Starting phenix.real_space_refine on Wed Mar 12 05:59:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cgy_30366/03_2025/7cgy_30366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cgy_30366/03_2025/7cgy_30366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cgy_30366/03_2025/7cgy_30366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cgy_30366/03_2025/7cgy_30366.map" model { file = "/net/cci-nas-00/data/ceres_data/7cgy_30366/03_2025/7cgy_30366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cgy_30366/03_2025/7cgy_30366.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.30, per 1000 atoms: 0.73 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: 1.55 Conformation dependent library (CDL) restraints added in 954.9 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: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.705A pdb=" N ILE A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.760A pdb=" N GLU A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.602A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.594A pdb=" N CYS A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.134A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 177 removed outlier: 4.318A pdb=" N ASP A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.656A pdb=" N VAL A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 201 Processing helix chain 'A' and resid 201 through 213 removed outlier: 4.469A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.674A pdb=" N ASP A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 233' Processing helix chain 'A' and resid 238 through 260 removed outlier: 4.042A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'B' and resid 27 through 31 removed outlier: 3.827A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 44 removed outlier: 3.562A pdb=" N LEU B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 42 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.513A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.794A pdb=" N ASP B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.603A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.593A pdb=" N CYS B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.134A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 177 removed outlier: 4.319A pdb=" N ASP B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.656A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 Processing helix chain 'B' and resid 201 through 213 removed outlier: 4.468A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.905A pdb=" N ASP B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 233' Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.912A pdb=" N GLN B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 260 removed outlier: 3.785A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'C' and resid 27 through 31 removed outlier: 3.828A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 44 removed outlier: 3.562A pdb=" N LEU C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.514A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.794A pdb=" N ASP C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.603A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.593A pdb=" N CYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 4.134A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 177 removed outlier: 4.318A pdb=" N ASP C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.656A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 Processing helix chain 'C' and resid 201 through 213 removed outlier: 4.468A pdb=" N TYR C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 238 removed outlier: 3.846A pdb=" N GLU C 238 " --> pdb=" O GLY C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 238' Processing helix chain 'C' and resid 239 through 260 removed outlier: 3.965A pdb=" N GLN C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 297 Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 336 removed outlier: 3.840A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR A 122 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN A 268 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA A 124 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 218 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N PHE A 265 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 220 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR A 267 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE A 222 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS A 155 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 219 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 156 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ALA A 191 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 158 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.532A pdb=" N LYS A 286 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 334 through 336 removed outlier: 5.980A pdb=" N THR B 122 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN B 268 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA B 124 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS B 218 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE B 265 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 220 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N THR B 267 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 222 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS B 155 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 219 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ALA B 191 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE B 158 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.532A pdb=" N LYS B 286 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.753A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ALA C 191 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE C 158 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS C 155 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU C 219 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS C 218 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE C 265 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 220 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N THR C 267 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE C 222 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR C 122 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN C 268 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA C 124 " --> pdb=" O ASN C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.532A pdb=" N LYS C 286 " --> pdb=" O THR C 271 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2357 1.34 - 1.46: 1134 1.46 - 1.57: 3762 1.57 - 1.69: 7 1.69 - 1.81: 63 Bond restraints: 7323 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 7318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 9725 4.12 - 8.24: 122 8.24 - 12.36: 8 12.36 - 16.49: 0 16.49 - 20.61: 3 Bond angle restraints: 9858 Sorted by residual: angle pdb=" N VAL B 231 " pdb=" CA VAL B 231 " pdb=" C VAL B 231 " ideal model delta sigma weight residual 110.62 118.33 -7.71 1.02e+00 9.61e-01 5.71e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 106.34 20.61 3.00e+00 1.11e-01 4.72e+01 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 111.36 118.01 -6.65 1.17e+00 7.31e-01 3.23e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 110.29 16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 110.30 16.65 3.00e+00 1.11e-01 3.08e+01 ... (remaining 9853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 4189 25.74 - 51.47: 230 51.47 - 77.20: 59 77.20 - 102.94: 14 102.94 - 128.67: 2 Dihedral angle restraints: 4494 sinusoidal: 1890 harmonic: 2604 Sorted by residual: dihedral pdb=" CA SER B 66 " pdb=" C SER B 66 " pdb=" N GLU B 67 " pdb=" CA GLU B 67 " ideal model delta harmonic sigma weight residual -180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA SER C 66 " pdb=" C SER C 66 " pdb=" N GLU C 67 " pdb=" CA GLU C 67 " ideal model delta harmonic sigma weight residual 180.00 -148.68 -31.32 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA ILE C 24 " pdb=" C ILE C 24 " pdb=" N ASP C 25 " pdb=" CA ASP C 25 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 4491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 896 0.069 - 0.139: 184 0.139 - 0.208: 28 0.208 - 0.277: 0 0.277 - 0.346: 5 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CA GLU B 241 " pdb=" N GLU B 241 " pdb=" C GLU B 241 " pdb=" CB GLU B 241 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA GLU C 241 " pdb=" N GLU C 241 " pdb=" C GLU C 241 " pdb=" CB GLU C 241 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1110 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 165 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C PHE A 165 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE A 165 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 166 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 165 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C PHE C 165 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE C 165 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 166 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 165 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C PHE B 165 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE B 165 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG B 166 " 0.013 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 13 2.22 - 2.89: 2683 2.89 - 3.56: 8834 3.56 - 4.23: 16163 4.23 - 4.90: 27660 Nonbonded interactions: 55353 Sorted by model distance: nonbonded pdb=" OE1 GLU B 238 " pdb=" OE2 GLU B 241 " model vdw 1.554 3.040 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.069 2.510 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.070 2.510 nonbonded pdb=" OG1 THR B 133 " pdb="CA CA B 401 " model vdw 2.074 2.510 nonbonded pdb=" OG1 THR A 133 " pdb="CA CA A 401 " model vdw 2.089 2.510 ... (remaining 55348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 4.680 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.980 Find NCS groups from input model: 0.330 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.154 7323 Z= 0.461 Angle : 1.151 20.608 9858 Z= 0.628 Chirality : 0.060 0.346 1113 Planarity : 0.005 0.034 1251 Dihedral : 18.085 128.673 2820 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.87 % Favored : 94.91 % Rotamer: Outliers : 0.27 % Allowed : 10.76 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.001 HIS A 295 PHE 0.025 0.003 PHE C 128 TYR 0.009 0.002 TYR A 194 ARG 0.006 0.001 ARG A 129 *********************** 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 : 0.748 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: 0.2625 time to fit residues: 83.9555 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 : 0.738 ------------------------------------------------------------------------------- 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 75 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114992 restraints weight = 10005.659| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.27 r_work: 0.3098 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2729 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= 0.158 Angle : 0.558 8.625 9858 Z= 0.294 Chirality : 0.045 0.160 1113 Planarity : 0.004 0.035 1251 Dihedral : 13.258 155.829 1085 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.99 % Allowed : 13.94 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.22), residues: 903 helix: -3.50 (0.17), residues: 408 sheet: -0.15 (0.35), residues: 162 loop : -2.46 (0.29), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 211 PHE 0.020 0.002 PHE B 128 TYR 0.010 0.001 TYR C 205 ARG 0.005 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.6359 (m-30) cc_final: 0.6130 (t0) REVERT: A 186 ASP cc_start: 0.8435 (m-30) cc_final: 0.8047 (p0) REVERT: A 211 HIS cc_start: 0.8103 (t-170) cc_final: 0.7886 (t-170) REVERT: A 241 GLU cc_start: 0.7279 (pt0) cc_final: 0.7079 (tt0) REVERT: A 304 ARG cc_start: 0.7765 (ptt90) cc_final: 0.7398 (ptt90) REVERT: B 49 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7883 (ttmm) REVERT: B 71 ASP cc_start: 0.7574 (m-30) cc_final: 0.7252 (t0) REVERT: B 72 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7818 (ttpp) REVERT: B 172 ASP cc_start: 0.7041 (m-30) cc_final: 0.6748 (m-30) REVERT: B 241 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 242 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8091 (ttp-170) REVERT: B 244 MET cc_start: 0.8266 (ptp) cc_final: 0.7576 (tmm) REVERT: B 252 ARG cc_start: 0.7572 (tpt90) cc_final: 0.7167 (tpt-90) REVERT: B 286 LYS cc_start: 0.7846 (pttt) cc_final: 0.7360 (pttm) REVERT: C 41 LYS cc_start: 0.6831 (mtpt) cc_final: 0.6091 (tptt) REVERT: C 107 GLU cc_start: 0.7853 (tp30) cc_final: 0.7629 (tp30) REVERT: C 116 ILE cc_start: 0.8762 (mt) cc_final: 0.8508 (mm) REVERT: C 123 GLU cc_start: 0.8536 (tt0) cc_final: 0.8189 (tt0) REVERT: C 175 ASP cc_start: 0.8112 (m-30) cc_final: 0.7826 (m-30) REVERT: C 241 GLU cc_start: 0.7988 (tt0) cc_final: 0.7726 (tt0) REVERT: C 244 MET cc_start: 0.8097 (ptt) cc_final: 0.7796 (tmm) REVERT: C 286 LYS cc_start: 0.7601 (pttt) cc_final: 0.7115 (ptmt) REVERT: C 300 ARG cc_start: 0.8787 (mtp180) cc_final: 0.8258 (mtp180) outliers start: 15 outliers final: 10 residues processed: 208 average time/residue: 0.2682 time to fit residues: 69.0560 Evaluate side-chains 175 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 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 25 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN 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 = 0.3561 r_free = 0.3561 target = 0.140471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113155 restraints weight = 10036.097| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.26 r_work: 0.2999 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7323 Z= 0.324 Angle : 0.658 8.694 9858 Z= 0.340 Chirality : 0.049 0.206 1113 Planarity : 0.004 0.046 1251 Dihedral : 12.067 154.703 1081 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.32 % Allowed : 15.67 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.24), residues: 903 helix: -2.78 (0.19), residues: 426 sheet: 0.14 (0.35), residues: 162 loop : -2.38 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 291 PHE 0.022 0.002 PHE B 128 TYR 0.012 0.001 TYR A 151 ARG 0.005 0.001 ARG A 176 *********************** 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 179 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.841 Fit side-chains REVERT: A 71 ASP cc_start: 0.6500 (m-30) cc_final: 0.6093 (t0) REVERT: A 90 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: A 110 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8444 (tttm) REVERT: A 186 ASP cc_start: 0.8484 (m-30) cc_final: 0.8052 (p0) REVERT: A 304 ARG cc_start: 0.7952 (ptt90) cc_final: 0.7473 (ptt180) REVERT: B 39 LYS cc_start: 0.6576 (ptpt) cc_final: 0.6317 (ptpt) REVERT: B 72 LYS cc_start: 0.8180 (ptmt) cc_final: 0.7891 (ttpp) REVERT: B 244 MET cc_start: 0.8566 (ptp) cc_final: 0.8240 (tmm) REVERT: C 116 ILE cc_start: 0.8822 (mt) cc_final: 0.8525 (mm) REVERT: C 175 ASP cc_start: 0.7933 (m-30) cc_final: 0.7654 (m-30) REVERT: C 286 LYS cc_start: 0.7858 (pttt) cc_final: 0.7232 (ptmt) outliers start: 25 outliers final: 20 residues processed: 171 average time/residue: 0.2535 time to fit residues: 54.5303 Evaluate side-chains 163 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 97 MET 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 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 331 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 268 ASN B 269 GLN C 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113737 restraints weight = 10164.674| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.27 r_work: 0.3032 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3751 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= 0.204 Angle : 0.548 7.306 9858 Z= 0.285 Chirality : 0.046 0.181 1113 Planarity : 0.003 0.032 1251 Dihedral : 11.804 156.335 1077 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.45 % Allowed : 16.47 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.25), residues: 903 helix: -2.31 (0.21), residues: 429 sheet: 0.26 (0.35), residues: 162 loop : -2.31 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 291 PHE 0.025 0.002 PHE C 89 TYR 0.009 0.001 TYR A 151 ARG 0.004 0.000 ARG A 242 *********************** 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 181 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.733 Fit side-chains REVERT: A 71 ASP cc_start: 0.6463 (m-30) cc_final: 0.6051 (t0) REVERT: A 110 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8391 (tttm) REVERT: A 186 ASP cc_start: 0.8396 (m-30) cc_final: 0.8017 (p0) REVERT: A 304 ARG cc_start: 0.8009 (ptt90) cc_final: 0.7597 (ptt90) REVERT: B 39 LYS cc_start: 0.6605 (ptpt) cc_final: 0.6379 (ptpt) REVERT: B 72 LYS cc_start: 0.8090 (ptmt) cc_final: 0.7795 (ttpp) REVERT: B 244 MET cc_start: 0.8483 (ptp) cc_final: 0.8234 (tmm) REVERT: C 52 GLN cc_start: 0.7988 (tt0) cc_final: 0.7743 (tt0) REVERT: C 175 ASP cc_start: 0.7878 (m-30) cc_final: 0.7621 (m-30) REVERT: C 205 TYR cc_start: 0.8741 (m-80) cc_final: 0.8197 (m-80) REVERT: C 244 MET cc_start: 0.8165 (ptt) cc_final: 0.7939 (tmm) REVERT: C 286 LYS cc_start: 0.7723 (pttt) cc_final: 0.7281 (ptmt) outliers start: 26 outliers final: 16 residues processed: 171 average time/residue: 0.2552 time to fit residues: 54.5470 Evaluate side-chains 162 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113308 restraints weight = 9966.252| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.22 r_work: 0.3014 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7323 Z= 0.257 Angle : 0.582 8.275 9858 Z= 0.299 Chirality : 0.047 0.190 1113 Planarity : 0.003 0.037 1251 Dihedral : 11.811 157.658 1077 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.59 % Allowed : 16.73 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.25), residues: 903 helix: -2.12 (0.22), residues: 429 sheet: 0.38 (0.36), residues: 162 loop : -2.28 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 181 PHE 0.023 0.002 PHE B 128 TYR 0.006 0.001 TYR A 194 ARG 0.002 0.000 ARG C 192 *********************** 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 177 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.118 Fit side-chains REVERT: A 71 ASP cc_start: 0.6399 (m-30) cc_final: 0.6051 (t0) REVERT: A 110 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8395 (tttm) REVERT: A 186 ASP cc_start: 0.8430 (m-30) cc_final: 0.8066 (p0) REVERT: A 304 ARG cc_start: 0.7985 (ptt90) cc_final: 0.7580 (ptt90) REVERT: B 72 LYS cc_start: 0.8147 (ptmt) cc_final: 0.7872 (ttpp) REVERT: B 230 ARG cc_start: 0.8416 (ptm160) cc_final: 0.7977 (ptm-80) REVERT: B 244 MET cc_start: 0.8468 (ptp) cc_final: 0.8201 (tmm) REVERT: C 175 ASP cc_start: 0.7856 (m-30) cc_final: 0.7613 (m-30) REVERT: C 205 TYR cc_start: 0.8731 (m-80) cc_final: 0.8149 (m-80) REVERT: C 286 LYS cc_start: 0.7806 (pttt) cc_final: 0.7392 (ptmt) outliers start: 27 outliers final: 22 residues processed: 166 average time/residue: 0.2378 time to fit residues: 49.9301 Evaluate side-chains 167 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 MET 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 231 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 34 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 243 GLN Chi-restraints excluded: chain C residue 249 MET 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 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.117031 restraints weight = 10048.399| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.22 r_work: 0.3157 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7323 Z= 0.119 Angle : 0.478 8.970 9858 Z= 0.247 Chirality : 0.044 0.163 1113 Planarity : 0.003 0.026 1251 Dihedral : 11.546 156.340 1077 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.39 % Allowed : 18.73 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.26), residues: 903 helix: -1.69 (0.23), residues: 429 sheet: 0.62 (0.37), residues: 162 loop : -2.10 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 181 PHE 0.023 0.001 PHE C 89 TYR 0.012 0.001 TYR A 151 ARG 0.003 0.000 ARG B 252 *********************** 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 185 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.745 Fit side-chains REVERT: A 71 ASP cc_start: 0.6530 (m-30) cc_final: 0.6129 (t0) REVERT: A 110 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8374 (tttm) REVERT: A 186 ASP cc_start: 0.8374 (m-30) cc_final: 0.8053 (p0) REVERT: A 259 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7125 (mt-10) REVERT: A 304 ARG cc_start: 0.7950 (ptt90) cc_final: 0.7593 (ptt90) REVERT: B 71 ASP cc_start: 0.7432 (m-30) cc_final: 0.6962 (t0) REVERT: B 72 LYS cc_start: 0.8044 (ptmt) cc_final: 0.7815 (ttpp) REVERT: B 200 MET cc_start: 0.8645 (tpt) cc_final: 0.8389 (tpt) REVERT: B 230 ARG cc_start: 0.8344 (ptm160) cc_final: 0.7934 (ptm-80) REVERT: B 244 MET cc_start: 0.8377 (ptp) cc_final: 0.8155 (tmm) REVERT: B 286 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7538 (pttm) REVERT: C 52 GLN cc_start: 0.7907 (tt0) cc_final: 0.7698 (tt0) REVERT: C 123 GLU cc_start: 0.8687 (tt0) cc_final: 0.8473 (tt0) REVERT: C 175 ASP cc_start: 0.7876 (m-30) cc_final: 0.7654 (m-30) REVERT: C 205 TYR cc_start: 0.8710 (m-80) cc_final: 0.8093 (m-80) REVERT: C 286 LYS cc_start: 0.7661 (pttt) cc_final: 0.7410 (ptmt) REVERT: C 300 ARG cc_start: 0.8713 (mtp180) cc_final: 0.8353 (mtp180) outliers start: 18 outliers final: 13 residues processed: 178 average time/residue: 0.2399 time to fit residues: 53.4772 Evaluate side-chains 167 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 87 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 226 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN C 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114378 restraints weight = 10073.546| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.22 r_work: 0.3081 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7323 Z= 0.280 Angle : 0.603 11.233 9858 Z= 0.304 Chirality : 0.047 0.191 1113 Planarity : 0.004 0.037 1251 Dihedral : 11.758 158.300 1077 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.32 % Allowed : 18.19 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.26), residues: 903 helix: -1.69 (0.23), residues: 426 sheet: 0.63 (0.37), residues: 162 loop : -2.15 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 291 PHE 0.026 0.002 PHE C 89 TYR 0.007 0.001 TYR A 151 ARG 0.003 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.752 Fit side-chains REVERT: A 71 ASP cc_start: 0.6463 (m-30) cc_final: 0.6078 (t0) REVERT: A 110 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8424 (tttm) REVERT: A 186 ASP cc_start: 0.8443 (m-30) cc_final: 0.8081 (p0) REVERT: A 304 ARG cc_start: 0.8001 (ptt90) cc_final: 0.7645 (ptt90) REVERT: B 72 LYS cc_start: 0.8063 (ptmt) cc_final: 0.7845 (ttpp) REVERT: B 244 MET cc_start: 0.8511 (ptp) cc_final: 0.8258 (tmm) REVERT: C 61 ASN cc_start: 0.7425 (m-40) cc_final: 0.7162 (m-40) REVERT: C 205 TYR cc_start: 0.8780 (m-80) cc_final: 0.8226 (m-80) REVERT: C 286 LYS cc_start: 0.7876 (pttt) cc_final: 0.7595 (ptmt) outliers start: 25 outliers final: 20 residues processed: 174 average time/residue: 0.2400 time to fit residues: 52.6842 Evaluate side-chains 174 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 179 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 87 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 243 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 32 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN B 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115572 restraints weight = 10102.701| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.26 r_work: 0.3093 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4351 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= 0.140 Angle : 0.495 10.822 9858 Z= 0.255 Chirality : 0.044 0.169 1113 Planarity : 0.003 0.024 1251 Dihedral : 11.569 157.384 1077 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.19 % Allowed : 17.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.26), residues: 903 helix: -1.28 (0.24), residues: 420 sheet: 0.75 (0.37), residues: 162 loop : -2.01 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 181 PHE 0.021 0.001 PHE C 89 TYR 0.004 0.001 TYR B 151 ARG 0.003 0.000 ARG B 252 *********************** 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: 24 poor density : 163 time to evaluate : 0.888 Fit side-chains REVERT: A 71 ASP cc_start: 0.6502 (m-30) cc_final: 0.6150 (t0) REVERT: A 110 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8451 (tttm) REVERT: A 186 ASP cc_start: 0.8385 (m-30) cc_final: 0.8058 (p0) REVERT: A 304 ARG cc_start: 0.7991 (ptt90) cc_final: 0.7654 (ptt90) REVERT: B 72 LYS cc_start: 0.8023 (ptmt) cc_final: 0.7783 (ttpp) REVERT: B 244 MET cc_start: 0.8429 (ptp) cc_final: 0.8161 (tmm) REVERT: B 286 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7520 (pttm) REVERT: C 52 GLN cc_start: 0.7942 (tt0) cc_final: 0.7562 (tt0) REVERT: C 57 ARG cc_start: 0.7786 (mtp180) cc_final: 0.6907 (ptm160) REVERT: C 61 ASN cc_start: 0.7477 (m-40) cc_final: 0.7163 (m-40) REVERT: C 175 ASP cc_start: 0.7784 (m-30) cc_final: 0.7497 (m-30) REVERT: C 205 TYR cc_start: 0.8752 (m-80) cc_final: 0.8132 (m-80) REVERT: C 231 VAL cc_start: 0.8611 (t) cc_final: 0.8307 (m) REVERT: C 286 LYS cc_start: 0.7768 (pttt) cc_final: 0.7511 (ptmt) REVERT: C 300 ARG cc_start: 0.8732 (mtp180) cc_final: 0.8371 (mtp180) outliers start: 24 outliers final: 17 residues processed: 179 average time/residue: 0.2416 time to fit residues: 54.8112 Evaluate side-chains 180 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 87 THR 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 226 MET Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 106 GLN A 178 ASN C 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112727 restraints weight = 10208.115| |-----------------------------------------------------------------------------| r_work (start): 0.3180 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: 4.79 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7323 Z= 0.279 Angle : 0.608 11.472 9858 Z= 0.306 Chirality : 0.047 0.189 1113 Planarity : 0.004 0.039 1251 Dihedral : 11.810 159.210 1077 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.72 % Allowed : 16.73 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.26), residues: 903 helix: -1.48 (0.23), residues: 426 sheet: 0.77 (0.37), residues: 162 loop : -2.06 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 291 PHE 0.024 0.002 PHE B 89 TYR 0.006 0.001 TYR B 205 ARG 0.003 0.000 ARG C 192 *********************** 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 187 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.817 Fit side-chains REVERT: A 71 ASP cc_start: 0.6532 (m-30) cc_final: 0.6141 (t0) REVERT: A 110 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8363 (tttm) REVERT: A 186 ASP cc_start: 0.8481 (m-30) cc_final: 0.8067 (p0) REVERT: A 304 ARG cc_start: 0.7991 (ptt90) cc_final: 0.7601 (ptt180) REVERT: B 72 LYS cc_start: 0.8009 (ptmt) cc_final: 0.7705 (ttpp) REVERT: B 244 MET cc_start: 0.8533 (ptp) cc_final: 0.8229 (tmm) REVERT: C 23 ASP cc_start: 0.8138 (p0) cc_final: 0.7831 (t70) REVERT: C 25 ASP cc_start: 0.7001 (m-30) cc_final: 0.6482 (m-30) REVERT: C 52 GLN cc_start: 0.7990 (tt0) cc_final: 0.7625 (tt0) REVERT: C 57 ARG cc_start: 0.7751 (mtp180) cc_final: 0.6949 (ptm160) REVERT: C 205 TYR cc_start: 0.8812 (m-80) cc_final: 0.8225 (m-80) REVERT: C 231 VAL cc_start: 0.8619 (t) cc_final: 0.8288 (m) REVERT: C 286 LYS cc_start: 0.7964 (pttt) cc_final: 0.7614 (ptmt) REVERT: C 300 ARG cc_start: 0.8756 (mtp180) cc_final: 0.8181 (mtp180) outliers start: 28 outliers final: 22 residues processed: 178 average time/residue: 0.2402 time to fit residues: 54.0747 Evaluate side-chains 181 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 179 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 87 THR 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 185 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117116 restraints weight = 10160.815| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.23 r_work: 0.3130 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4519 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= 0.128 Angle : 0.489 10.714 9858 Z= 0.251 Chirality : 0.044 0.166 1113 Planarity : 0.003 0.024 1251 Dihedral : 11.508 157.739 1077 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.39 % Allowed : 18.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 903 helix: -1.05 (0.24), residues: 420 sheet: 0.87 (0.38), residues: 162 loop : -1.93 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.020 0.001 PHE C 89 TYR 0.013 0.001 TYR A 151 ARG 0.002 0.000 ARG C 192 ********************** 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 188 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.762 Fit side-chains REVERT: A 71 ASP cc_start: 0.6529 (m-30) cc_final: 0.6221 (t0) REVERT: A 110 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8371 (tttm) REVERT: A 186 ASP cc_start: 0.8390 (m-30) cc_final: 0.8078 (p0) REVERT: A 304 ARG cc_start: 0.7964 (ptt90) cc_final: 0.7631 (ptt90) REVERT: B 71 ASP cc_start: 0.7456 (m-30) cc_final: 0.7060 (t0) REVERT: B 72 LYS cc_start: 0.7993 (ptmt) cc_final: 0.7715 (ttpp) REVERT: B 244 MET cc_start: 0.8435 (ptp) cc_final: 0.8166 (tmm) REVERT: B 286 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7492 (pttm) REVERT: C 23 ASP cc_start: 0.8110 (p0) cc_final: 0.7822 (t70) REVERT: C 57 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7025 (ptm160) REVERT: C 175 ASP cc_start: 0.7681 (m-30) cc_final: 0.7424 (m-30) REVERT: C 204 ASP cc_start: 0.8269 (m-30) cc_final: 0.7926 (m-30) REVERT: C 205 TYR cc_start: 0.8738 (m-80) cc_final: 0.8094 (m-80) REVERT: C 231 VAL cc_start: 0.8626 (t) cc_final: 0.8305 (m) REVERT: C 236 ARG cc_start: 0.6299 (ttm170) cc_final: 0.5119 (tpt170) REVERT: C 300 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8319 (mtp180) outliers start: 18 outliers final: 16 residues processed: 181 average time/residue: 0.2449 time to fit residues: 55.5421 Evaluate side-chains 180 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 267 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 106 GLN A 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111153 restraints weight = 10165.940| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.22 r_work: 0.3077 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4490 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= 0.216 Angle : 0.554 11.790 9858 Z= 0.280 Chirality : 0.046 0.181 1113 Planarity : 0.003 0.030 1251 Dihedral : 11.621 158.065 1077 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.39 % Allowed : 18.99 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.26), residues: 903 helix: -1.09 (0.24), residues: 423 sheet: 0.84 (0.38), residues: 162 loop : -1.91 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 30 PHE 0.022 0.002 PHE B 128 TYR 0.012 0.001 TYR A 151 ARG 0.003 0.000 ARG C 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4341.04 seconds wall clock time: 74 minutes 55.15 seconds (4495.15 seconds total)