Starting phenix.real_space_refine on Tue Jul 29 19:57:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o0y_12683/07_2025/7o0y_12683.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o0y_12683/07_2025/7o0y_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_12683/07_2025/7o0y_12683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o0y_12683/07_2025/7o0y_12683.map" model { file = "/net/cci-nas-00/data/ceres_data/7o0y_12683/07_2025/7o0y_12683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o0y_12683/07_2025/7o0y_12683.cif" } resolution = 3.3 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: 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.11, per 1000 atoms: 0.70 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: 2.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.76 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: 4.33 Time building geometry restraints manager: 3.11 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: 2.670 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.060 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.011 0.002 TRP C 240 HIS 0.009 0.001 HIS A 163 PHE 0.024 0.002 PHE E 64 TYR 0.016 0.002 TYR A 204 ARG 0.005 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.29887 ( 498) hydrogen bonds : angle 11.30550 ( 1392) covalent geometry : bond 0.00641 (11871) covalent geometry : angle 1.03888 (16116) *********************** 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 : 1.368 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: 0.8742 (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: 0.2643 time to fit residues: 41.7036 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 : 1.377 ------------------------------------------------------------------------------- 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 124 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN B 11 GLN B 20 HIS B 25 ASN B 270 GLN C 82 ASN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN D 225 ASN E 108 HIS E 225 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053017 restraints weight = 36460.292| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.17 r_work: 0.2865 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1755 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= 0.172 Angle : 0.603 8.137 16116 Z= 0.313 Chirality : 0.043 0.170 1861 Planarity : 0.005 0.041 2063 Dihedral : 5.323 51.588 1645 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.74 % Allowed : 12.91 % Favored : 86.36 % 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: -3.76 (0.18), residues: 1498 helix: -2.20 (0.15), residues: 669 sheet: -3.22 (0.33), residues: 171 loop : -2.46 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 253 HIS 0.004 0.001 HIS B 245 PHE 0.012 0.001 PHE E 157 TYR 0.013 0.001 TYR B 86 ARG 0.003 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 498) hydrogen bonds : angle 5.19382 ( 1392) covalent geometry : bond 0.00381 (11871) covalent geometry : angle 0.60338 (16116) *********************** 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 95 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8391 (m100) cc_final: 0.7796 (m100) REVERT: A 235 LYS cc_start: 0.9378 (mmtt) cc_final: 0.9139 (tppp) REVERT: A 305 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8736 (mtmt) REVERT: C 47 LYS cc_start: 0.9121 (mttt) cc_final: 0.8846 (mttp) REVERT: C 287 LEU cc_start: 0.9399 (tp) cc_final: 0.9109 (tp) REVERT: D 201 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8448 (mm-30) REVERT: D 219 ASP cc_start: 0.8820 (m-30) cc_final: 0.8418 (m-30) REVERT: D 222 ARG cc_start: 0.9068 (mmm-85) cc_final: 0.8866 (mtt90) REVERT: D 230 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7423 (mm-30) REVERT: E 3 GLN cc_start: 0.8447 (mt0) cc_final: 0.7971 (mt0) REVERT: E 221 TYR cc_start: 0.9558 (t80) cc_final: 0.9326 (t80) outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 0.2333 time to fit residues: 32.4841 Evaluate side-chains 79 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 109 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 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** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN B 25 ASN C 82 ASN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.071712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.053697 restraints weight = 36337.681| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.21 r_work: 0.2890 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2107 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= 0.142 Angle : 0.556 7.211 16116 Z= 0.283 Chirality : 0.042 0.158 1861 Planarity : 0.004 0.033 2063 Dihedral : 4.833 30.102 1643 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.65 % Allowed : 14.30 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.51 (0.20), residues: 1498 helix: -0.59 (0.19), residues: 685 sheet: -2.98 (0.33), residues: 176 loop : -2.42 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 236 HIS 0.002 0.001 HIS A 163 PHE 0.012 0.001 PHE E 157 TYR 0.010 0.001 TYR B 86 ARG 0.002 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 498) hydrogen bonds : angle 4.45699 ( 1392) covalent geometry : bond 0.00320 (11871) covalent geometry : angle 0.55565 (16116) *********************** 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 84 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8403 (m100) cc_final: 0.7776 (m100) REVERT: A 235 LYS cc_start: 0.9396 (mmtt) cc_final: 0.9192 (tppp) REVERT: A 305 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8762 (mtmt) REVERT: B 16 MET cc_start: 0.8429 (pmm) cc_final: 0.8172 (pmm) REVERT: C 47 LYS cc_start: 0.9067 (mttt) cc_final: 0.8850 (mttp) REVERT: D 201 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8552 (mm-30) REVERT: D 219 ASP cc_start: 0.8848 (m-30) cc_final: 0.8433 (m-30) REVERT: D 222 ARG cc_start: 0.9051 (mmm-85) cc_final: 0.8819 (mtt90) REVERT: E 3 GLN cc_start: 0.8451 (mt0) cc_final: 0.7908 (mt0) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.2494 time to fit residues: 30.4075 Evaluate side-chains 79 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 C residue 13 TYR Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.069224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.051494 restraints weight = 36618.687| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.12 r_work: 0.2826 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11871 Z= 0.217 Angle : 0.597 7.023 16116 Z= 0.301 Chirality : 0.043 0.156 1861 Planarity : 0.003 0.032 2063 Dihedral : 4.830 29.605 1643 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.47 % Allowed : 15.11 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.81 (0.22), residues: 1498 helix: 0.16 (0.20), residues: 688 sheet: -2.83 (0.33), residues: 191 loop : -2.20 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 37 HIS 0.003 0.001 HIS C 263 PHE 0.015 0.001 PHE E 157 TYR 0.016 0.001 TYR B 86 ARG 0.003 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 498) hydrogen bonds : angle 4.31303 ( 1392) covalent geometry : bond 0.00488 (11871) covalent geometry : angle 0.59717 (16116) *********************** 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 93 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8465 (m100) cc_final: 0.7823 (m100) REVERT: A 125 MET cc_start: 0.8899 (mtt) cc_final: 0.8465 (mtm) REVERT: A 305 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8818 (mtmt) REVERT: B 16 MET cc_start: 0.8459 (pmm) cc_final: 0.8211 (pmm) REVERT: D 201 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8593 (mm-30) REVERT: D 219 ASP cc_start: 0.8853 (m-30) cc_final: 0.8350 (m-30) REVERT: E 3 GLN cc_start: 0.8606 (mt0) cc_final: 0.8127 (mt0) outliers start: 18 outliers final: 7 residues processed: 92 average time/residue: 0.2275 time to fit residues: 31.3570 Evaluate side-chains 74 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 20 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 128 optimal weight: 0.0870 chunk 93 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 C 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.071985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053979 restraints weight = 35980.963| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.15 r_work: 0.2896 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2529 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= 0.124 Angle : 0.538 7.991 16116 Z= 0.273 Chirality : 0.042 0.155 1861 Planarity : 0.003 0.032 2063 Dihedral : 4.612 29.854 1643 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.98 % Allowed : 16.50 % Favored : 82.52 % 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: -1.30 (0.22), residues: 1498 helix: 0.73 (0.21), residues: 688 sheet: -2.81 (0.34), residues: 190 loop : -2.03 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 240 HIS 0.002 0.001 HIS B 97 PHE 0.012 0.001 PHE E 157 TYR 0.014 0.001 TYR B 86 ARG 0.002 0.000 ARG D 222 Details of bonding type rmsd hydrogen bonds : bond 0.02833 ( 498) hydrogen bonds : angle 3.98377 ( 1392) covalent geometry : bond 0.00281 (11871) covalent geometry : angle 0.53803 (16116) *********************** 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 87 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8424 (m100) cc_final: 0.7767 (m100) REVERT: A 174 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6808 (m-70) REVERT: A 305 LYS cc_start: 0.9203 (mmtt) cc_final: 0.8808 (mtmt) REVERT: B 181 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9198 (pt) REVERT: D 219 ASP cc_start: 0.8815 (m-30) cc_final: 0.8392 (m-30) REVERT: D 222 ARG cc_start: 0.9034 (mmm-85) cc_final: 0.8799 (mtt90) REVERT: E 3 GLN cc_start: 0.8574 (mt0) cc_final: 0.8026 (mt0) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 0.2280 time to fit residues: 29.3597 Evaluate side-chains 75 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 B residue 181 ILE 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 111 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 417 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.049484 restraints weight = 37560.478| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.12 r_work: 0.2759 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 11871 Z= 0.386 Angle : 0.739 11.316 16116 Z= 0.365 Chirality : 0.048 0.172 1861 Planarity : 0.004 0.033 2063 Dihedral : 5.023 30.023 1643 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.72 % Allowed : 16.75 % 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: -1.33 (0.22), residues: 1498 helix: 0.65 (0.21), residues: 683 sheet: -2.79 (0.34), residues: 189 loop : -1.99 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 400 HIS 0.005 0.001 HIS C 263 PHE 0.019 0.002 PHE E 157 TYR 0.022 0.002 TYR B 86 ARG 0.006 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 498) hydrogen bonds : angle 4.47174 ( 1392) covalent geometry : bond 0.00869 (11871) covalent geometry : angle 0.73898 (16116) *********************** 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 92 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9031 (mtt) cc_final: 0.8648 (mtm) REVERT: A 174 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6558 (m-70) REVERT: A 305 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8865 (mtmt) REVERT: B 57 GLU cc_start: 0.7327 (tt0) cc_final: 0.7038 (tp30) REVERT: B 181 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9219 (pt) REVERT: C 38 ASN cc_start: 0.8273 (m110) cc_final: 0.7989 (m110) REVERT: E 224 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9207 (pt) outliers start: 21 outliers final: 10 residues processed: 91 average time/residue: 0.2301 time to fit residues: 31.2492 Evaluate side-chains 80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 225 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 224 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053033 restraints weight = 36742.358| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.16 r_work: 0.2860 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11871 Z= 0.118 Angle : 0.555 10.764 16116 Z= 0.279 Chirality : 0.042 0.151 1861 Planarity : 0.003 0.032 2063 Dihedral : 4.685 29.960 1643 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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 (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: -0.99 (0.23), residues: 1498 helix: 1.03 (0.21), residues: 691 sheet: -2.79 (0.35), residues: 170 loop : -1.96 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 253 HIS 0.003 0.001 HIS B 97 PHE 0.012 0.001 PHE E 157 TYR 0.016 0.001 TYR B 86 ARG 0.004 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 498) hydrogen bonds : angle 3.95948 ( 1392) covalent geometry : bond 0.00268 (11871) covalent geometry : angle 0.55502 (16116) *********************** 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 85 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8453 (m100) cc_final: 0.7835 (m100) REVERT: A 125 MET cc_start: 0.8893 (mtt) cc_final: 0.8418 (mtm) REVERT: A 174 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.6756 (m-70) REVERT: A 305 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8830 (mtmm) REVERT: A 426 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8205 (mtmt) REVERT: B 181 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9182 (pt) REVERT: D 219 ASP cc_start: 0.8853 (m-30) cc_final: 0.8498 (m-30) REVERT: E 3 GLN cc_start: 0.8576 (mt0) cc_final: 0.8040 (mt0) outliers start: 12 outliers final: 5 residues processed: 84 average time/residue: 0.2382 time to fit residues: 29.9604 Evaluate side-chains 75 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 417 HIS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 61 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.070763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052817 restraints weight = 36972.967| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.18 r_work: 0.2834 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2806 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= 0.145 Angle : 0.562 10.539 16116 Z= 0.280 Chirality : 0.042 0.152 1861 Planarity : 0.003 0.040 2063 Dihedral : 4.566 29.607 1643 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.65 % Allowed : 18.38 % Favored : 80.96 % 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: -0.81 (0.23), residues: 1498 helix: 1.24 (0.21), residues: 690 sheet: -2.77 (0.34), residues: 181 loop : -1.89 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.003 0.001 HIS B 245 PHE 0.012 0.001 PHE E 157 TYR 0.018 0.001 TYR B 86 ARG 0.009 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 498) hydrogen bonds : angle 3.87087 ( 1392) covalent geometry : bond 0.00330 (11871) covalent geometry : angle 0.56160 (16116) *********************** 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 78 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8489 (m100) cc_final: 0.7845 (m100) REVERT: A 125 MET cc_start: 0.8947 (mtt) cc_final: 0.8480 (mtm) REVERT: A 174 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6731 (m-70) REVERT: A 305 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8799 (mtmt) REVERT: A 426 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8221 (mtmt) REVERT: B 181 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9188 (pt) REVERT: C 263 HIS cc_start: 0.7622 (m-70) cc_final: 0.7416 (m-70) REVERT: D 219 ASP cc_start: 0.8926 (m-30) cc_final: 0.8446 (m-30) REVERT: E 3 GLN cc_start: 0.8628 (mt0) cc_final: 0.8078 (mt0) outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 0.2267 time to fit residues: 26.7281 Evaluate side-chains 75 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 417 HIS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.072541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054587 restraints weight = 36400.264| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.18 r_work: 0.2904 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2868 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= 0.119 Angle : 0.550 10.457 16116 Z= 0.273 Chirality : 0.042 0.151 1861 Planarity : 0.003 0.035 2063 Dihedral : 4.468 29.613 1643 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.82 % Allowed : 18.55 % Favored : 80.64 % 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: -0.67 (0.23), residues: 1498 helix: 1.38 (0.21), residues: 690 sheet: -2.71 (0.34), residues: 181 loop : -1.84 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 98 HIS 0.003 0.001 HIS B 245 PHE 0.011 0.001 PHE E 157 TYR 0.017 0.001 TYR B 86 ARG 0.005 0.000 ARG D 222 Details of bonding type rmsd hydrogen bonds : bond 0.02701 ( 498) hydrogen bonds : angle 3.74354 ( 1392) covalent geometry : bond 0.00274 (11871) covalent geometry : angle 0.55034 (16116) *********************** 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 80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8473 (m100) cc_final: 0.7876 (m100) REVERT: A 125 MET cc_start: 0.8855 (mtt) cc_final: 0.8402 (mtm) REVERT: A 174 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6750 (m-70) REVERT: A 231 MET cc_start: 0.8659 (ptp) cc_final: 0.8413 (ptp) REVERT: A 305 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8808 (mtmt) REVERT: B 181 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9205 (pt) REVERT: D 219 ASP cc_start: 0.8843 (m-30) cc_final: 0.8449 (m-30) REVERT: E 3 GLN cc_start: 0.8606 (mt0) cc_final: 0.8066 (mt0) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.2176 time to fit residues: 26.1359 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 : 1.231 ------------------------------------------------------------------------------- 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 417 HIS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 64 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.072052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054011 restraints weight = 36492.203| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.21 r_work: 0.2886 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2891 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= 0.140 Angle : 0.554 10.421 16116 Z= 0.274 Chirality : 0.042 0.151 1861 Planarity : 0.003 0.033 2063 Dihedral : 4.447 29.423 1643 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.82 % Allowed : 18.46 % Favored : 80.72 % 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: -0.59 (0.23), residues: 1498 helix: 1.44 (0.21), residues: 689 sheet: -2.62 (0.34), residues: 186 loop : -1.79 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.003 0.001 HIS B 245 PHE 0.012 0.001 PHE E 157 TYR 0.017 0.001 TYR B 86 ARG 0.004 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.02762 ( 498) hydrogen bonds : angle 3.75140 ( 1392) covalent geometry : bond 0.00321 (11871) covalent geometry : angle 0.55376 (16116) ********************** 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 78 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 2.356 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8501 (m100) cc_final: 0.7867 (m100) REVERT: A 125 MET cc_start: 0.8854 (mtt) cc_final: 0.8424 (mtm) REVERT: A 174 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6758 (m-70) REVERT: A 231 MET cc_start: 0.8716 (ptp) cc_final: 0.8450 (ptp) REVERT: A 305 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8801 (mtmt) REVERT: B 181 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9207 (pt) REVERT: D 219 ASP cc_start: 0.8854 (m-30) cc_final: 0.8437 (m-30) REVERT: E 3 GLN cc_start: 0.8618 (mt0) cc_final: 0.8096 (mt0) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.2846 time to fit residues: 34.7763 Evaluate side-chains 76 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 13 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.073125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055320 restraints weight = 36290.655| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.21 r_work: 0.2921 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2963 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= 0.107 Angle : 0.533 10.353 16116 Z= 0.264 Chirality : 0.042 0.150 1861 Planarity : 0.003 0.031 2063 Dihedral : 4.327 29.437 1643 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.82 % Allowed : 18.71 % Favored : 80.47 % 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: -0.45 (0.23), residues: 1498 helix: 1.56 (0.21), residues: 690 sheet: -2.55 (0.35), residues: 182 loop : -1.75 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 98 HIS 0.003 0.001 HIS B 245 PHE 0.011 0.001 PHE E 157 TYR 0.014 0.001 TYR B 86 ARG 0.004 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.02604 ( 498) hydrogen bonds : angle 3.61633 ( 1392) covalent geometry : bond 0.00245 (11871) covalent geometry : angle 0.53338 (16116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5116.31 seconds wall clock time: 91 minutes 14.28 seconds (5474.28 seconds total)