0.7844 (tp40) REVERT: A 261 ASN cc_start: 0.8745 (t0) cc_final: 0.8501 (t0) REVERT: A 304 ARG cc_start: 0.7298 (ptt90) cc_final: 0.6970 (ptt90) REVERT: B 49 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8026 (ttmm) REVERT: B 72 LYS cc_start: 0.7929 (ptmt) cc_final: 0.7607 (ttpp) REVERT: B 155 LYS cc_start: 0.8257 (mttt) cc_final: 0.7912 (mtpt) REVERT: B 242 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7219 (mtp180) REVERT: B 249 MET cc_start: 0.8404 (ptm) cc_final: 0.8005 (ptp) REVERT: C 175 ASP cc_start: 0.7675 (m-30) cc_final: 0.7444 (m-30) REVERT: C 286 LYS cc_start: 0.7713 (pttt) cc_final: 0.7146 (ptmm) REVERT: C 320 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7029 (mt-10) outliers start: 2 outliers final: 0 residues processed: 260 average time/residue: 0.1166 time to fit residues: 37.3188 Evaluate side-chains 162 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 242 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 199 GLN A 269 GLN B 22 GLN C 22 GLN C 52 GLN C 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.145806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118176 restraints weight = 10031.909| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.31 r_work: 0.3101 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7323 Z= 0.107 Angle : 0.552 8.669 9858 Z= 0.291 Chirality : 0.045 0.160 1113 Planarity : 0.004 0.035 1251 Dihedral : 13.188 156.673 1085 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.99 % Allowed : 14.08 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.22), residues: 903 helix: -3.48 (0.17), residues: 408 sheet: -0.13 (0.35), residues: 162 loop : -2.46 (0.29), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.010 0.001 TYR C 205 PHE 0.019 0.002 PHE B 128 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7323) covalent geometry : angle 0.55247 ( 9858) hydrogen bonds : bond 0.03712 ( 222) hydrogen bonds : angle 5.61203 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.6349 (m-30) cc_final: 0.6121 (t0) REVERT: A 186 ASP cc_start: 0.8425 (m-30) cc_final: 0.8031 (p0) REVERT: A 211 HIS cc_start: 0.8106 (t-170) cc_final: 0.7825 (t-170) REVERT: A 304 ARG cc_start: 0.7773 (ptt90) cc_final: 0.7405 (ptt90) REVERT: B 49 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7875 (ttmm) REVERT: B 71 ASP cc_start: 0.7569 (m-30) cc_final: 0.7182 (t0) REVERT: B 72 LYS cc_start: 0.8075 (ptmt) cc_final: 0.7818 (ttpp) REVERT: B 108 PHE cc_start: 0.8130 (t80) cc_final: 0.7697 (t80) REVERT: B 172 ASP cc_start: 0.7002 (m-30) cc_final: 0.6710 (m-30) REVERT: B 241 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 242 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8102 (ttp-170) REVERT: B 244 MET cc_start: 0.8270 (ptp) cc_final: 0.7609 (tmm) REVERT: B 252 ARG cc_start: 0.7577 (tpt90) cc_final: 0.7185 (tpt-90) REVERT: B 286 LYS cc_start: 0.7839 (pttt) cc_final: 0.7539 (pttt) REVERT: C 41 LYS cc_start: 0.6857 (mtpt) cc_final: 0.6118 (tptt) REVERT: C 107 GLU cc_start: 0.7874 (tp30) cc_final: 0.7647 (tp30) REVERT: C 116 ILE cc_start: 0.8759 (mt) cc_final: 0.8504 (mm) REVERT: C 123 GLU cc_start: 0.8534 (tt0) cc_final: 0.8242 (tt0) REVERT: C 175 ASP cc_start: 0.8109 (m-30) cc_final: 0.7848 (m-30) REVERT: C 186 ASP cc_start: 0.7201 (p0) cc_final: 0.6992 (p0) REVERT: C 241 GLU cc_start: 0.7996 (tt0) cc_final: 0.7730 (tt0) REVERT: C 244 MET cc_start: 0.8107 (ptt) cc_final: 0.7826 (tmm) REVERT: C 286 LYS cc_start: 0.7602 (pttt) cc_final: 0.7131 (ptmt) REVERT: C 300 ARG cc_start: 0.8786 (mtp180) cc_final: 0.8265 (mtp180) outliers start: 15 outliers final: 9 residues processed: 209 average time/residue: 0.1127 time to fit residues: 29.3310 Evaluate side-chains 174 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 21 optimal weight: 0.0770 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120958 restraints weight = 9988.055| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.26 r_work: 0.3098 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7323 Z= 0.093 Angle : 0.488 6.794 9858 Z= 0.257 Chirality : 0.044 0.162 1113 Planarity : 0.003 0.027 1251 Dihedral : 11.610 147.416 1081 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.99 % Allowed : 15.67 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.25), residues: 903 helix: -2.39 (0.21), residues: 426 sheet: 0.03 (0.34), residues: 174 loop : -2.26 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 192 TYR 0.007 0.001 TYR A 151 PHE 0.020 0.001 PHE B 128 HIS 0.004 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7323) covalent geometry : angle 0.48823 ( 9858) hydrogen bonds : bond 0.03378 ( 222) hydrogen bonds : angle 4.83811 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.234 Fit side-chains REVERT: A 71 ASP cc_start: 0.6512 (m-30) cc_final: 0.6142 (t0) REVERT: A 90 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: A 110 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8424 (tttm) REVERT: A 186 ASP cc_start: 0.8399 (m-30) cc_final: 0.8088 (p0) REVERT: A 211 HIS cc_start: 0.8083 (t-170) cc_final: 0.7803 (t-170) REVERT: A 304 ARG cc_start: 0.7895 (ptt90) cc_final: 0.7494 (ptt90) REVERT: A 320 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6714 (mt-10) REVERT: B 71 ASP cc_start: 0.7574 (m-30) cc_final: 0.7102 (t0) REVERT: B 72 LYS cc_start: 0.7974 (ptmt) cc_final: 0.7691 (ttpp) REVERT: B 108 PHE cc_start: 0.8076 (t80) cc_final: 0.7757 (t80) REVERT: B 241 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 244 MET cc_start: 0.8381 (ptp) cc_final: 0.7925 (tmm) REVERT: B 252 ARG cc_start: 0.7747 (tpt90) cc_final: 0.7404 (ttt90) REVERT: C 175 ASP cc_start: 0.7969 (m-30) cc_final: 0.7650 (m-30) REVERT: C 286 LYS cc_start: 0.7680 (pttt) cc_final: 0.7308 (ptmt) outliers start: 15 outliers final: 11 residues processed: 178 average time/residue: 0.1145 time to fit residues: 25.4871 Evaluate side-chains 174 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 268 ASN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS C 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115621 restraints weight = 10137.415| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.25 r_work: 0.3121 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7323 Z= 0.154 Angle : 0.556 6.895 9858 Z= 0.289 Chirality : 0.046 0.185 1113 Planarity : 0.003 0.037 1251 Dihedral : 11.703 154.268 1077 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.92 % Allowed : 15.94 % Favored : 81.14 % 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: -2.83 (0.24), residues: 903 helix: -2.21 (0.21), residues: 426 sheet: 0.23 (0.34), residues: 168 loop : -2.34 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.009 0.001 TYR A 151 PHE 0.023 0.002 PHE B 128 HIS 0.004 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7323) covalent geometry : angle 0.55602 ( 9858) hydrogen bonds : bond 0.03900 ( 222) hydrogen bonds : angle 4.95707 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.265 Fit side-chains REVERT: A 71 ASP cc_start: 0.6518 (m-30) cc_final: 0.6097 (t0) REVERT: A 110 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8404 (tttm) REVERT: A 186 ASP cc_start: 0.8391 (m-30) cc_final: 0.8087 (p0) REVERT: A 304 ARG cc_start: 0.7947 (ptt90) cc_final: 0.7523 (ptt90) REVERT: A 320 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6593 (mt-10) REVERT: B 72 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7747 (ttpp) REVERT: B 108 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7998 (t80) REVERT: B 242 ARG cc_start: 0.8936 (tmm160) cc_final: 0.8707 (ttt-90) REVERT: B 244 MET cc_start: 0.8484 (ptp) cc_final: 0.8215 (tmm) REVERT: B 252 ARG cc_start: 0.7860 (tpt90) cc_final: 0.7608 (ttt90) REVERT: B 286 LYS cc_start: 0.8085 (pttp) cc_final: 0.7399 (ptpt) REVERT: C 286 LYS cc_start: 0.7658 (pttt) cc_final: 0.7361 (ptmt) outliers start: 22 outliers final: 14 residues processed: 165 average time/residue: 0.1155 time to fit residues: 23.7609 Evaluate side-chains 159 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.0010 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117302 restraints weight = 10132.614| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.28 r_work: 0.3045 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7323 Z= 0.119 Angle : 0.509 8.531 9858 Z= 0.263 Chirality : 0.045 0.175 1113 Planarity : 0.003 0.027 1251 Dihedral : 11.595 154.587 1077 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.59 % Allowed : 15.94 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.25), residues: 903 helix: -1.82 (0.23), residues: 435 sheet: 0.48 (0.35), residues: 162 loop : -2.30 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.010 0.001 TYR A 151 PHE 0.021 0.002 PHE B 128 HIS 0.003 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7323) covalent geometry : angle 0.50867 ( 9858) hydrogen bonds : bond 0.03346 ( 222) hydrogen bonds : angle 4.67113 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.287 Fit side-chains REVERT: A 71 ASP cc_start: 0.6503 (m-30) cc_final: 0.6084 (t0) REVERT: A 110 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8395 (tttm) REVERT: A 186 ASP cc_start: 0.8352 (m-30) cc_final: 0.8035 (p0) REVERT: A 259 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 304 ARG cc_start: 0.7948 (ptt90) cc_final: 0.7548 (ptt90) REVERT: B 79 LYS cc_start: 0.8226 (ptpp) cc_final: 0.7893 (ptpp) REVERT: B 108 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7972 (t80) REVERT: B 230 ARG cc_start: 0.8392 (ptm160) cc_final: 0.8035 (ptm-80) REVERT: B 244 MET cc_start: 0.8440 (ptp) cc_final: 0.8238 (tmm) REVERT: B 252 ARG cc_start: 0.7788 (tpt90) cc_final: 0.7501 (ttt90) REVERT: B 286 LYS cc_start: 0.7973 (pttp) cc_final: 0.7771 (pttm) REVERT: C 123 GLU cc_start: 0.8733 (tt0) cc_final: 0.8421 (tt0) REVERT: C 205 TYR cc_start: 0.8728 (m-80) cc_final: 0.8103 (m-80) REVERT: C 286 LYS cc_start: 0.7717 (pttt) cc_final: 0.7424 (ptmt) REVERT: C 300 ARG cc_start: 0.8760 (mtp180) cc_final: 0.8325 (mtp180) REVERT: C 312 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8343 (mp) outliers start: 27 outliers final: 18 residues processed: 168 average time/residue: 0.1177 time to fit residues: 24.6942 Evaluate side-chains 167 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 0.0980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 268 ASN B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115409 restraints weight = 10185.237| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.26 r_work: 0.3077 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7323 Z= 0.129 Angle : 0.524 7.886 9858 Z= 0.270 Chirality : 0.045 0.180 1113 Planarity : 0.003 0.029 1251 Dihedral : 11.627 155.724 1077 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.19 % Allowed : 16.47 % Favored : 80.35 % 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: -2.24 (0.25), residues: 903 helix: -1.60 (0.23), residues: 432 sheet: 0.56 (0.36), residues: 162 loop : -2.26 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 192 TYR 0.009 0.001 TYR A 151 PHE 0.021 0.002 PHE B 128 HIS 0.003 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7323) covalent geometry : angle 0.52367 ( 9858) hydrogen bonds : bond 0.03454 ( 222) hydrogen bonds : angle 4.64060 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.283 Fit side-chains REVERT: A 71 ASP cc_start: 0.6447 (m-30) cc_final: 0.6032 (t0) REVERT: A 110 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8407 (tttm) REVERT: A 186 ASP cc_start: 0.8410 (m-30) cc_final: 0.8066 (p0) REVERT: A 304 ARG cc_start: 0.7948 (ptt90) cc_final: 0.7560 (ptt90) REVERT: B 71 ASP cc_start: 0.7489 (m-30) cc_final: 0.7035 (t0) REVERT: B 79 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7813 (ptpp) REVERT: B 108 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8014 (t80) REVERT: B 230 ARG cc_start: 0.8379 (ptm160) cc_final: 0.8043 (ptm-80) REVERT: B 252 ARG cc_start: 0.7659 (tpt90) cc_final: 0.7439 (ttt90) REVERT: C 123 GLU cc_start: 0.8695 (tt0) cc_final: 0.8251 (tt0) REVERT: C 175 ASP cc_start: 0.7499 (m-30) cc_final: 0.7253 (m-30) REVERT: C 205 TYR cc_start: 0.8732 (m-80) cc_final: 0.8108 (m-80) REVERT: C 286 LYS cc_start: 0.7590 (pttt) cc_final: 0.7267 (ptmt) REVERT: C 300 ARG cc_start: 0.8750 (mtp180) cc_final: 0.8282 (mtp180) REVERT: C 312 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8378 (mp) outliers start: 24 outliers final: 19 residues processed: 160 average time/residue: 0.1115 time to fit residues: 22.5195 Evaluate side-chains 165 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 0.0270 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN B 269 GLN C 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118352 restraints weight = 10024.415| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.27 r_work: 0.3144 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7323 Z= 0.085 Angle : 0.473 9.101 9858 Z= 0.243 Chirality : 0.043 0.165 1113 Planarity : 0.003 0.024 1251 Dihedral : 11.457 154.938 1077 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.66 % Allowed : 17.26 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.26), residues: 903 helix: -1.29 (0.24), residues: 429 sheet: 0.60 (0.36), residues: 162 loop : -2.14 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.004 0.001 TYR A 194 PHE 0.023 0.001 PHE C 89 HIS 0.002 0.000 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 7323) covalent geometry : angle 0.47309 ( 9858) hydrogen bonds : bond 0.02751 ( 222) hydrogen bonds : angle 4.35265 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.209 Fit side-chains REVERT: A 71 ASP cc_start: 0.6526 (m-30) cc_final: 0.6114 (t0) REVERT: A 110 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8412 (tttm) REVERT: A 186 ASP cc_start: 0.8326 (m-30) cc_final: 0.8039 (p0) REVERT: A 304 ARG cc_start: 0.7902 (ptt90) cc_final: 0.7542 (ptt90) REVERT: B 71 ASP cc_start: 0.7473 (m-30) cc_final: 0.7093 (t0) REVERT: B 108 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7950 (t80) REVERT: B 200 MET cc_start: 0.8652 (tpt) cc_final: 0.8390 (tpt) REVERT: B 230 ARG cc_start: 0.8331 (ptm160) cc_final: 0.7985 (ptm-80) REVERT: B 252 ARG cc_start: 0.7710 (tpt90) cc_final: 0.7386 (ttt90) REVERT: C 123 GLU cc_start: 0.8640 (tt0) cc_final: 0.8379 (tt0) REVERT: C 205 TYR cc_start: 0.8707 (m-80) cc_final: 0.8061 (m-80) REVERT: C 300 ARG cc_start: 0.8740 (mtp180) cc_final: 0.8389 (mtp180) REVERT: C 312 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8379 (mp) outliers start: 20 outliers final: 13 residues processed: 172 average time/residue: 0.1125 time to fit residues: 24.4305 Evaluate side-chains 163 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 0.0040 chunk 70 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 106 GLN A 178 ASN A 261 ASN A 268 ASN B 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120114 restraints weight = 10148.988| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.25 r_work: 0.3091 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7323 Z= 0.090 Angle : 0.479 9.817 9858 Z= 0.245 Chirality : 0.044 0.166 1113 Planarity : 0.003 0.024 1251 Dihedral : 11.355 154.516 1077 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.92 % Allowed : 16.87 % Favored : 80.21 % 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: -1.68 (0.26), residues: 903 helix: -1.07 (0.24), residues: 429 sheet: 0.63 (0.37), residues: 165 loop : -1.99 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.004 0.001 TYR B 151 PHE 0.022 0.001 PHE C 89 HIS 0.010 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7323) covalent geometry : angle 0.47928 ( 9858) hydrogen bonds : bond 0.02821 ( 222) hydrogen bonds : angle 4.29850 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.268 Fit side-chains REVERT: A 71 ASP cc_start: 0.6506 (m-30) cc_final: 0.6093 (t0) REVERT: A 110 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8398 (tttm) REVERT: A 186 ASP cc_start: 0.8377 (m-30) cc_final: 0.8043 (p0) REVERT: A 304 ARG cc_start: 0.7920 (ptt90) cc_final: 0.7571 (ptt90) REVERT: B 71 ASP cc_start: 0.7472 (m-30) cc_final: 0.7077 (t0) REVERT: B 108 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7934 (t80) REVERT: B 200 MET cc_start: 0.8684 (tpt) cc_final: 0.8451 (tpt) REVERT: B 230 ARG cc_start: 0.8282 (ptm160) cc_final: 0.7934 (ptm-80) REVERT: B 252 ARG cc_start: 0.7682 (tpt90) cc_final: 0.7378 (ttt90) REVERT: C 123 GLU cc_start: 0.8681 (tt0) cc_final: 0.8358 (tt0) REVERT: C 175 ASP cc_start: 0.7535 (m-30) cc_final: 0.7217 (m-30) REVERT: C 205 TYR cc_start: 0.8706 (m-80) cc_final: 0.8023 (m-80) REVERT: C 300 ARG cc_start: 0.8767 (mtp180) cc_final: 0.8375 (mtp180) REVERT: C 312 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8337 (mp) outliers start: 22 outliers final: 18 residues processed: 168 average time/residue: 0.1100 time to fit residues: 23.3762 Evaluate side-chains 171 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115006 restraints weight = 10053.050| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.26 r_work: 0.3098 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7323 Z= 0.150 Angle : 0.549 9.735 9858 Z= 0.280 Chirality : 0.046 0.183 1113 Planarity : 0.003 0.032 1251 Dihedral : 11.595 157.064 1077 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.59 % Allowed : 16.07 % Favored : 80.35 % 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: -1.76 (0.26), residues: 903 helix: -1.23 (0.24), residues: 429 sheet: 0.65 (0.37), residues: 162 loop : -1.89 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.004 0.001 TYR A 151 PHE 0.023 0.002 PHE C 89 HIS 0.009 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7323) covalent geometry : angle 0.54919 ( 9858) hydrogen bonds : bond 0.03613 ( 222) hydrogen bonds : angle 4.58155 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.195 Fit side-chains REVERT: A 71 ASP cc_start: 0.6533 (m-30) cc_final: 0.6161 (t0) REVERT: A 110 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8429 (tttm) REVERT: A 186 ASP cc_start: 0.8454 (m-30) cc_final: 0.8092 (p0) REVERT: A 304 ARG cc_start: 0.7967 (ptt90) cc_final: 0.7626 (ptm-80) REVERT: B 108 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8050 (t80) REVERT: B 230 ARG cc_start: 0.8293 (ptm160) cc_final: 0.7960 (ptm-80) REVERT: B 252 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7382 (ttt90) REVERT: C 123 GLU cc_start: 0.8695 (tt0) cc_final: 0.8212 (tt0) REVERT: C 205 TYR cc_start: 0.8738 (m-80) cc_final: 0.8162 (m-80) REVERT: C 300 ARG cc_start: 0.8753 (mtp180) cc_final: 0.8250 (mtp180) outliers start: 27 outliers final: 21 residues processed: 164 average time/residue: 0.1033 time to fit residues: 21.4817 Evaluate side-chains 171 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN A 268 ASN C 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119517 restraints weight = 10117.341| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.26 r_work: 0.3130 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7323 Z= 0.084 Angle : 0.475 9.976 9858 Z= 0.246 Chirality : 0.044 0.163 1113 Planarity : 0.003 0.022 1251 Dihedral : 11.472 156.553 1077 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.12 % Allowed : 18.06 % Favored : 79.81 % 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: -1.42 (0.27), residues: 903 helix: -0.80 (0.24), residues: 429 sheet: 0.67 (0.38), residues: 165 loop : -1.89 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 304 TYR 0.015 0.001 TYR A 151 PHE 0.026 0.001 PHE C 89 HIS 0.009 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 7323) covalent geometry : angle 0.47509 ( 9858) hydrogen bonds : bond 0.02706 ( 222) hydrogen bonds : angle 4.26302 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.219 Fit side-chains REVERT: A 71 ASP cc_start: 0.6514 (m-30) cc_final: 0.6202 (t0) REVERT: A 110 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8426 (tttm) REVERT: A 186 ASP cc_start: 0.8370 (m-30) cc_final: 0.8056 (p0) REVERT: A 211 HIS cc_start: 0.8004 (t-170) cc_final: 0.7785 (t-170) REVERT: A 304 ARG cc_start: 0.7928 (ptt90) cc_final: 0.7580 (ptt90) REVERT: B 71 ASP cc_start: 0.7469 (m-30) cc_final: 0.7192 (t0) REVERT: B 108 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7953 (t80) REVERT: B 230 ARG cc_start: 0.8297 (ptm160) cc_final: 0.7981 (ptm-80) REVERT: B 232 ASP cc_start: 0.7965 (m-30) cc_final: 0.7670 (m-30) REVERT: B 252 ARG cc_start: 0.7620 (tpt90) cc_final: 0.7360 (ttt90) REVERT: C 52 GLN cc_start: 0.7634 (mt0) cc_final: 0.7388 (mt0) REVERT: C 61 ASN cc_start: 0.7471 (m-40) cc_final: 0.7268 (m-40) REVERT: C 123 GLU cc_start: 0.8645 (tt0) cc_final: 0.8369 (tt0) REVERT: C 205 TYR cc_start: 0.8727 (m-80) cc_final: 0.8049 (m-80) REVERT: C 300 ARG cc_start: 0.8710 (mtp180) cc_final: 0.8363 (mtp180) outliers start: 16 outliers final: 14 residues processed: 160 average time/residue: 0.1069 time to fit residues: 21.6537 Evaluate side-chains 169 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.0170 chunk 36 optimal weight: 0.0070 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN A 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.145015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118113 restraints weight = 10086.063| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.29 r_work: 0.3150 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7323 Z= 0.078 Angle : 0.453 9.549 9858 Z= 0.234 Chirality : 0.043 0.160 1113 Planarity : 0.002 0.022 1251 Dihedral : 11.161 154.376 1077 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.66 % Allowed : 17.66 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.27), residues: 903 helix: -0.57 (0.25), residues: 429 sheet: 0.68 (0.38), residues: 165 loop : -1.76 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.015 0.001 TYR A 151 PHE 0.025 0.001 PHE C 89 HIS 0.008 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 7323) covalent geometry : angle 0.45252 ( 9858) hydrogen bonds : bond 0.02490 ( 222) hydrogen bonds : angle 4.08817 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.74 seconds wall clock time: 36 minutes 2.41 seconds (2162.41 seconds total)