Starting phenix.real_space_refine on Wed Mar 4 06:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o0y_12683/03_2026/7o0y_12683.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o0y_12683/03_2026/7o0y_12683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o0y_12683/03_2026/7o0y_12683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o0y_12683/03_2026/7o0y_12683.map" model { file = "/net/cci-nas-00/data/ceres_data/7o0y_12683/03_2026/7o0y_12683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o0y_12683/03_2026/7o0y_12683.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 37 5.16 5 C 7466 2.51 5 N 2038 2.21 5 O 2109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3140 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain: "B" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2303 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.48, per 1000 atoms: 0.21 Number of scatterers: 11651 At special positions: 0 Unit cell: (86.184, 164.16, 138.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 Mg 1 11.99 O 2109 8.00 N 2038 7.00 C 7466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 525.3 milliseconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 11 sheets defined 48.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.256A pdb=" N GLY A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.773A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.529A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 removed outlier: 4.000A pdb=" N SER B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.856A pdb=" N GLY B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.527A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.735A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.730A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.952A pdb=" N ALA B 193 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 232 through 244 removed outlier: 4.237A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.885A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.682A pdb=" N GLU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 3.717A pdb=" N SER C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.547A pdb=" N ARG C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.558A pdb=" N VAL C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 178 removed outlier: 3.718A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.776A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.826A pdb=" N ALA C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.687A pdb=" N GLU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.853A pdb=" N GLU C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.626A pdb=" N ILE D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.500A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 Processing helix chain 'D' and resid 57 through 75 Proline residue: D 67 - end of helix removed outlier: 3.545A pdb=" N TYR D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.721A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.104A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 146 through 167 removed outlier: 3.544A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.546A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.567A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.527A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.626A pdb=" N LEU D 239 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.639A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.562A pdb=" N ILE E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 7' Processing helix chain 'E' and resid 7 through 16 Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.613A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.626A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.917A pdb=" N THR E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.665A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.753A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.555A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 208 through 213 removed outlier: 3.590A pdb=" N LEU E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.586A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 3.908A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.102A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.750A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE A 199 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.475A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.663A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 7.627A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 12 removed outlier: 3.684A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER B 10 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS B 20 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG B 12 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 18 " --> pdb=" O ARG B 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.405A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 249 removed outlier: 4.057A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 25 removed outlier: 5.646A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 8 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.348A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP C 153 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 79 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.974A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 225 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1392 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: 1.62 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3399 1.33 - 1.45: 1837 1.45 - 1.57: 6568 1.57 - 1.69: 3 1.69 - 1.81: 64 Bond restraints: 11871 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.595 -0.070 2.10e-02 2.27e+03 1.11e+01 bond pdb=" CB ASN B 261 " pdb=" CG ASN B 261 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.20e+00 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.600 -0.060 2.70e-02 1.37e+03 5.00e+00 bond pdb=" C ILE E 51 " pdb=" N PRO E 52 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.25e-02 6.40e+03 3.78e+00 bond pdb=" CG LEU D 21 " pdb=" CD1 LEU D 21 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.69e+00 ... (remaining 11866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 15916 3.91 - 7.83: 174 7.83 - 11.74: 22 11.74 - 15.66: 2 15.66 - 19.57: 2 Bond angle restraints: 16116 Sorted by residual: angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 135.87 -19.57 3.50e+00 8.16e-02 3.13e+01 angle pdb=" CA MET A 105 " pdb=" CB MET A 105 " pdb=" CG MET A 105 " ideal model delta sigma weight residual 114.10 124.00 -9.90 2.00e+00 2.50e-01 2.45e+01 angle pdb=" C VAL B 260 " pdb=" N ASN B 261 " pdb=" CA ASN B 261 " ideal model delta sigma weight residual 122.08 129.22 -7.14 1.47e+00 4.63e-01 2.36e+01 angle pdb=" CA ASN B 261 " pdb=" CB ASN B 261 " pdb=" CG ASN B 261 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" CA LEU A 89 " pdb=" CB LEU A 89 " pdb=" CG LEU A 89 " ideal model delta sigma weight residual 116.30 132.73 -16.43 3.50e+00 8.16e-02 2.20e+01 ... (remaining 16111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6262 17.62 - 35.25: 606 35.25 - 52.87: 132 52.87 - 70.49: 19 70.49 - 88.12: 2 Dihedral angle restraints: 7021 sinusoidal: 2752 harmonic: 4269 Sorted by residual: dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual 180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PRO B 277 " pdb=" C PRO B 277 " pdb=" N GLU B 278 " pdb=" CA GLU B 278 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA VAL C 83 " pdb=" C VAL C 83 " pdb=" N THR C 84 " pdb=" CA THR C 84 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 7018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1728 0.106 - 0.213: 120 0.213 - 0.319: 12 0.319 - 0.426: 0 0.426 - 0.532: 1 Chirality restraints: 1861 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA ASP A 182 " pdb=" N ASP A 182 " pdb=" C ASP A 182 " pdb=" CB ASP A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL D 116 " pdb=" CA VAL D 116 " pdb=" CG1 VAL D 116 " pdb=" CG2 VAL D 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1858 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO D 67 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " -0.049 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO E 67 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO E 210 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " 0.038 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 53 2.47 - 3.07: 6413 3.07 - 3.68: 18333 3.68 - 4.29: 27148 4.29 - 4.90: 45133 Nonbonded interactions: 97080 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 1.857 2.170 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 2.087 2.170 nonbonded pdb=" OD1 ASP A 363 " pdb="MG MG A 501 " model vdw 2.287 2.170 nonbonded pdb=" O TRP E 259 " pdb=" OG SER E 263 " model vdw 2.327 3.040 nonbonded pdb=" OE1 GLU B 218 " pdb=" OH TYR B 294 " model vdw 2.344 3.040 ... (remaining 97075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 2 through 299) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.006 0.083 11871 Z= 0.283 Angle : 1.039 19.574 16116 Z= 0.538 Chirality : 0.060 0.532 1861 Planarity : 0.007 0.075 2063 Dihedral : 14.350 88.116 4299 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.41 % Allowed : 8.17 % Favored : 91.42 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.81 (0.15), residues: 1498 helix: -4.65 (0.07), residues: 657 sheet: -3.40 (0.31), residues: 179 loop : -2.92 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 360 TYR 0.016 0.002 TYR A 204 PHE 0.024 0.002 PHE E 64 TRP 0.011 0.002 TRP C 240 HIS 0.009 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00641 (11871) covalent geometry : angle 1.03888 (16116) hydrogen bonds : bond 0.29887 ( 498) hydrogen bonds : angle 11.30550 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9312 (mmtt) cc_final: 0.9085 (tppt) REVERT: A 305 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8760 (mtmt) REVERT: B 287 LEU cc_start: 0.9376 (tp) cc_final: 0.9084 (tt) REVERT: C 47 LYS cc_start: 0.8931 (mttt) cc_final: 0.8623 (mttp) REVERT: C 61 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8225 (mtpp) REVERT: C 133 MET cc_start: 0.8952 (mtm) cc_final: 0.8678 (ttm) outliers start: 5 outliers final: 2 residues processed: 111 average time/residue: 0.1121 time to fit residues: 17.7321 Evaluate side-chains 80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 188 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS A 190 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN A 341 GLN B 11 GLN B 20 HIS B 25 ASN C 82 ASN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN D 225 ASN E 225 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054469 restraints weight = 36408.204| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.18 r_work: 0.2890 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11871 Z= 0.121 Angle : 0.574 8.325 16116 Z= 0.298 Chirality : 0.042 0.168 1861 Planarity : 0.005 0.042 2063 Dihedral : 5.263 50.307 1645 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.74 % Allowed : 12.50 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.18), residues: 1498 helix: -2.20 (0.15), residues: 669 sheet: -3.21 (0.32), residues: 176 loop : -2.48 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 138 TYR 0.011 0.001 TYR B 86 PHE 0.011 0.001 PHE E 157 TRP 0.010 0.001 TRP D 253 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00263 (11871) covalent geometry : angle 0.57393 (16116) hydrogen bonds : bond 0.03645 ( 498) hydrogen bonds : angle 5.13737 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8337 (m100) cc_final: 0.7743 (m100) REVERT: A 235 LYS cc_start: 0.9367 (mmtt) cc_final: 0.9114 (tppp) REVERT: A 305 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8660 (mtmt) REVERT: B 295 MET cc_start: 0.9028 (mmp) cc_final: 0.8824 (mmp) REVERT: C 47 LYS cc_start: 0.9097 (mttt) cc_final: 0.8812 (mttp) REVERT: C 287 LEU cc_start: 0.9387 (tp) cc_final: 0.9091 (tp) REVERT: D 201 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 219 ASP cc_start: 0.8863 (m-30) cc_final: 0.8434 (m-30) REVERT: D 244 ASP cc_start: 0.8535 (m-30) cc_final: 0.8331 (m-30) REVERT: E 3 GLN cc_start: 0.8384 (mt0) cc_final: 0.7866 (mt0) REVERT: E 221 TYR cc_start: 0.9560 (t80) cc_final: 0.9308 (t80) outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 0.1054 time to fit residues: 14.4546 Evaluate side-chains 80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 114 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 82 ASN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053374 restraints weight = 36592.873| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.17 r_work: 0.2881 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11871 Z= 0.177 Angle : 0.580 7.616 16116 Z= 0.296 Chirality : 0.043 0.159 1861 Planarity : 0.004 0.033 2063 Dihedral : 4.879 30.140 1643 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.74 % Allowed : 14.05 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.20), residues: 1498 helix: -0.65 (0.19), residues: 683 sheet: -2.97 (0.33), residues: 176 loop : -2.43 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 17 TYR 0.011 0.001 TYR B 86 PHE 0.013 0.001 PHE E 157 TRP 0.012 0.001 TRP C 236 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00399 (11871) covalent geometry : angle 0.58036 (16116) hydrogen bonds : bond 0.03280 ( 498) hydrogen bonds : angle 4.52973 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8414 (m100) cc_final: 0.7788 (m100) REVERT: A 235 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9202 (tppp) REVERT: A 305 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8761 (mtmt) REVERT: B 295 MET cc_start: 0.9020 (mmp) cc_final: 0.8793 (mmp) REVERT: C 47 LYS cc_start: 0.9040 (mttt) cc_final: 0.8751 (mttm) REVERT: D 201 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8551 (mm-30) REVERT: D 219 ASP cc_start: 0.8882 (m-30) cc_final: 0.8435 (m-30) REVERT: D 244 ASP cc_start: 0.8573 (m-30) cc_final: 0.8346 (m-30) REVERT: E 3 GLN cc_start: 0.8541 (mt0) cc_final: 0.8048 (mt0) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.0946 time to fit residues: 11.1303 Evaluate side-chains 72 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 114 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.069694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051637 restraints weight = 36911.405| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.15 r_work: 0.2811 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11871 Z= 0.225 Angle : 0.605 7.375 16116 Z= 0.306 Chirality : 0.044 0.157 1861 Planarity : 0.003 0.032 2063 Dihedral : 4.870 29.991 1643 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.14 % Allowed : 15.60 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.22), residues: 1498 helix: 0.10 (0.20), residues: 688 sheet: -2.82 (0.33), residues: 191 loop : -2.24 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.011 0.001 TYR B 86 PHE 0.015 0.001 PHE E 157 TRP 0.007 0.001 TRP C 240 HIS 0.003 0.001 HIS C 263 Details of bonding type rmsd covalent geometry : bond 0.00507 (11871) covalent geometry : angle 0.60495 (16116) hydrogen bonds : bond 0.03265 ( 498) hydrogen bonds : angle 4.34608 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8461 (m100) cc_final: 0.7818 (m100) REVERT: A 305 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8769 (mtmt) REVERT: B 1 MET cc_start: 0.6701 (tpt) cc_final: 0.6185 (tpt) REVERT: B 16 MET cc_start: 0.8414 (pmm) cc_final: 0.8173 (pmm) REVERT: D 201 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8617 (mm-30) REVERT: D 219 ASP cc_start: 0.8919 (m-30) cc_final: 0.8422 (m-30) outliers start: 14 outliers final: 6 residues processed: 85 average time/residue: 0.0949 time to fit residues: 12.2242 Evaluate side-chains 73 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 32 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 49 optimal weight: 0.2980 chunk 126 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 54 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.072944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.054968 restraints weight = 36082.212| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.21 r_work: 0.2917 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11871 Z= 0.105 Angle : 0.529 8.560 16116 Z= 0.267 Chirality : 0.041 0.151 1861 Planarity : 0.003 0.031 2063 Dihedral : 4.572 29.849 1643 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.14 % Allowed : 16.67 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.22), residues: 1498 helix: 0.72 (0.21), residues: 690 sheet: -2.84 (0.34), residues: 191 loop : -2.06 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.014 0.001 TYR B 86 PHE 0.011 0.001 PHE E 157 TRP 0.008 0.001 TRP A 98 HIS 0.002 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00238 (11871) covalent geometry : angle 0.52924 (16116) hydrogen bonds : bond 0.02728 ( 498) hydrogen bonds : angle 3.93333 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8453 (m100) cc_final: 0.7831 (m100) REVERT: A 125 MET cc_start: 0.8842 (mtt) cc_final: 0.8378 (mtm) REVERT: A 174 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6798 (m-70) REVERT: A 305 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8744 (mtmm) REVERT: B 1 MET cc_start: 0.6315 (tpt) cc_final: 0.5741 (tpt) REVERT: C 295 MET cc_start: 0.8927 (mmm) cc_final: 0.8690 (mmm) REVERT: D 219 ASP cc_start: 0.8885 (m-30) cc_final: 0.8500 (m-30) REVERT: E 3 GLN cc_start: 0.8474 (mt0) cc_final: 0.7902 (mt0) outliers start: 14 outliers final: 5 residues processed: 88 average time/residue: 0.0928 time to fit residues: 12.3393 Evaluate side-chains 76 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 143 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.070860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053321 restraints weight = 36426.326| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.12 r_work: 0.2863 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11871 Z= 0.140 Angle : 0.550 10.801 16116 Z= 0.275 Chirality : 0.042 0.147 1861 Planarity : 0.003 0.031 2063 Dihedral : 4.516 29.664 1643 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.74 % Allowed : 17.08 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1498 helix: 0.98 (0.21), residues: 691 sheet: -2.70 (0.35), residues: 175 loop : -2.02 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.016 0.001 TYR B 86 PHE 0.012 0.001 PHE D 157 TRP 0.007 0.001 TRP A 98 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00318 (11871) covalent geometry : angle 0.55005 (16116) hydrogen bonds : bond 0.02819 ( 498) hydrogen bonds : angle 3.85922 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8470 (m100) cc_final: 0.7806 (m100) REVERT: A 174 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6738 (m-70) REVERT: A 305 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8722 (mtmm) REVERT: B 1 MET cc_start: 0.6320 (tpt) cc_final: 0.5750 (tpt) REVERT: B 181 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9174 (pt) REVERT: D 219 ASP cc_start: 0.8912 (m-30) cc_final: 0.8487 (m-30) REVERT: E 3 GLN cc_start: 0.8622 (mt0) cc_final: 0.8111 (mt0) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.0914 time to fit residues: 11.2584 Evaluate side-chains 77 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.068285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050273 restraints weight = 37082.129| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.12 r_work: 0.2795 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 11871 Z= 0.367 Angle : 0.731 10.503 16116 Z= 0.360 Chirality : 0.047 0.170 1861 Planarity : 0.004 0.062 2063 Dihedral : 4.979 29.969 1643 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.47 % Allowed : 16.91 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1498 helix: 0.84 (0.21), residues: 688 sheet: -2.76 (0.34), residues: 190 loop : -2.00 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.022 0.002 TYR B 86 PHE 0.019 0.002 PHE D 157 TRP 0.008 0.001 TRP D 37 HIS 0.004 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00826 (11871) covalent geometry : angle 0.73111 (16116) hydrogen bonds : bond 0.03560 ( 498) hydrogen bonds : angle 4.39111 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.8990 (mtt) cc_final: 0.8619 (mtm) REVERT: A 174 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6559 (m-70) REVERT: A 305 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8905 (mtmt) REVERT: B 1 MET cc_start: 0.6922 (tpt) cc_final: 0.6392 (tpt) REVERT: B 57 GLU cc_start: 0.7345 (tt0) cc_final: 0.6978 (tp30) REVERT: B 181 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9229 (pt) REVERT: C 38 ASN cc_start: 0.8311 (m110) cc_final: 0.8019 (m110) REVERT: C 46 MET cc_start: 0.8423 (tpp) cc_final: 0.8178 (tpp) REVERT: D 219 ASP cc_start: 0.8905 (m-30) cc_final: 0.8507 (m-30) REVERT: E 224 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9224 (pt) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 0.0912 time to fit residues: 12.0129 Evaluate side-chains 77 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 224 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 18 optimal weight: 0.0020 chunk 74 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.072421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054642 restraints weight = 36246.932| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.17 r_work: 0.2906 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11871 Z= 0.106 Angle : 0.549 10.486 16116 Z= 0.276 Chirality : 0.042 0.151 1861 Planarity : 0.003 0.034 2063 Dihedral : 4.590 30.149 1643 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.98 % Allowed : 17.73 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1498 helix: 1.26 (0.21), residues: 685 sheet: -2.69 (0.35), residues: 170 loop : -1.82 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.015 0.001 TYR B 86 PHE 0.013 0.001 PHE E 157 TRP 0.010 0.001 TRP D 253 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00238 (11871) covalent geometry : angle 0.54917 (16116) hydrogen bonds : bond 0.02697 ( 498) hydrogen bonds : angle 3.86088 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8470 (m100) cc_final: 0.7896 (m100) REVERT: A 125 MET cc_start: 0.8807 (mtt) cc_final: 0.8319 (mtm) REVERT: A 174 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6710 (m-70) REVERT: A 305 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8837 (mtmt) REVERT: B 1 MET cc_start: 0.6430 (tpt) cc_final: 0.5850 (tpt) REVERT: B 181 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9183 (pt) REVERT: C 46 MET cc_start: 0.8212 (tpp) cc_final: 0.7992 (tpp) REVERT: D 219 ASP cc_start: 0.8863 (m-30) cc_final: 0.8450 (m-30) REVERT: E 3 GLN cc_start: 0.8575 (mt0) cc_final: 0.8046 (mt0) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 0.0886 time to fit residues: 11.1067 Evaluate side-chains 75 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 229 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 4 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.053466 restraints weight = 36128.994| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.13 r_work: 0.2869 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11871 Z= 0.173 Angle : 0.576 10.421 16116 Z= 0.287 Chirality : 0.043 0.148 1861 Planarity : 0.003 0.037 2063 Dihedral : 4.586 29.626 1643 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.98 % Allowed : 17.65 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.23), residues: 1498 helix: 1.34 (0.21), residues: 684 sheet: -2.79 (0.34), residues: 183 loop : -1.75 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.020 0.001 TYR B 86 PHE 0.014 0.001 PHE E 157 TRP 0.007 0.001 TRP A 98 HIS 0.003 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00395 (11871) covalent geometry : angle 0.57642 (16116) hydrogen bonds : bond 0.02903 ( 498) hydrogen bonds : angle 3.91114 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8500 (m100) cc_final: 0.7879 (m100) REVERT: A 125 MET cc_start: 0.8899 (mtt) cc_final: 0.8479 (mtm) REVERT: A 174 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.6773 (m-70) REVERT: A 279 MET cc_start: 0.6638 (ptt) cc_final: 0.6433 (ptt) REVERT: A 305 LYS cc_start: 0.9241 (mmtt) cc_final: 0.8849 (mtmm) REVERT: B 1 MET cc_start: 0.6668 (tpt) cc_final: 0.6108 (tpt) REVERT: B 181 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9208 (pt) REVERT: C 46 MET cc_start: 0.8319 (tpp) cc_final: 0.8063 (tpp) REVERT: D 219 ASP cc_start: 0.8857 (m-30) cc_final: 0.8433 (m-30) REVERT: E 3 GLN cc_start: 0.8625 (mt0) cc_final: 0.8119 (mt0) REVERT: E 147 MET cc_start: 0.8376 (mmt) cc_final: 0.7987 (mmt) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 0.0879 time to fit residues: 10.4726 Evaluate side-chains 77 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 22 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054883 restraints weight = 36270.821| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.19 r_work: 0.2911 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11871 Z= 0.116 Angle : 0.541 10.327 16116 Z= 0.269 Chirality : 0.042 0.146 1861 Planarity : 0.003 0.032 2063 Dihedral : 4.447 29.788 1643 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.82 % Allowed : 17.97 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.23), residues: 1498 helix: 1.48 (0.21), residues: 684 sheet: -2.64 (0.35), residues: 181 loop : -1.71 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.017 0.001 TYR B 86 PHE 0.012 0.001 PHE E 157 TRP 0.008 0.001 TRP A 98 HIS 0.002 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00264 (11871) covalent geometry : angle 0.54085 (16116) hydrogen bonds : bond 0.02668 ( 498) hydrogen bonds : angle 3.74600 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8473 (m100) cc_final: 0.7883 (m100) REVERT: A 125 MET cc_start: 0.8832 (mtt) cc_final: 0.8380 (mtm) REVERT: A 174 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6753 (m-70) REVERT: A 305 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8817 (mtmt) REVERT: B 1 MET cc_start: 0.6501 (tpt) cc_final: 0.5961 (tpt) REVERT: B 181 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9184 (pt) REVERT: C 46 MET cc_start: 0.8263 (tpp) cc_final: 0.8025 (tpp) REVERT: D 219 ASP cc_start: 0.8862 (m-30) cc_final: 0.8444 (m-30) REVERT: E 3 GLN cc_start: 0.8609 (mt0) cc_final: 0.8036 (mt0) REVERT: E 147 MET cc_start: 0.8275 (mmt) cc_final: 0.7945 (mmt) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.0809 time to fit residues: 9.9253 Evaluate side-chains 78 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.072864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055208 restraints weight = 36220.497| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.13 r_work: 0.2916 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11871 Z= 0.118 Angle : 0.539 10.287 16116 Z= 0.268 Chirality : 0.042 0.145 1861 Planarity : 0.003 0.032 2063 Dihedral : 4.389 29.622 1643 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.82 % Allowed : 18.14 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1498 helix: 1.56 (0.21), residues: 684 sheet: -2.67 (0.34), residues: 194 loop : -1.64 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.017 0.001 TYR B 86 PHE 0.012 0.001 PHE E 157 TRP 0.009 0.001 TRP A 98 HIS 0.002 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00271 (11871) covalent geometry : angle 0.53901 (16116) hydrogen bonds : bond 0.02670 ( 498) hydrogen bonds : angle 3.69272 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2081.53 seconds wall clock time: 36 minutes 38.87 seconds (2198.87 seconds total)