Starting phenix.real_space_refine on Fri Sep 11 03:49:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cgy_30366/09_2026/7cgy_30366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cgy_30366/09_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_30366/09_2026/7cgy_30366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cgy_30366/09_2026/7cgy_30366.map" model { file = "/net/cci-nas-00/data/ceres_data/7cgy_30366/09_2026/7cgy_30366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cgy_30366/09_2026/7cgy_30366.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cgy_30366/09_2026/7cgy_30366.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cgy_30366/09_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-2.2.1-6174/lib/python3.11/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: 1.77, 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: 0.59 Conformation dependent library (CDL) restraints added in 384.7 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: 0.25 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: 0.99 Time building geometry restraints manager: 0.78 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: 4166 25.74 - 51.47: 207 51.47 - 77.20: 28 77.20 - 102.94: 7 102.94 - 128.67: 2 Dihedral angle restraints: 4410 sinusoidal: 1806 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 4407 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: 0.02 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: 4.160 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.040 Find NCS groups from input model: 0.160 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 15.888 128.673 2736 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/Z covalent geometry : bond 0.00757 / 0.36 ( 7323) covalent geometry : angle 1.15087 / 0.63 ( 9858) hydrogen bonds : bond 0.30550 / 20.21 ( 222) hydrogen bonds : angle 10.54914 / 7.55 ( 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 : 0.273 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: 0.1201 time to fit residues: 38.9319 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 : 0.281 ------------------------------------------------------------------------------- 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... 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 = 0.3658 r_free = 0.3658 target = 0.148579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121159 restraints weight = 9942.275| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.28 r_work: 0.3101 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7323 Z= 0.109 Angle : 0.543 8.524 9858 Z= 0.290 Chirality : 0.045 0.163 1113 Planarity : 0.004 0.035 1251 Dihedral : 11.945 161.632 1001 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.86 % Allowed : 13.94 % Favored : 84.20 % 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: -3.91 (0.22), residues: 903 helix: -3.47 (0.17), residues: 408 sheet: -0.12 (0.35), residues: 162 loop : -2.44 (0.29), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.009 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/Z covalent geometry : bond 0.00241 / 0.11 ( 7323) covalent geometry : angle 0.54273 / 0.29 ( 9858) hydrogen bonds : bond 0.03870 / 2.55 ( 222) hydrogen bonds : angle 5.63005 / 3.93 ( 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 211 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.6338 (m-30) cc_final: 0.6115 (t0) REVERT: A 186 ASP cc_start: 0.8427 (m-30) cc_final: 0.8042 (p0) REVERT: A 211 HIS cc_start: 0.8112 (t-170) cc_final: 0.7826 (t-170) REVERT: A 304 ARG cc_start: 0.7772 (ptt90) cc_final: 0.7406 (ptt90) REVERT: B 41 LYS cc_start: 0.6875 (mttt) cc_final: 0.6670 (mmtt) REVERT: B 49 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7879 (ttmm) REVERT: B 71 ASP cc_start: 0.7555 (m-30) cc_final: 0.7207 (t0) REVERT: B 72 LYS cc_start: 0.8051 (ptmt) cc_final: 0.7820 (ttpp) REVERT: B 108 PHE cc_start: 0.8104 (t80) cc_final: 0.7680 (t80) REVERT: B 172 ASP cc_start: 0.7005 (m-30) cc_final: 0.6720 (m-30) REVERT: B 186 ASP cc_start: 0.7337 (p0) cc_final: 0.7041 (p0) REVERT: B 241 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 242 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8110 (ttp-170) REVERT: B 244 MET cc_start: 0.8283 (ptp) cc_final: 0.7637 (tmm) REVERT: B 252 ARG cc_start: 0.7618 (tpt90) cc_final: 0.7230 (tpt-90) REVERT: B 286 LYS cc_start: 0.7786 (pttt) cc_final: 0.7329 (pttm) REVERT: C 41 LYS cc_start: 0.6854 (mtpt) cc_final: 0.6113 (tptt) REVERT: C 116 ILE cc_start: 0.8757 (mt) cc_final: 0.8497 (mm) REVERT: C 123 GLU cc_start: 0.8547 (tt0) cc_final: 0.8300 (tt0) REVERT: C 175 ASP cc_start: 0.8090 (m-30) cc_final: 0.7834 (m-30) REVERT: C 186 ASP cc_start: 0.7191 (p0) cc_final: 0.6987 (p0) REVERT: C 241 GLU cc_start: 0.7977 (tt0) cc_final: 0.7755 (tt0) REVERT: C 244 MET cc_start: 0.8101 (ptt) cc_final: 0.7802 (tmm) REVERT: C 286 LYS cc_start: 0.7593 (pttt) cc_final: 0.7120 (ptmt) REVERT: C 300 ARG cc_start: 0.8782 (mtp180) cc_final: 0.8254 (mtp180) outliers start: 14 outliers final: 9 residues processed: 204 average time/residue: 0.1187 time to fit residues: 30.3698 Evaluate side-chains 175 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 249 MET 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: 2.9990 chunk 69 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN B 100 HIS C 30 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 = 0.3616 r_free = 0.3616 target = 0.144776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118056 restraints weight = 10009.808| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.26 r_work: 0.3055 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7323 Z= 0.126 Angle : 0.529 7.278 9858 Z= 0.278 Chirality : 0.045 0.178 1113 Planarity : 0.003 0.032 1251 Dihedral : 11.403 164.239 997 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.39 % Allowed : 15.80 % Favored : 81.81 % 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: -3.12 (0.24), residues: 903 helix: -2.61 (0.20), residues: 429 sheet: 0.18 (0.35), residues: 162 loop : -2.23 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 192 TYR 0.009 0.001 TYR A 151 PHE 0.022 0.002 PHE B 128 HIS 0.003 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7323) covalent geometry : angle 0.52875 / 0.28 ( 9858) hydrogen bonds : bond 0.03969 / 2.62 ( 222) hydrogen bonds : angle 5.05157 / 3.49 ( 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 180 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.285 Fit side-chains REVERT: A 71 ASP cc_start: 0.6447 (m-30) cc_final: 0.6054 (t0) REVERT: A 110 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8422 (tttm) REVERT: A 186 ASP cc_start: 0.8420 (m-30) cc_final: 0.8072 (p0) REVERT: A 304 ARG cc_start: 0.7957 (ptt90) cc_final: 0.7515 (ptt90) REVERT: B 71 ASP cc_start: 0.7586 (m-30) cc_final: 0.7140 (t0) REVERT: B 72 LYS cc_start: 0.8028 (ptmt) cc_final: 0.7739 (ttpp) REVERT: B 108 PHE cc_start: 0.8233 (t80) cc_final: 0.7908 (t80) REVERT: B 244 MET cc_start: 0.8550 (ptp) cc_final: 0.8182 (tmm) REVERT: B 252 ARG cc_start: 0.7757 (tpt90) cc_final: 0.7429 (ttt90) REVERT: B 286 LYS cc_start: 0.7806 (pttt) cc_final: 0.7553 (ptmt) REVERT: C 116 ILE cc_start: 0.8746 (mt) cc_final: 0.8452 (mm) REVERT: C 175 ASP cc_start: 0.7927 (m-30) cc_final: 0.7605 (m-30) REVERT: C 286 LYS cc_start: 0.7638 (pttt) cc_final: 0.7280 (ptmt) outliers start: 18 outliers final: 14 residues processed: 170 average time/residue: 0.1164 time to fit residues: 24.8897 Evaluate side-chains 156 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 179 VAL 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 225 ILE 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: 0.9980 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.0000 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.145772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118889 restraints weight = 10117.269| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.28 r_work: 0.3176 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3754 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= 0.087 Angle : 0.450 4.531 9858 Z= 0.241 Chirality : 0.043 0.162 1113 Planarity : 0.003 0.026 1251 Dihedral : 11.077 166.535 993 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.66 % Allowed : 16.73 % Favored : 80.61 % 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: -2.65 (0.25), residues: 903 helix: -2.03 (0.22), residues: 432 sheet: 0.28 (0.35), residues: 165 loop : -2.26 (0.32), residues: 306 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 0.003 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 7323) covalent geometry : angle 0.44991 / 0.24 ( 9858) hydrogen bonds : bond 0.02874 / 1.90 ( 222) hydrogen bonds : angle 4.57916 / 3.13 ( 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 180 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.296 Fit side-chains REVERT: A 71 ASP cc_start: 0.6504 (m-30) cc_final: 0.6108 (t0) REVERT: A 110 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8413 (tttm) REVERT: A 186 ASP cc_start: 0.8332 (m-30) cc_final: 0.8055 (p0) REVERT: A 200 MET cc_start: 0.8539 (tpt) cc_final: 0.8243 (tpt) REVERT: A 243 GLN cc_start: 0.8450 (mm110) cc_final: 0.8217 (mm110) REVERT: A 304 ARG cc_start: 0.7880 (ptt90) cc_final: 0.7497 (ptt90) REVERT: B 71 ASP cc_start: 0.7519 (m-30) cc_final: 0.7055 (t0) REVERT: B 72 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7674 (ttpp) REVERT: B 79 LYS cc_start: 0.8369 (mttm) cc_final: 0.8048 (mtmt) REVERT: B 108 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7867 (t80) REVERT: B 244 MET cc_start: 0.8405 (ptp) cc_final: 0.8142 (tmm) REVERT: B 252 ARG cc_start: 0.7828 (tpt90) cc_final: 0.7469 (ttt90) REVERT: C 52 GLN cc_start: 0.7797 (tt0) cc_final: 0.7536 (tt0) REVERT: C 175 ASP cc_start: 0.7864 (m-30) cc_final: 0.7572 (m-30) REVERT: C 205 TYR cc_start: 0.8660 (m-80) cc_final: 0.8057 (m-80) REVERT: C 286 LYS cc_start: 0.7700 (pttt) cc_final: 0.7410 (ptmt) REVERT: C 300 ARG cc_start: 0.8732 (mtp180) cc_final: 0.8375 (mtp180) outliers start: 20 outliers final: 10 residues processed: 170 average time/residue: 0.1164 time to fit residues: 24.9635 Evaluate side-chains 162 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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 103 THR Chi-restraints excluded: chain C residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.0070 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117305 restraints weight = 10138.329| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.30 r_work: 0.3103 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3930 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= 0.087 Angle : 0.451 5.946 9858 Z= 0.239 Chirality : 0.044 0.161 1113 Planarity : 0.003 0.024 1251 Dihedral : 10.893 166.425 993 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.66 % Allowed : 16.47 % Favored : 80.88 % 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: -2.26 (0.25), residues: 903 helix: -1.63 (0.23), residues: 429 sheet: 0.47 (0.36), residues: 165 loop : -2.21 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.007 0.001 TYR A 151 PHE 0.020 0.001 PHE C 89 HIS 0.008 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 ( 7323) covalent geometry : angle 0.45074 / 0.24 ( 9858) hydrogen bonds : bond 0.02865 / 1.89 ( 222) hydrogen bonds : angle 4.45765 / 3.04 ( 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 186 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.256 Fit side-chains REVERT: A 71 ASP cc_start: 0.6486 (m-30) cc_final: 0.6083 (t0) REVERT: A 110 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8418 (tttm) REVERT: A 186 ASP cc_start: 0.8323 (m-30) cc_final: 0.8034 (p0) REVERT: A 200 MET cc_start: 0.8566 (tpt) cc_final: 0.8252 (tpt) REVERT: A 211 HIS cc_start: 0.8075 (t-170) cc_final: 0.7854 (t-170) REVERT: A 243 GLN cc_start: 0.8489 (mm110) cc_final: 0.8259 (mm110) REVERT: A 304 ARG cc_start: 0.7886 (ptt90) cc_final: 0.7501 (ptt90) REVERT: B 71 ASP cc_start: 0.7511 (m-30) cc_final: 0.7059 (t0) REVERT: B 72 LYS cc_start: 0.7925 (ptmt) cc_final: 0.7705 (ttpp) REVERT: B 108 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7921 (t80) REVERT: B 244 MET cc_start: 0.8416 (ptp) cc_final: 0.8179 (tmm) REVERT: B 252 ARG cc_start: 0.7829 (tpt90) cc_final: 0.7538 (ttt90) REVERT: C 52 GLN cc_start: 0.7856 (tt0) cc_final: 0.7570 (tt0) REVERT: C 175 ASP cc_start: 0.7840 (m-30) cc_final: 0.7630 (m-30) REVERT: C 205 TYR cc_start: 0.8646 (m-80) cc_final: 0.7991 (m-80) REVERT: C 286 LYS cc_start: 0.7563 (pttt) cc_final: 0.7181 (ptmt) REVERT: C 300 ARG cc_start: 0.8739 (mtp180) cc_final: 0.8372 (mtp180) outliers start: 20 outliers final: 16 residues processed: 176 average time/residue: 0.1104 time to fit residues: 24.7390 Evaluate side-chains 170 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 B residue 270 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 103 THR 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 258 GLU Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115889 restraints weight = 10152.475| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.27 r_work: 0.3033 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7323 Z= 0.139 Angle : 0.523 6.576 9858 Z= 0.272 Chirality : 0.046 0.180 1113 Planarity : 0.003 0.029 1251 Dihedral : 10.971 166.775 993 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.32 % Allowed : 16.20 % 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: -2.15 (0.25), residues: 903 helix: -1.54 (0.23), residues: 432 sheet: 0.60 (0.35), residues: 162 loop : -2.19 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.008 0.001 TYR A 151 PHE 0.021 0.002 PHE B 128 HIS 0.006 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7323) covalent geometry : angle 0.52335 / 0.27 ( 9858) hydrogen bonds : bond 0.03564 / 2.32 ( 222) hydrogen bonds : angle 4.66524 / 3.19 ( 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 173 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.302 Fit side-chains REVERT: A 71 ASP cc_start: 0.6471 (m-30) cc_final: 0.6034 (t0) REVERT: A 90 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: A 110 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8418 (tttm) REVERT: A 186 ASP cc_start: 0.8379 (m-30) cc_final: 0.8057 (p0) REVERT: A 211 HIS cc_start: 0.8053 (t-170) cc_final: 0.7831 (t-170) REVERT: A 304 ARG cc_start: 0.7947 (ptt90) cc_final: 0.7546 (ptt90) REVERT: B 230 ARG cc_start: 0.8377 (ptm160) cc_final: 0.8041 (ptm-80) REVERT: B 252 ARG cc_start: 0.7975 (tpt90) cc_final: 0.7694 (ttt90) REVERT: C 52 GLN cc_start: 0.7966 (tt0) cc_final: 0.7610 (tt0) REVERT: C 175 ASP cc_start: 0.7795 (m-30) cc_final: 0.7583 (m-30) REVERT: C 205 TYR cc_start: 0.8708 (m-80) cc_final: 0.8058 (m-80) REVERT: C 286 LYS cc_start: 0.7556 (pttt) cc_final: 0.7220 (ptmt) REVERT: C 300 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8288 (mtp180) outliers start: 25 outliers final: 18 residues processed: 162 average time/residue: 0.1096 time to fit residues: 22.5633 Evaluate side-chains 165 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 185 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 119 MET 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 B residue 270 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3609 r_free = 0.3609 target = 0.144562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117446 restraints weight = 9983.799| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.29 r_work: 0.3068 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4164 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= 0.101 Angle : 0.480 7.696 9858 Z= 0.250 Chirality : 0.044 0.169 1113 Planarity : 0.003 0.025 1251 Dihedral : 10.903 168.014 993 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.92 % Allowed : 17.66 % Favored : 79.42 % 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: -1.89 (0.26), residues: 903 helix: -1.23 (0.24), residues: 429 sheet: 0.64 (0.36), residues: 162 loop : -2.16 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.012 0.001 TYR A 151 PHE 0.023 0.001 PHE C 89 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 7323) covalent geometry : angle 0.47988 / 0.25 ( 9858) hydrogen bonds : bond 0.03021 / 1.98 ( 222) hydrogen bonds : angle 4.39792 / 2.98 ( 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 182 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.332 Fit side-chains REVERT: A 71 ASP cc_start: 0.6490 (m-30) cc_final: 0.6081 (t0) REVERT: A 110 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8405 (tttm) REVERT: A 186 ASP cc_start: 0.8341 (m-30) cc_final: 0.8040 (p0) REVERT: A 211 HIS cc_start: 0.8051 (t-170) cc_final: 0.7842 (t-170) REVERT: A 304 ARG cc_start: 0.7905 (ptt90) cc_final: 0.7522 (ptt90) REVERT: B 71 ASP cc_start: 0.7394 (m-30) cc_final: 0.7011 (t0) REVERT: B 108 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 230 ARG cc_start: 0.8343 (ptm160) cc_final: 0.8005 (ptm-80) REVERT: B 252 ARG cc_start: 0.7668 (tpt90) cc_final: 0.7379 (ttt90) REVERT: B 286 LYS cc_start: 0.8266 (ptpt) cc_final: 0.7633 (pttm) REVERT: C 52 GLN cc_start: 0.7925 (tt0) cc_final: 0.7613 (tt0) REVERT: C 175 ASP cc_start: 0.7761 (m-30) cc_final: 0.7548 (m-30) REVERT: C 205 TYR cc_start: 0.8707 (m-80) cc_final: 0.8050 (m-80) REVERT: C 300 ARG cc_start: 0.8741 (mtp180) cc_final: 0.8318 (mtp180) outliers start: 22 outliers final: 19 residues processed: 172 average time/residue: 0.1056 time to fit residues: 23.2810 Evaluate side-chains 175 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR 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 B residue 270 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 179 VAL 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 258 GLU Chi-restraints excluded: chain C residue 297 SER 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: 0.9980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 106 GLN A 178 ASN A 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.143736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117175 restraints weight = 10161.313| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.28 r_work: 0.3097 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7323 Z= 0.104 Angle : 0.484 8.276 9858 Z= 0.251 Chirality : 0.044 0.170 1113 Planarity : 0.003 0.024 1251 Dihedral : 10.794 167.841 993 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.45 % Allowed : 17.40 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.26), residues: 903 helix: -1.00 (0.24), residues: 429 sheet: 0.66 (0.37), residues: 162 loop : -2.06 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.012 0.001 TYR A 151 PHE 0.023 0.002 PHE C 89 HIS 0.005 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 7323) covalent geometry : angle 0.48441 / 0.25 ( 9858) hydrogen bonds : bond 0.03053 / 1.99 ( 222) hydrogen bonds : angle 4.37042 / 2.95 ( 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 187 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.344 Fit side-chains REVERT: A 71 ASP cc_start: 0.6488 (m-30) cc_final: 0.6126 (t0) REVERT: A 110 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8433 (tttm) REVERT: A 186 ASP cc_start: 0.8331 (m-30) cc_final: 0.8041 (p0) REVERT: A 304 ARG cc_start: 0.7916 (ptt90) cc_final: 0.7554 (ptt90) REVERT: B 71 ASP cc_start: 0.7498 (m-30) cc_final: 0.7095 (t0) REVERT: B 108 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7993 (t80) REVERT: B 230 ARG cc_start: 0.8321 (ptm160) cc_final: 0.7992 (ptm-80) REVERT: B 252 ARG cc_start: 0.7743 (tpt90) cc_final: 0.7448 (ttt90) REVERT: C 52 GLN cc_start: 0.7895 (tt0) cc_final: 0.7582 (tt0) REVERT: C 175 ASP cc_start: 0.7790 (m-30) cc_final: 0.7572 (m-30) REVERT: C 205 TYR cc_start: 0.8718 (m-80) cc_final: 0.8047 (m-80) REVERT: C 231 VAL cc_start: 0.8610 (t) cc_final: 0.8268 (m) REVERT: C 300 ARG cc_start: 0.8724 (mtp180) cc_final: 0.8320 (mtp180) outliers start: 26 outliers final: 22 residues processed: 175 average time/residue: 0.1048 time to fit residues: 23.3665 Evaluate side-chains 187 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 B residue 270 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 179 VAL 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 258 GLU Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 178 ASN ** A 268 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 = 0.3560 r_free = 0.3560 target = 0.140609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113854 restraints weight = 10044.171| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.24 r_work: 0.3094 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7323 Z= 0.166 Angle : 0.566 8.715 9858 Z= 0.289 Chirality : 0.047 0.188 1113 Planarity : 0.003 0.034 1251 Dihedral : 10.962 168.365 993 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.92 % Allowed : 17.66 % Favored : 79.42 % 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: -1.18 (0.24), residues: 429 sheet: 0.71 (0.37), residues: 162 loop : -2.00 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.008 0.001 TYR A 151 PHE 0.025 0.002 PHE C 89 HIS 0.009 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 7323) covalent geometry : angle 0.56634 / 0.29 ( 9858) hydrogen bonds : bond 0.03779 / 2.44 ( 222) hydrogen bonds : angle 4.63213 / 3.14 ( 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 177 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.281 Fit side-chains REVERT: A 71 ASP cc_start: 0.6532 (m-30) cc_final: 0.6159 (t0) REVERT: A 110 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8421 (tttm) REVERT: A 186 ASP cc_start: 0.8412 (m-30) cc_final: 0.8060 (p0) REVERT: A 304 ARG cc_start: 0.7963 (ptt90) cc_final: 0.7591 (ptm-80) REVERT: A 320 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6571 (mt-10) REVERT: B 71 ASP cc_start: 0.7488 (m-30) cc_final: 0.7093 (t0) REVERT: B 108 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8131 (t80) REVERT: B 230 ARG cc_start: 0.8361 (ptm160) cc_final: 0.8023 (ptm-80) REVERT: B 252 ARG cc_start: 0.7719 (tpt90) cc_final: 0.7427 (ttt90) REVERT: B 286 LYS cc_start: 0.8307 (ptpt) cc_final: 0.7782 (pttt) REVERT: C 52 GLN cc_start: 0.7912 (tt0) cc_final: 0.7571 (tt0) REVERT: C 61 ASN cc_start: 0.7466 (m-40) cc_final: 0.7255 (m-40) REVERT: C 205 TYR cc_start: 0.8756 (m-80) cc_final: 0.8185 (m-80) REVERT: C 231 VAL cc_start: 0.8617 (t) cc_final: 0.8270 (m) REVERT: C 300 ARG cc_start: 0.8725 (mtp180) cc_final: 0.8247 (mtp180) outliers start: 22 outliers final: 20 residues processed: 168 average time/residue: 0.1097 time to fit residues: 23.5153 Evaluate side-chains 173 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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 B residue 270 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 179 VAL 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 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: 6.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3586 r_free = 0.3586 target = 0.142610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115881 restraints weight = 10116.878| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.26 r_work: 0.3081 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7323 Z= 0.148 Angle : 0.548 8.483 9858 Z= 0.280 Chirality : 0.046 0.184 1113 Planarity : 0.003 0.032 1251 Dihedral : 11.004 169.316 993 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.05 % Allowed : 17.93 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.26), residues: 903 helix: -1.14 (0.24), residues: 432 sheet: 0.72 (0.37), residues: 162 loop : -2.01 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 176 TYR 0.005 0.001 TYR B 151 PHE 0.024 0.002 PHE C 89 HIS 0.008 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7323) covalent geometry : angle 0.54822 / 0.28 ( 9858) hydrogen bonds : bond 0.03545 / 2.29 ( 222) hydrogen bonds : angle 4.59158 / 3.09 ( 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 179 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.324 Fit side-chains REVERT: A 71 ASP cc_start: 0.6494 (m-30) cc_final: 0.6097 (t0) REVERT: A 110 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8391 (tttm) REVERT: A 186 ASP cc_start: 0.8390 (m-30) cc_final: 0.8020 (p0) REVERT: A 304 ARG cc_start: 0.7976 (ptt90) cc_final: 0.7614 (ptm-80) REVERT: A 320 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6435 (mt-10) REVERT: B 71 ASP cc_start: 0.7533 (m-30) cc_final: 0.7104 (t0) REVERT: B 108 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8123 (t80) REVERT: B 230 ARG cc_start: 0.8361 (ptm160) cc_final: 0.8024 (ptm-80) REVERT: B 252 ARG cc_start: 0.7702 (tpt90) cc_final: 0.7392 (ttt90) REVERT: B 286 LYS cc_start: 0.8252 (ptpt) cc_final: 0.7759 (pttt) REVERT: C 52 GLN cc_start: 0.7909 (tt0) cc_final: 0.7567 (tt0) REVERT: C 61 ASN cc_start: 0.7422 (m-40) cc_final: 0.7206 (m-40) REVERT: C 175 ASP cc_start: 0.7566 (m-30) cc_final: 0.7209 (m-30) REVERT: C 205 TYR cc_start: 0.8773 (m-80) cc_final: 0.8171 (m-80) REVERT: C 231 VAL cc_start: 0.8636 (t) cc_final: 0.8303 (m) REVERT: C 300 ARG cc_start: 0.8707 (mtp180) cc_final: 0.8208 (mtp180) outliers start: 23 outliers final: 21 residues processed: 169 average time/residue: 0.1088 time to fit residues: 23.5386 Evaluate side-chains 176 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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 B residue 270 MET Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 179 VAL 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 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 34 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 178 ASN B 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116346 restraints weight = 10067.130| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.29 r_work: 0.3106 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7323 Z= 0.110 Angle : 0.503 8.513 9858 Z= 0.259 Chirality : 0.045 0.174 1113 Planarity : 0.003 0.027 1251 Dihedral : 10.850 169.132 993 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.05 % Allowed : 17.93 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.27), residues: 903 helix: -0.82 (0.24), residues: 435 sheet: 0.75 (0.38), residues: 162 loop : -2.02 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.005 0.001 TYR B 260 PHE 0.022 0.002 PHE C 89 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 7323) covalent geometry : angle 0.50322 / 0.26 ( 9858) hydrogen bonds : bond 0.03089 / 2.01 ( 222) hydrogen bonds : angle 4.42634 / 2.97 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.43 seconds wall clock time: 38 minutes 2.43 seconds (2282.43 seconds total)