Starting phenix.real_space_refine on Wed Feb 12 05:48:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cgy_30366/02_2025/7cgy_30366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cgy_30366/02_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_30366/02_2025/7cgy_30366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cgy_30366/02_2025/7cgy_30366.map" model { file = "/net/cci-nas-00/data/ceres_data/7cgy_30366/02_2025/7cgy_30366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cgy_30366/02_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-5592/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: 5.47, per 1000 atoms: 0.76 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 2.01 Time building geometry restraints manager: 2.03 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: 3.530 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.640 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.070 ------------------------------------------------------------------------------- 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 : 0.872 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: 0.2830 time to fit residues: 90.0425 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 : 0.743 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.147735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120626 restraints weight = 9874.424| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.26 r_work: 0.3104 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.6349 (m-30) cc_final: 0.6123 (t0) REVERT: A 186 ASP cc_start: 0.8433 (m-30) cc_final: 0.8048 (p0) REVERT: A 211 HIS cc_start: 0.8102 (t-170) cc_final: 0.7885 (t-170) REVERT: A 241 GLU cc_start: 0.7278 (pt0) cc_final: 0.7076 (tt0) REVERT: A 304 ARG cc_start: 0.7766 (ptt90) cc_final: 0.7401 (ptt90) REVERT: B 49 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7878 (ttmm) REVERT: B 71 ASP cc_start: 0.7577 (m-30) cc_final: 0.7253 (t0) REVERT: B 72 LYS cc_start: 0.8079 (ptmt) cc_final: 0.7827 (ttpp) REVERT: B 172 ASP cc_start: 0.7031 (m-30) cc_final: 0.6736 (m-30) REVERT: B 241 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 242 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8092 (ttp-170) REVERT: B 244 MET cc_start: 0.8264 (ptp) cc_final: 0.7575 (tmm) REVERT: B 252 ARG cc_start: 0.7577 (tpt90) cc_final: 0.7174 (tpt-90) REVERT: B 286 LYS cc_start: 0.7844 (pttt) cc_final: 0.7360 (pttm) REVERT: C 41 LYS cc_start: 0.6828 (mtpt) cc_final: 0.6088 (tptt) REVERT: C 107 GLU cc_start: 0.7851 (tp30) cc_final: 0.7627 (tp30) REVERT: C 116 ILE cc_start: 0.8763 (mt) cc_final: 0.8510 (mm) REVERT: C 123 GLU cc_start: 0.8534 (tt0) cc_final: 0.8185 (tt0) REVERT: C 175 ASP cc_start: 0.8104 (m-30) cc_final: 0.7819 (m-30) REVERT: C 241 GLU cc_start: 0.7987 (tt0) cc_final: 0.7725 (tt0) REVERT: C 244 MET cc_start: 0.8097 (ptt) cc_final: 0.7796 (tmm) REVERT: C 286 LYS cc_start: 0.7602 (pttt) cc_final: 0.7118 (ptmt) REVERT: C 300 ARG cc_start: 0.8785 (mtp180) cc_final: 0.8257 (mtp180) outliers start: 15 outliers final: 10 residues processed: 208 average time/residue: 0.2706 time to fit residues: 69.4556 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 : 0.813 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 268 ASN C 30 HIS C 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120212 restraints weight = 9993.779| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.28 r_work: 0.3156 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7323 Z= 0.116 Angle : 0.472 6.777 9858 Z= 0.249 Chirality : 0.043 0.154 1113 Planarity : 0.003 0.027 1251 Dihedral : 11.607 146.660 1081 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.86 % Allowed : 15.41 % Favored : 82.74 % 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: -2.97 (0.25), residues: 903 helix: -2.38 (0.21), residues: 423 sheet: 0.00 (0.34), residues: 174 loop : -2.27 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 30 PHE 0.019 0.001 PHE B 128 TYR 0.006 0.001 TYR C 205 ARG 0.003 0.000 ARG B 192 *********************** 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 198 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.6500 (m-30) cc_final: 0.6175 (t0) REVERT: A 110 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8423 (tttm) REVERT: A 186 ASP cc_start: 0.8367 (m-30) cc_final: 0.8077 (p0) REVERT: A 211 HIS cc_start: 0.8082 (t-170) cc_final: 0.7806 (t-170) REVERT: A 241 GLU cc_start: 0.7640 (pt0) cc_final: 0.7409 (tt0) REVERT: A 304 ARG cc_start: 0.7870 (ptt90) cc_final: 0.7480 (ptt90) REVERT: A 320 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6663 (mt-10) REVERT: B 71 ASP cc_start: 0.7556 (m-30) cc_final: 0.7136 (t0) REVERT: B 72 LYS cc_start: 0.7989 (ptmt) cc_final: 0.7707 (ttpp) REVERT: B 241 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7888 (mm-30) REVERT: B 244 MET cc_start: 0.8293 (ptp) cc_final: 0.7808 (tmm) REVERT: B 252 ARG cc_start: 0.7720 (tpt90) cc_final: 0.7364 (ttt90) REVERT: C 123 GLU cc_start: 0.8515 (tt0) cc_final: 0.8247 (tt0) REVERT: C 175 ASP cc_start: 0.8008 (m-30) cc_final: 0.7690 (m-30) REVERT: C 286 LYS cc_start: 0.7674 (pttt) cc_final: 0.7154 (ptmt) REVERT: C 300 ARG cc_start: 0.8841 (mtp180) cc_final: 0.8264 (mtp180) outliers start: 14 outliers final: 10 residues processed: 192 average time/residue: 0.2631 time to fit residues: 62.8905 Evaluate side-chains 168 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 267 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 249 MET 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: 7.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.0000 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 268 ASN B 100 HIS C 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117178 restraints weight = 10124.725| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.27 r_work: 0.3063 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3672 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= 0.185 Angle : 0.517 6.422 9858 Z= 0.271 Chirality : 0.045 0.173 1113 Planarity : 0.003 0.031 1251 Dihedral : 11.520 151.792 1077 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.92 % Allowed : 15.54 % Favored : 81.54 % 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: -2.69 (0.25), residues: 903 helix: -2.10 (0.22), residues: 426 sheet: 0.26 (0.35), residues: 168 loop : -2.25 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 30 PHE 0.022 0.002 PHE B 128 TYR 0.009 0.001 TYR A 151 ARG 0.002 0.000 ARG A 176 *********************** 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 178 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.803 Fit side-chains REVERT: A 71 ASP cc_start: 0.6512 (m-30) cc_final: 0.6093 (t0) REVERT: A 110 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8415 (tttm) REVERT: A 186 ASP cc_start: 0.8390 (m-30) cc_final: 0.8073 (p0) REVERT: A 200 MET cc_start: 0.8585 (tpt) cc_final: 0.8302 (tpt) REVERT: A 304 ARG cc_start: 0.7909 (ptt90) cc_final: 0.7549 (ptm-80) REVERT: A 320 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6584 (mt-10) REVERT: B 71 ASP cc_start: 0.7551 (m-30) cc_final: 0.7052 (t0) REVERT: B 72 LYS cc_start: 0.8003 (ptmt) cc_final: 0.7791 (ttpp) REVERT: B 242 ARG cc_start: 0.8889 (ttm170) cc_final: 0.8656 (ttt-90) REVERT: B 244 MET cc_start: 0.8441 (ptp) cc_final: 0.8167 (tmm) REVERT: B 252 ARG cc_start: 0.7771 (tpt90) cc_final: 0.7520 (ttt90) REVERT: B 286 LYS cc_start: 0.8084 (pttp) cc_final: 0.7392 (ptpt) REVERT: C 205 TYR cc_start: 0.8647 (m-80) cc_final: 0.7994 (m-80) REVERT: C 270 MET cc_start: 0.8355 (mtp) cc_final: 0.8139 (ttt) REVERT: C 286 LYS cc_start: 0.7812 (pttt) cc_final: 0.7461 (ptmt) outliers start: 22 outliers final: 15 residues processed: 171 average time/residue: 0.2676 time to fit residues: 57.0258 Evaluate side-chains 160 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 80 LEU 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 37 ILE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112830 restraints weight = 9926.214| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.24 r_work: 0.3046 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7323 Z= 0.265 Angle : 0.584 8.588 9858 Z= 0.301 Chirality : 0.047 0.195 1113 Planarity : 0.004 0.038 1251 Dihedral : 11.725 155.857 1077 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.32 % Allowed : 15.94 % Favored : 80.74 % 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: -2.58 (0.25), residues: 903 helix: -2.01 (0.22), residues: 429 sheet: 0.45 (0.35), residues: 162 loop : -2.24 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 211 PHE 0.023 0.002 PHE B 128 TYR 0.010 0.001 TYR A 151 ARG 0.004 0.000 ARG A 242 *********************** 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 175 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.905 Fit side-chains REVERT: A 71 ASP cc_start: 0.6502 (m-30) cc_final: 0.6067 (t0) REVERT: A 110 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8418 (tttm) REVERT: A 186 ASP cc_start: 0.8399 (m-30) cc_final: 0.8068 (p0) REVERT: A 304 ARG cc_start: 0.7996 (ptt90) cc_final: 0.7551 (ptt180) REVERT: B 72 LYS cc_start: 0.8006 (ptmt) cc_final: 0.7803 (ttpp) REVERT: B 200 MET cc_start: 0.8646 (tpt) cc_final: 0.8306 (tpt) REVERT: B 230 ARG cc_start: 0.8441 (ptm160) cc_final: 0.8079 (ptm-80) REVERT: B 244 MET cc_start: 0.8483 (ptp) cc_final: 0.8263 (tmm) REVERT: B 249 MET cc_start: 0.8284 (ptp) cc_final: 0.8054 (ttm) REVERT: B 252 ARG cc_start: 0.7858 (tpt90) cc_final: 0.7630 (ttt90) REVERT: B 286 LYS cc_start: 0.8002 (pttp) cc_final: 0.7309 (ptpt) REVERT: C 175 ASP cc_start: 0.7450 (m-30) cc_final: 0.7161 (m-30) REVERT: C 286 LYS cc_start: 0.7636 (pttt) cc_final: 0.7267 (ptmt) REVERT: C 312 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8412 (mp) outliers start: 25 outliers final: 20 residues processed: 166 average time/residue: 0.2559 time to fit residues: 53.6751 Evaluate side-chains 165 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 37 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 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 312 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 85 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 268 ASN B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117797 restraints weight = 10013.095| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.19 r_work: 0.3089 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4119 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= 0.196 Angle : 0.526 8.426 9858 Z= 0.271 Chirality : 0.045 0.180 1113 Planarity : 0.003 0.030 1251 Dihedral : 11.673 156.353 1077 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.05 % Allowed : 16.87 % 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: -2.34 (0.25), residues: 903 helix: -1.77 (0.23), residues: 429 sheet: 0.51 (0.35), residues: 162 loop : -2.17 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 211 PHE 0.025 0.002 PHE C 89 TYR 0.010 0.001 TYR A 151 ARG 0.002 0.000 ARG C 192 *********************** 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 177 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.878 Fit side-chains REVERT: A 71 ASP cc_start: 0.6488 (m-30) cc_final: 0.6149 (t0) REVERT: A 110 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8405 (tttm) REVERT: A 186 ASP cc_start: 0.8376 (m-30) cc_final: 0.8061 (p0) REVERT: A 259 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7045 (mt-10) REVERT: A 304 ARG cc_start: 0.7941 (ptt90) cc_final: 0.7546 (ptt90) REVERT: B 71 ASP cc_start: 0.7479 (m-30) cc_final: 0.7032 (t0) REVERT: B 72 LYS cc_start: 0.8033 (ptmt) cc_final: 0.7792 (ttpp) REVERT: B 230 ARG cc_start: 0.8403 (ptm160) cc_final: 0.8050 (ptm-80) REVERT: B 252 ARG cc_start: 0.7713 (tpt90) cc_final: 0.7497 (ttt90) REVERT: C 205 TYR cc_start: 0.8698 (m-80) cc_final: 0.8128 (m-80) REVERT: C 286 LYS cc_start: 0.7585 (pttt) cc_final: 0.7330 (pttm) REVERT: C 312 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8395 (mp) outliers start: 23 outliers final: 18 residues processed: 169 average time/residue: 0.2520 time to fit residues: 54.2483 Evaluate side-chains 167 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 80 LEU 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 37 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117241 restraints weight = 9973.787| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.22 r_work: 0.3058 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: 0.8250 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7323 Z= 0.146 Angle : 0.494 9.097 9858 Z= 0.254 Chirality : 0.044 0.172 1113 Planarity : 0.003 0.025 1251 Dihedral : 11.531 155.676 1077 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.24 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: -2.02 (0.26), residues: 903 helix: -1.43 (0.24), residues: 423 sheet: 0.56 (0.36), residues: 162 loop : -2.05 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 211 PHE 0.022 0.001 PHE C 89 TYR 0.011 0.001 TYR A 151 ARG 0.002 0.000 ARG B 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 199 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.855 Fit side-chains REVERT: A 71 ASP cc_start: 0.6477 (m-30) cc_final: 0.6141 (t0) REVERT: A 110 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8396 (tttm) REVERT: A 186 ASP cc_start: 0.8323 (m-30) cc_final: 0.8001 (p0) REVERT: A 211 HIS cc_start: 0.8037 (t-170) cc_final: 0.7824 (t-170) REVERT: A 304 ARG cc_start: 0.7906 (ptt90) cc_final: 0.7519 (ptt90) REVERT: B 71 ASP cc_start: 0.7474 (m-30) cc_final: 0.7046 (t0) REVERT: B 72 LYS cc_start: 0.8069 (ptmt) cc_final: 0.7861 (ttpp) REVERT: B 230 ARG cc_start: 0.8335 (ptm160) cc_final: 0.7986 (ptm-80) REVERT: B 252 ARG cc_start: 0.7599 (tpt90) cc_final: 0.7248 (ttt90) REVERT: C 123 GLU cc_start: 0.8732 (tt0) cc_final: 0.8501 (tt0) REVERT: C 175 ASP cc_start: 0.7554 (m-30) cc_final: 0.7236 (m-30) REVERT: C 205 TYR cc_start: 0.8688 (m-80) cc_final: 0.8064 (m-80) REVERT: C 300 ARG cc_start: 0.8749 (mtp180) cc_final: 0.8396 (mtp180) REVERT: C 312 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (mp) outliers start: 26 outliers final: 19 residues processed: 188 average time/residue: 0.2430 time to fit residues: 57.9149 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 : 0.799 ------------------------------------------------------------------------------- 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 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 37 ILE 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 226 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 32 optimal weight: 0.0770 chunk 68 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 178 ASN A 268 ASN B 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120036 restraints weight = 10069.084| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.26 r_work: 0.3163 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4436 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= 0.122 Angle : 0.475 9.990 9858 Z= 0.245 Chirality : 0.044 0.164 1113 Planarity : 0.003 0.024 1251 Dihedral : 11.412 155.000 1077 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.79 % Allowed : 16.60 % 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 (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: -1.74 (0.26), residues: 903 helix: -1.18 (0.24), residues: 423 sheet: 0.59 (0.37), residues: 165 loop : -1.90 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS A 211 PHE 0.022 0.001 PHE C 89 TYR 0.019 0.001 TYR A 260 ARG 0.002 0.000 ARG B 192 *********************** 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: 21 poor density : 166 time to evaluate : 0.765 Fit side-chains REVERT: A 71 ASP cc_start: 0.6488 (m-30) cc_final: 0.6137 (t0) REVERT: A 110 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8419 (tttm) REVERT: A 186 ASP cc_start: 0.8346 (m-30) cc_final: 0.8027 (p0) REVERT: A 304 ARG cc_start: 0.7933 (ptt90) cc_final: 0.7584 (ptt90) REVERT: B 71 ASP cc_start: 0.7529 (m-30) cc_final: 0.7049 (t0) REVERT: B 72 LYS cc_start: 0.8054 (ptmt) cc_final: 0.7812 (ttpp) REVERT: B 230 ARG cc_start: 0.8295 (ptm160) cc_final: 0.7957 (ptm-80) REVERT: B 252 ARG cc_start: 0.7629 (tpt90) cc_final: 0.7352 (ttt90) REVERT: C 123 GLU cc_start: 0.8661 (tt0) cc_final: 0.8354 (tt0) REVERT: C 175 ASP cc_start: 0.7525 (m-30) cc_final: 0.7202 (m-30) REVERT: C 205 TYR cc_start: 0.8697 (m-80) cc_final: 0.8025 (m-80) REVERT: C 300 ARG cc_start: 0.8733 (mtp180) cc_final: 0.8345 (mtp180) REVERT: C 312 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8360 (mp) REVERT: C 320 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7349 (mt-10) outliers start: 21 outliers final: 18 residues processed: 180 average time/residue: 0.2389 time to fit residues: 54.3204 Evaluate side-chains 170 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 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 226 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.0870 chunk 65 optimal weight: 7.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121321 restraints weight = 10117.646| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.24 r_work: 0.3104 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4635 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= 0.108 Angle : 0.449 8.823 9858 Z= 0.234 Chirality : 0.043 0.155 1113 Planarity : 0.002 0.023 1251 Dihedral : 11.223 154.211 1077 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.39 % Allowed : 16.47 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.43 (0.27), residues: 903 helix: -0.88 (0.25), residues: 420 sheet: 0.67 (0.38), residues: 165 loop : -1.76 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 211 PHE 0.021 0.001 PHE C 89 TYR 0.006 0.001 TYR A 260 ARG 0.002 0.000 ARG A 230 *********************** 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 192 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.827 Fit side-chains REVERT: A 71 ASP cc_start: 0.6544 (m-30) cc_final: 0.6119 (t0) REVERT: A 110 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8405 (tttm) REVERT: A 182 ASP cc_start: 0.8219 (m-30) cc_final: 0.7680 (p0) REVERT: A 186 ASP cc_start: 0.8311 (m-30) cc_final: 0.8000 (p0) REVERT: A 304 ARG cc_start: 0.7890 (ptt90) cc_final: 0.7532 (ptt90) REVERT: B 71 ASP cc_start: 0.7510 (m-30) cc_final: 0.7048 (t0) REVERT: B 72 LYS cc_start: 0.7960 (ptmt) cc_final: 0.7704 (ttpp) REVERT: B 230 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7989 (ptm-80) REVERT: B 252 ARG cc_start: 0.7588 (tpt90) cc_final: 0.7091 (tpt-90) REVERT: B 304 ARG cc_start: 0.8349 (ptt90) cc_final: 0.8002 (ptt180) REVERT: C 25 ASP cc_start: 0.6734 (m-30) cc_final: 0.6121 (t70) REVERT: C 123 GLU cc_start: 0.8685 (tt0) cc_final: 0.8427 (tt0) REVERT: C 175 ASP cc_start: 0.7422 (m-30) cc_final: 0.7098 (m-30) REVERT: C 204 ASP cc_start: 0.8218 (m-30) cc_final: 0.7905 (m-30) REVERT: C 205 TYR cc_start: 0.8654 (m-80) cc_final: 0.7953 (m-80) REVERT: C 300 ARG cc_start: 0.8717 (mtp180) cc_final: 0.8332 (mtp180) REVERT: C 304 ARG cc_start: 0.8620 (ptt90) cc_final: 0.8197 (mtm-85) REVERT: C 312 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8309 (mp) REVERT: C 320 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7324 (mt-10) outliers start: 18 outliers final: 16 residues processed: 185 average time/residue: 0.2407 time to fit residues: 56.0023 Evaluate side-chains 183 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 87 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 297 SER Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119646 restraints weight = 10206.046| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.27 r_work: 0.3093 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4654 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= 0.118 Angle : 0.466 9.510 9858 Z= 0.239 Chirality : 0.044 0.158 1113 Planarity : 0.002 0.021 1251 Dihedral : 11.169 154.201 1077 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.26 % Allowed : 17.13 % 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 (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: -1.27 (0.27), residues: 903 helix: -0.76 (0.25), residues: 426 sheet: 0.68 (0.38), residues: 165 loop : -1.64 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 211 PHE 0.020 0.001 PHE B 128 TYR 0.008 0.001 TYR A 260 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 184 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.679 Fit side-chains REVERT: A 71 ASP cc_start: 0.6532 (m-30) cc_final: 0.6094 (t0) REVERT: A 110 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8409 (tttm) REVERT: A 182 ASP cc_start: 0.8202 (m-30) cc_final: 0.7667 (p0) REVERT: A 186 ASP cc_start: 0.8315 (m-30) cc_final: 0.8025 (p0) REVERT: A 241 GLU cc_start: 0.8156 (pt0) cc_final: 0.7721 (tt0) REVERT: A 252 ARG cc_start: 0.7627 (mmm160) cc_final: 0.7048 (tpt-90) REVERT: A 304 ARG cc_start: 0.7900 (ptt90) cc_final: 0.7546 (ptt90) REVERT: B 29 LYS cc_start: 0.7932 (ptpp) cc_final: 0.7694 (pptt) REVERT: B 71 ASP cc_start: 0.7518 (m-30) cc_final: 0.7099 (t0) REVERT: B 72 LYS cc_start: 0.7966 (ptmt) cc_final: 0.7695 (ttpp) REVERT: B 230 ARG cc_start: 0.8314 (ptm160) cc_final: 0.7984 (ptm-80) REVERT: B 252 ARG cc_start: 0.7598 (tpt90) cc_final: 0.7136 (tpt-90) REVERT: B 304 ARG cc_start: 0.8353 (ptt90) cc_final: 0.8011 (ptt180) REVERT: C 25 ASP cc_start: 0.6685 (m-30) cc_final: 0.6181 (t70) REVERT: C 123 GLU cc_start: 0.8669 (tt0) cc_final: 0.8404 (tt0) REVERT: C 204 ASP cc_start: 0.8216 (m-30) cc_final: 0.7770 (m-30) REVERT: C 205 TYR cc_start: 0.8671 (m-80) cc_final: 0.7945 (m-80) REVERT: C 300 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8366 (mtp180) REVERT: C 304 ARG cc_start: 0.8607 (ptt90) cc_final: 0.8215 (mtm-85) REVERT: C 312 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8382 (mt) REVERT: C 320 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7306 (mt-10) outliers start: 17 outliers final: 15 residues processed: 177 average time/residue: 0.2544 time to fit residues: 56.5975 Evaluate side-chains 173 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 185 LEU Chi-restraints excluded: chain B residue 267 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 226 MET Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115235 restraints weight = 10113.957| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.24 r_work: 0.3160 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7323 Z= 0.196 Angle : 0.530 10.130 9858 Z= 0.271 Chirality : 0.047 0.377 1113 Planarity : 0.003 0.026 1251 Dihedral : 11.418 156.495 1077 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.66 % Allowed : 17.13 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.27), residues: 903 helix: -0.84 (0.25), residues: 423 sheet: 0.71 (0.37), residues: 162 loop : -1.71 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 211 PHE 0.021 0.002 PHE B 128 TYR 0.005 0.001 TYR C 91 ARG 0.002 0.000 ARG C 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4324.70 seconds wall clock time: 77 minutes 18.45 seconds (4638.45 seconds total)