Starting phenix.real_space_refine on Wed Mar 4 10:20:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7osf_13049/03_2026/7osf_13049.cif Found real_map, /net/cci-nas-00/data/ceres_data/7osf_13049/03_2026/7osf_13049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7osf_13049/03_2026/7osf_13049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7osf_13049/03_2026/7osf_13049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7osf_13049/03_2026/7osf_13049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7osf_13049/03_2026/7osf_13049.map" } resolution = 3.8 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8200 2.51 5 N 2249 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 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: 12826 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2375 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} 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: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1092 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11839 SG CYS H 45 45.459 41.805 48.159 1.00122.68 S ATOM 11862 SG CYS H 48 43.354 42.911 45.783 1.00122.45 S ATOM 12043 SG CYS H 72 46.189 43.837 44.237 1.00129.62 S Time building chain proxies: 2.52, per 1000 atoms: 0.20 Number of scatterers: 12826 At special positions: 0 Unit cell: (80.352, 90.72, 194.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 45 16.00 Mg 1 11.99 O 2329 8.00 N 2249 7.00 C 8200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 588.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 13 sheets defined 43.7% alpha, 11.2% 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 375 through 383 removed outlier: 3.662A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.511A pdb=" N MET A 390 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.656A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.512A pdb=" N ARG B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.657A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.247A pdb=" N ASP B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.844A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.570A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.529A pdb=" N TYR B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.868A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.600A 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 108 through 113 removed outlier: 3.546A pdb=" N LEU C 113 " --> pdb=" O VAL C 109 " (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 177 removed outlier: 3.851A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.564A pdb=" N GLN C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.531A pdb=" N LEU C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.504A pdb=" N GLY C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.166A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.536A pdb=" N PHE D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.661A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.778A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.159A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.531A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.788A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.513A pdb=" N LEU D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.597A 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 Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.844A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.613A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.755A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.630A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.572A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.506A pdb=" N TYR E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.605A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.508A pdb=" N ILE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.097A 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: 3.788A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.512A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.553A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.593A pdb=" N LEU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 213 removed outlier: 4.515A pdb=" N TRP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.513A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.158A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.800A pdb=" N ASP H 54 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.683A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.602A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.226A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.586A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.291A 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: 6.317A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 23 removed outlier: 5.933A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN B 23 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLN B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.650A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 228 Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 26 removed outlier: 5.583A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.752A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 249 through 251 removed outlier: 6.890A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.552A pdb=" N VAL H 121 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG H 152 " --> pdb=" O VAL H 121 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1425 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: 1.63 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4117 1.34 - 1.46: 2180 1.46 - 1.57: 6691 1.57 - 1.69: 2 1.69 - 1.81: 77 Bond restraints: 13067 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.587 -0.062 2.10e-02 2.27e+03 8.70e+00 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.597 -0.057 2.70e-02 1.37e+03 4.39e+00 bond pdb=" C LEU E 209 " pdb=" N PRO E 210 " ideal model delta sigma weight residual 1.335 1.363 -0.027 1.36e-02 5.41e+03 4.05e+00 bond pdb=" CB GLN A 232 " pdb=" CG GLN A 232 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.04e+00 bond pdb=" CB VAL A 407 " pdb=" CG2 VAL A 407 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.67e+00 ... (remaining 13062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 17372 3.32 - 6.65: 299 6.65 - 9.97: 48 9.97 - 13.30: 6 13.30 - 16.62: 1 Bond angle restraints: 17726 Sorted by residual: angle pdb=" C VAL C 260 " pdb=" N ASN C 261 " pdb=" CA ASN C 261 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" C GLU H 64 " pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta sigma weight residual 125.02 133.56 -8.54 1.76e+00 3.23e-01 2.35e+01 angle pdb=" C GLU H 138 " pdb=" N GLU H 139 " pdb=" CA GLU H 139 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 132.92 -16.62 3.50e+00 8.16e-02 2.26e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 ... (remaining 17721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 6649 14.86 - 29.72: 818 29.72 - 44.57: 221 44.57 - 59.43: 32 59.43 - 74.29: 16 Dihedral angle restraints: 7736 sinusoidal: 3041 harmonic: 4695 Sorted by residual: dihedral pdb=" CA VAL B 266 " pdb=" C VAL B 266 " pdb=" N LEU B 267 " pdb=" CA LEU B 267 " ideal model delta harmonic sigma weight residual -180.00 -121.50 -58.50 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA HIS B 263 " pdb=" C HIS B 263 " pdb=" N LYS B 264 " pdb=" CA LYS B 264 " ideal model delta harmonic sigma weight residual -180.00 -131.64 -48.36 0 5.00e+00 4.00e-02 9.35e+01 dihedral pdb=" CA ASP H 108 " pdb=" C ASP H 108 " pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta harmonic sigma weight residual 180.00 149.17 30.83 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1787 0.092 - 0.184: 209 0.184 - 0.276: 27 0.276 - 0.368: 5 0.368 - 0.460: 2 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CG LEU B 265 " pdb=" CB LEU B 265 " pdb=" CD1 LEU B 265 " pdb=" CD2 LEU B 265 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.29e+00 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 -2.22 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB THR A 297 " pdb=" CA THR A 297 " pdb=" OG1 THR A 297 " pdb=" CG2 THR A 297 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2027 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " -0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO E 210 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 192 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C VAL E 192 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL E 192 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU E 193 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.051 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO D 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.043 5.00e-02 4.00e+02 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 107 2.56 - 3.15: 9202 3.15 - 3.73: 19932 3.73 - 4.32: 28121 4.32 - 4.90: 46425 Nonbonded interactions: 103787 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.976 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 2.000 2.320 nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 2.111 2.170 nonbonded pdb=" SD MET H 50 " pdb="CU CU A 502 " model vdw 2.130 2.600 nonbonded pdb=" OD1 ASN A 361 " pdb="MG MG A 501 " model vdw 2.163 2.170 ... (remaining 103782 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 308) 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 group one per residue 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.007 0.073 13070 Z= 0.334 Angle : 1.113 16.623 17726 Z= 0.588 Chirality : 0.066 0.460 2030 Planarity : 0.007 0.094 2276 Dihedral : 14.292 74.290 4740 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 0.52 % Allowed : 9.16 % Favored : 90.32 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.56 (0.14), residues: 1645 helix: -4.44 (0.08), residues: 696 sheet: -2.91 (0.28), residues: 250 loop : -2.94 (0.19), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 378 TYR 0.012 0.002 TYR A 249 PHE 0.025 0.002 PHE E 204 TRP 0.027 0.002 TRP E 211 HIS 0.015 0.003 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00737 (13067) covalent geometry : angle 1.11312 (17726) hydrogen bonds : bond 0.29947 ( 502) hydrogen bonds : angle 10.50904 ( 1425) metal coordination : bond 0.04653 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8955 (tp) cc_final: 0.8648 (tp) REVERT: B 86 TYR cc_start: 0.8972 (m-80) cc_final: 0.8537 (m-10) REVERT: B 196 ASN cc_start: 0.8851 (t0) cc_final: 0.8448 (m-40) REVERT: B 279 ASP cc_start: 0.8613 (m-30) cc_final: 0.8258 (t0) REVERT: B 283 HIS cc_start: 0.6549 (m-70) cc_final: 0.5736 (m-70) REVERT: D 66 MET cc_start: 0.8978 (mmm) cc_final: 0.8645 (mmm) REVERT: D 81 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8052 (mt-10) REVERT: D 83 GLU cc_start: 0.9103 (pt0) cc_final: 0.8890 (pt0) REVERT: D 135 GLU cc_start: 0.8932 (tp30) cc_final: 0.8588 (pm20) REVERT: D 171 LYS cc_start: 0.9433 (ttmt) cc_final: 0.8894 (ttmm) REVERT: D 190 ASP cc_start: 0.8229 (m-30) cc_final: 0.7943 (t0) REVERT: D 238 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8842 (t) REVERT: E 11 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8086 (mm-30) REVERT: E 66 MET cc_start: 0.9157 (mmm) cc_final: 0.8835 (mmp) REVERT: E 76 ASP cc_start: 0.9054 (p0) cc_final: 0.8744 (p0) REVERT: H 65 LYS cc_start: 0.8851 (pttm) cc_final: 0.8319 (tmtt) REVERT: H 94 TYR cc_start: 0.8941 (m-80) cc_final: 0.8197 (m-10) REVERT: H 143 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9072 (mmtp) outliers start: 7 outliers final: 1 residues processed: 184 average time/residue: 0.1536 time to fit residues: 37.2999 Evaluate side-chains 105 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN 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 174 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 190 ASN A 212 ASN A 241 ASN A 245 GLN A 301 ASN A 324 ASN A 417 HIS B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 176 GLN C 20 HIS C 25 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 261 ASN C 270 GLN D 225 ASN E 108 HIS E 225 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.045760 restraints weight = 50353.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.047469 restraints weight = 25383.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.048602 restraints weight = 16183.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049337 restraints weight = 11963.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049873 restraints weight = 9749.489| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13070 Z= 0.162 Angle : 0.642 12.319 17726 Z= 0.331 Chirality : 0.043 0.201 2030 Planarity : 0.005 0.056 2276 Dihedral : 5.283 42.754 1805 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 1.19 % Allowed : 14.59 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.50 (0.17), residues: 1645 helix: -1.99 (0.15), residues: 704 sheet: -2.62 (0.29), residues: 245 loop : -2.40 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 66 TYR 0.015 0.001 TYR C 13 PHE 0.012 0.001 PHE D 157 TRP 0.018 0.001 TRP B 240 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00351 (13067) covalent geometry : angle 0.64215 (17726) hydrogen bonds : bond 0.03857 ( 502) hydrogen bonds : angle 4.95084 ( 1425) metal coordination : bond 0.00504 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8851 (mp) REVERT: A 89 LEU cc_start: 0.9005 (tp) cc_final: 0.8656 (tp) REVERT: A 125 MET cc_start: 0.8325 (mpp) cc_final: 0.8043 (mpp) REVERT: A 253 MET cc_start: 0.8314 (ptp) cc_final: 0.7954 (mtm) REVERT: A 305 LYS cc_start: 0.9195 (mttt) cc_final: 0.8824 (mttp) REVERT: D 81 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7874 (mt-10) REVERT: D 82 ASP cc_start: 0.8807 (t0) cc_final: 0.8385 (m-30) REVERT: D 88 MET cc_start: 0.8101 (tpp) cc_final: 0.7899 (tpp) REVERT: D 219 ASP cc_start: 0.7832 (m-30) cc_final: 0.7532 (m-30) REVERT: E 194 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9077 (tt) REVERT: H 50 MET cc_start: 0.8443 (ptt) cc_final: 0.8211 (ptt) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.1120 time to fit residues: 19.3372 Evaluate side-chains 97 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 260 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 157 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 HIS H 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.042873 restraints weight = 51530.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.044570 restraints weight = 25178.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.045674 restraints weight = 15970.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.046450 restraints weight = 11847.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.046914 restraints weight = 9568.285| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13070 Z= 0.257 Angle : 0.694 7.125 17726 Z= 0.351 Chirality : 0.045 0.187 2030 Planarity : 0.004 0.042 2276 Dihedral : 5.248 49.961 1804 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.86 % Allowed : 17.05 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.22 (0.20), residues: 1645 helix: -0.31 (0.19), residues: 706 sheet: -2.49 (0.29), residues: 263 loop : -2.23 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 66 TYR 0.015 0.002 TYR C 13 PHE 0.016 0.001 PHE H 71 TRP 0.010 0.001 TRP E 20 HIS 0.009 0.001 HIS H 149 Details of bonding type rmsd covalent geometry : bond 0.00562 (13067) covalent geometry : angle 0.69400 (17726) hydrogen bonds : bond 0.03598 ( 502) hydrogen bonds : angle 4.54931 ( 1425) metal coordination : bond 0.00351 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8986 (tp) cc_final: 0.8688 (tp) REVERT: A 125 MET cc_start: 0.8545 (mpp) cc_final: 0.8071 (mpp) REVERT: A 253 MET cc_start: 0.8451 (ptp) cc_final: 0.7865 (mtm) REVERT: A 305 LYS cc_start: 0.9164 (mttt) cc_final: 0.8732 (mttt) REVERT: B 57 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: D 81 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7952 (mt-10) REVERT: D 88 MET cc_start: 0.8196 (tpp) cc_final: 0.7899 (tpp) REVERT: E 11 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8071 (tp30) REVERT: H 64 GLU cc_start: 0.7480 (tt0) cc_final: 0.6919 (tm-30) outliers start: 25 outliers final: 16 residues processed: 108 average time/residue: 0.1010 time to fit residues: 16.3774 Evaluate side-chains 98 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 245 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.056337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.044741 restraints weight = 50394.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.046482 restraints weight = 24606.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047639 restraints weight = 15505.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048436 restraints weight = 11407.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.048826 restraints weight = 9210.770| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13070 Z= 0.116 Angle : 0.569 9.123 17726 Z= 0.289 Chirality : 0.042 0.272 2030 Planarity : 0.003 0.039 2276 Dihedral : 4.803 44.673 1804 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.49 % Allowed : 18.17 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.45 (0.21), residues: 1645 helix: 0.57 (0.21), residues: 702 sheet: -2.20 (0.30), residues: 264 loop : -2.07 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 272 TYR 0.016 0.001 TYR C 13 PHE 0.013 0.001 PHE D 157 TRP 0.006 0.001 TRP E 20 HIS 0.003 0.001 HIS E 108 Details of bonding type rmsd covalent geometry : bond 0.00255 (13067) covalent geometry : angle 0.56931 (17726) hydrogen bonds : bond 0.02825 ( 502) hydrogen bonds : angle 4.03229 ( 1425) metal coordination : bond 0.00247 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9063 (tp) cc_final: 0.8785 (tp) REVERT: A 125 MET cc_start: 0.8482 (mpp) cc_final: 0.7904 (mpp) REVERT: A 253 MET cc_start: 0.8409 (ptp) cc_final: 0.7833 (mtm) REVERT: A 305 LYS cc_start: 0.9184 (mttt) cc_final: 0.8836 (mttt) REVERT: B 264 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7083 (pttp) REVERT: D 66 MET cc_start: 0.8963 (mmp) cc_final: 0.8721 (mmm) REVERT: D 148 ILE cc_start: 0.8739 (pt) cc_final: 0.8460 (mm) REVERT: E 11 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8226 (tp30) REVERT: H 44 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7499 (mt-10) outliers start: 20 outliers final: 13 residues processed: 113 average time/residue: 0.1149 time to fit residues: 18.8520 Evaluate side-chains 102 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 85 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 116 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 261 ASN E 205 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.055176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.043807 restraints weight = 51240.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045503 restraints weight = 25859.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046602 restraints weight = 16625.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047274 restraints weight = 12346.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.047827 restraints weight = 10149.144| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13070 Z= 0.225 Angle : 0.647 9.441 17726 Z= 0.325 Chirality : 0.045 0.212 2030 Planarity : 0.004 0.040 2276 Dihedral : 4.952 49.448 1804 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.16 % Allowed : 18.62 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.16 (0.21), residues: 1645 helix: 0.97 (0.21), residues: 703 sheet: -2.35 (0.30), residues: 263 loop : -1.96 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.015 0.001 TYR C 13 PHE 0.015 0.001 PHE D 157 TRP 0.009 0.001 TRP E 20 HIS 0.003 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00495 (13067) covalent geometry : angle 0.64670 (17726) hydrogen bonds : bond 0.03122 ( 502) hydrogen bonds : angle 4.18458 ( 1425) metal coordination : bond 0.00331 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9112 (tp) cc_final: 0.8788 (tt) REVERT: A 125 MET cc_start: 0.8537 (mpp) cc_final: 0.7926 (mpp) REVERT: A 305 LYS cc_start: 0.9174 (mttt) cc_final: 0.8844 (mttt) REVERT: B 57 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: B 264 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7542 (pttp) REVERT: D 66 MET cc_start: 0.9045 (mmp) cc_final: 0.8773 (mmm) REVERT: E 11 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8326 (tp30) REVERT: H 44 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7533 (mt-10) REVERT: H 140 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8559 (mm-40) outliers start: 29 outliers final: 19 residues processed: 120 average time/residue: 0.1072 time to fit residues: 19.1017 Evaluate side-chains 107 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN E 169 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.044432 restraints weight = 50642.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046131 restraints weight = 25559.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.047224 restraints weight = 16430.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.047908 restraints weight = 12231.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.048440 restraints weight = 10063.213| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13070 Z= 0.155 Angle : 0.597 8.986 17726 Z= 0.299 Chirality : 0.043 0.201 2030 Planarity : 0.003 0.040 2276 Dihedral : 4.806 45.036 1804 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 2.23 % Allowed : 18.69 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.86 (0.22), residues: 1645 helix: 1.24 (0.21), residues: 702 sheet: -2.09 (0.30), residues: 275 loop : -1.87 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.017 0.001 TYR C 13 PHE 0.013 0.001 PHE D 157 TRP 0.005 0.001 TRP E 20 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00347 (13067) covalent geometry : angle 0.59662 (17726) hydrogen bonds : bond 0.02861 ( 502) hydrogen bonds : angle 3.97858 ( 1425) metal coordination : bond 0.00207 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7580 (mmm) cc_final: 0.7091 (mpp) REVERT: A 89 LEU cc_start: 0.9085 (tp) cc_final: 0.8732 (tt) REVERT: A 125 MET cc_start: 0.8517 (mpp) cc_final: 0.7818 (mpp) REVERT: B 7 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8229 (mm110) REVERT: B 57 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: B 264 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7335 (pttp) REVERT: B 269 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7419 (mmm160) REVERT: B 272 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9042 (tp) REVERT: C 61 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8371 (mmmm) REVERT: D 66 MET cc_start: 0.9006 (mmp) cc_final: 0.8737 (mmm) REVERT: D 81 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 222 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8564 (ttm110) REVERT: E 11 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8181 (tp30) REVERT: H 90 ASP cc_start: 0.8683 (t0) cc_final: 0.8349 (t0) REVERT: H 140 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8563 (mm-40) outliers start: 30 outliers final: 20 residues processed: 119 average time/residue: 0.1165 time to fit residues: 20.1490 Evaluate side-chains 111 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 85 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 135 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.043474 restraints weight = 50850.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.045147 restraints weight = 25653.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.046251 restraints weight = 16513.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.046982 restraints weight = 12294.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.047384 restraints weight = 10024.406| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13070 Z= 0.218 Angle : 0.645 9.086 17726 Z= 0.322 Chirality : 0.044 0.198 2030 Planarity : 0.004 0.051 2276 Dihedral : 4.901 44.673 1804 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.63 % Favored : 93.31 % Rotamer: Outliers : 2.83 % Allowed : 18.47 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.81 (0.22), residues: 1645 helix: 1.35 (0.21), residues: 701 sheet: -2.16 (0.30), residues: 278 loop : -1.86 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 66 TYR 0.015 0.001 TYR C 13 PHE 0.015 0.001 PHE D 157 TRP 0.007 0.001 TRP H 103 HIS 0.003 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00484 (13067) covalent geometry : angle 0.64462 (17726) hydrogen bonds : bond 0.03053 ( 502) hydrogen bonds : angle 4.10766 ( 1425) metal coordination : bond 0.00343 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9052 (tp) cc_final: 0.8716 (tt) REVERT: A 125 MET cc_start: 0.8527 (mpp) cc_final: 0.7821 (mpp) REVERT: B 7 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8223 (mm110) REVERT: B 57 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: B 264 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7679 (pttp) REVERT: C 61 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8753 (mmmm) REVERT: D 66 MET cc_start: 0.9036 (mmp) cc_final: 0.8742 (mmm) REVERT: D 81 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7767 (mt-10) REVERT: D 222 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8618 (ttm110) REVERT: E 11 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8124 (tp30) REVERT: E 64 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8673 (t80) REVERT: H 72 CYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7701 (p) REVERT: H 105 LYS cc_start: 0.9268 (tptp) cc_final: 0.8675 (tptp) REVERT: H 140 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8571 (mm-40) outliers start: 38 outliers final: 22 residues processed: 122 average time/residue: 0.1150 time to fit residues: 20.3838 Evaluate side-chains 116 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 144 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.055108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.043824 restraints weight = 50374.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.045503 restraints weight = 25544.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.046615 restraints weight = 16447.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047283 restraints weight = 12243.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.047827 restraints weight = 10068.391| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13070 Z= 0.177 Angle : 0.639 12.259 17726 Z= 0.314 Chirality : 0.044 0.200 2030 Planarity : 0.003 0.041 2276 Dihedral : 4.865 44.264 1804 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.31 % Allowed : 19.43 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.22), residues: 1645 helix: 1.46 (0.21), residues: 701 sheet: -2.11 (0.30), residues: 280 loop : -1.78 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 66 TYR 0.017 0.001 TYR C 13 PHE 0.014 0.001 PHE D 157 TRP 0.007 0.001 TRP E 20 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00395 (13067) covalent geometry : angle 0.63928 (17726) hydrogen bonds : bond 0.02915 ( 502) hydrogen bonds : angle 4.01330 ( 1425) metal coordination : bond 0.00238 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9039 (tp) cc_final: 0.8709 (tt) REVERT: A 125 MET cc_start: 0.8478 (mpp) cc_final: 0.7735 (mpp) REVERT: B 7 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8280 (mm110) REVERT: B 57 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: B 264 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7434 (pttp) REVERT: C 61 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8787 (mmmm) REVERT: D 81 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7726 (mt-10) REVERT: D 222 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8599 (ttm110) REVERT: E 11 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8238 (tp30) REVERT: E 64 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8687 (t80) REVERT: E 81 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7124 (mt-10) REVERT: H 105 LYS cc_start: 0.9280 (tptp) cc_final: 0.8782 (tptp) outliers start: 31 outliers final: 23 residues processed: 118 average time/residue: 0.1153 time to fit residues: 19.7748 Evaluate side-chains 114 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 85 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 151 optimal weight: 0.0050 chunk 20 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045360 restraints weight = 50021.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047080 restraints weight = 25147.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.048225 restraints weight = 16124.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.048994 restraints weight = 11925.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.049374 restraints weight = 9670.385| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13070 Z= 0.114 Angle : 0.602 11.688 17726 Z= 0.297 Chirality : 0.043 0.199 2030 Planarity : 0.003 0.042 2276 Dihedral : 4.696 42.061 1804 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.31 % Allowed : 19.81 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.47 (0.22), residues: 1645 helix: 1.61 (0.21), residues: 707 sheet: -2.01 (0.31), residues: 280 loop : -1.67 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 66 TYR 0.022 0.001 TYR C 13 PHE 0.013 0.001 PHE D 157 TRP 0.009 0.001 TRP E 20 HIS 0.003 0.000 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00258 (13067) covalent geometry : angle 0.60187 (17726) hydrogen bonds : bond 0.02620 ( 502) hydrogen bonds : angle 3.78918 ( 1425) metal coordination : bond 0.00644 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7689 (mmm) cc_final: 0.7062 (mpp) REVERT: A 89 LEU cc_start: 0.8991 (tp) cc_final: 0.8655 (tt) REVERT: A 125 MET cc_start: 0.8475 (mpp) cc_final: 0.7711 (mpp) REVERT: A 253 MET cc_start: 0.8428 (ptp) cc_final: 0.7819 (mtm) REVERT: B 7 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8174 (mm110) REVERT: B 57 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: B 264 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7049 (pttp) REVERT: C 61 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8755 (mmmm) REVERT: D 148 ILE cc_start: 0.8729 (pt) cc_final: 0.8509 (mm) REVERT: D 222 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8557 (ttm110) REVERT: E 11 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8265 (tp30) REVERT: E 64 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8717 (t80) REVERT: E 81 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7155 (mt-10) REVERT: H 51 ILE cc_start: 0.9517 (mm) cc_final: 0.9309 (mm) REVERT: H 105 LYS cc_start: 0.9262 (tptp) cc_final: 0.8845 (tptp) REVERT: H 140 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8441 (mp10) outliers start: 31 outliers final: 18 residues processed: 120 average time/residue: 0.1043 time to fit residues: 18.4737 Evaluate side-chains 113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 156 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 119 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.044459 restraints weight = 50948.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.046171 restraints weight = 25586.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.047299 restraints weight = 16369.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.048045 restraints weight = 12123.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.048435 restraints weight = 9867.480| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13070 Z= 0.158 Angle : 0.635 11.201 17726 Z= 0.311 Chirality : 0.043 0.198 2030 Planarity : 0.003 0.041 2276 Dihedral : 4.741 43.978 1804 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.16 % Allowed : 19.66 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.42 (0.22), residues: 1645 helix: 1.67 (0.21), residues: 706 sheet: -2.09 (0.30), residues: 275 loop : -1.62 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 66 TYR 0.022 0.001 TYR C 13 PHE 0.014 0.001 PHE D 157 TRP 0.007 0.001 TRP E 20 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00353 (13067) covalent geometry : angle 0.63533 (17726) hydrogen bonds : bond 0.02773 ( 502) hydrogen bonds : angle 3.86219 ( 1425) metal coordination : bond 0.00802 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7690 (mmm) cc_final: 0.7067 (mpp) REVERT: A 89 LEU cc_start: 0.8998 (tp) cc_final: 0.8664 (tt) REVERT: A 125 MET cc_start: 0.8489 (mpp) cc_final: 0.7779 (mpp) REVERT: B 7 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8202 (mm110) REVERT: B 57 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: B 264 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7126 (pttp) REVERT: C 61 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8769 (mmmm) REVERT: D 222 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8563 (ttm110) REVERT: E 11 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8245 (tp30) REVERT: E 64 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8761 (t80) REVERT: H 51 ILE cc_start: 0.9621 (mm) cc_final: 0.9413 (mm) REVERT: H 105 LYS cc_start: 0.9273 (tptp) cc_final: 0.8837 (tptp) REVERT: H 140 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8458 (mp10) outliers start: 29 outliers final: 20 residues processed: 114 average time/residue: 0.1094 time to fit residues: 18.1616 Evaluate side-chains 112 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 92 optimal weight: 1.9990 chunk 161 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 131 optimal weight: 0.0670 chunk 95 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.056594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045359 restraints weight = 50021.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047071 restraints weight = 25063.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.048216 restraints weight = 16050.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.048921 restraints weight = 11845.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.049490 restraints weight = 9666.711| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13070 Z= 0.117 Angle : 0.615 10.802 17726 Z= 0.301 Chirality : 0.043 0.202 2030 Planarity : 0.003 0.041 2276 Dihedral : 4.653 42.208 1804 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.01 % Allowed : 20.10 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.33 (0.22), residues: 1645 helix: 1.75 (0.21), residues: 706 sheet: -2.02 (0.30), residues: 277 loop : -1.59 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 66 TYR 0.023 0.001 TYR C 13 PHE 0.013 0.001 PHE D 157 TRP 0.007 0.001 TRP A 98 HIS 0.003 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00264 (13067) covalent geometry : angle 0.61497 (17726) hydrogen bonds : bond 0.02634 ( 502) hydrogen bonds : angle 3.76651 ( 1425) metal coordination : bond 0.00597 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1593.01 seconds wall clock time: 28 minutes 25.46 seconds (1705.46 seconds total)