Starting phenix.real_space_refine on Fri Jul 3 03:51:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ef5_28066/07_2026/8ef5_28066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ef5_28066/07_2026/8ef5_28066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2026/8ef5_28066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2026/8ef5_28066.map" model { file = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2026/8ef5_28066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2026/8ef5_28066.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2026/8ef5_28066.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2026/8ef5_28066.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 7619 2.51 5 N 1899 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11705 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 436 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2315 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain: "R" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 165 Unusual residues: {'7V7': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 165 Unusual residues: {'7V7': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.97, per 1000 atoms: 0.25 Number of scatterers: 11705 At special positions: 0 Unit cell: (107.1, 130.662, 141.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2088 8.00 N 1899 7.00 C 7619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " distance=2.03 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: 1.13 Conformation dependent library (CDL) restraints added in 610.9 milliseconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 15 sheets defined 50.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'R' and resid 66 through 98 Processing helix chain 'R' and resid 103 through 122 removed outlier: 3.587A pdb=" N ILE R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 133 removed outlier: 3.512A pdb=" N ASN R 129 " --> pdb=" O PHE R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.518A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.390A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix removed outlier: 3.525A pdb=" N PHE R 206 " --> pdb=" O LEU R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 243 removed outlier: 3.636A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN R 232 " --> pdb=" O TRP R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 264 removed outlier: 3.504A pdb=" N LEU R 259 " --> pdb=" O GLY R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 338 removed outlier: 3.851A pdb=" N HIS R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 removed outlier: 3.582A pdb=" N CYS R 348 " --> pdb=" O ASN R 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.545A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.462A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.934A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.566A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.507A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.189A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.604A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.512A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.537A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.192A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.721A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.132A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 98 removed outlier: 3.539A pdb=" N VAL M 96 " --> pdb=" O MET M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 122 removed outlier: 3.576A pdb=" N TYR M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 133 removed outlier: 3.612A pdb=" N GLN M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.799A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 4.237A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.543A pdb=" N ILE M 188 " --> pdb=" O ARG M 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP M 194 " --> pdb=" O ASN M 190 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix removed outlier: 3.634A pdb=" N PHE M 206 " --> pdb=" O LEU M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 243 removed outlier: 3.774A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 264 removed outlier: 3.574A pdb=" N LEU M 259 " --> pdb=" O GLY M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 308 removed outlier: 3.662A pdb=" N ASN M 276 " --> pdb=" O GLU M 272 " (cutoff:3.500A) Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 339 removed outlier: 3.552A pdb=" N ASN M 330 " --> pdb=" O LEU M 326 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'F' and resid 338 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.539A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.365A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.748A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.792A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.685A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.346A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.737A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.875A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.608A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.740A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.740A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.577A pdb=" N VAL E 148 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 156 through 161 Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 removed outlier: 3.522A pdb=" N THR M 220 " --> pdb=" O THR M 209 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.45 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: 3020 1.34 - 1.46: 2424 1.46 - 1.58: 6394 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 11984 Sorted by residual: bond pdb=" C02 7V7 M 501 " pdb=" N05 7V7 M 501 " ideal model delta sigma weight residual 1.359 1.436 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C02 7V7 R 501 " pdb=" N05 7V7 R 501 " ideal model delta sigma weight residual 1.359 1.435 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C20 7V7 M 501 " pdb=" N05 7V7 M 501 " ideal model delta sigma weight residual 1.423 1.493 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C20 7V7 R 501 " pdb=" N05 7V7 R 501 " ideal model delta sigma weight residual 1.423 1.492 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 CLR R 505 " pdb=" C6 CLR R 505 " ideal model delta sigma weight residual 1.332 1.298 0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 11979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 15848 2.43 - 4.85: 408 4.85 - 7.28: 42 7.28 - 9.70: 6 9.70 - 12.13: 1 Bond angle restraints: 16305 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 133.67 -12.13 1.91e+00 2.74e-01 4.03e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" N ASP E 74 " pdb=" CA ASP E 74 " pdb=" C ASP E 74 " ideal model delta sigma weight residual 109.81 116.71 -6.90 2.21e+00 2.05e-01 9.76e+00 angle pdb=" N LEU M 123 " pdb=" CA LEU M 123 " pdb=" C LEU M 123 " ideal model delta sigma weight residual 109.81 116.39 -6.58 2.21e+00 2.05e-01 8.86e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 124.31 129.22 -4.91 1.67e+00 3.59e-01 8.64e+00 ... (remaining 16300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 6812 16.39 - 32.78: 168 32.78 - 49.18: 20 49.18 - 65.57: 3 65.57 - 81.96: 2 Dihedral angle restraints: 7005 sinusoidal: 2792 harmonic: 4213 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CB CYS M 142 " pdb=" SG CYS M 142 " pdb=" SG CYS M 219 " pdb=" CB CYS M 219 " ideal model delta sinusoidal sigma weight residual 93.00 123.38 -30.38 1 1.00e+01 1.00e-02 1.32e+01 ... (remaining 7002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1694 0.085 - 0.169: 164 0.169 - 0.254: 26 0.254 - 0.339: 11 0.339 - 0.424: 10 Chirality restraints: 1905 Sorted by residual: chirality pdb=" C14 CLR M 502 " pdb=" C13 CLR M 502 " pdb=" C15 CLR M 502 " pdb=" C8 CLR M 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C14 CLR M 504 " pdb=" C13 CLR M 504 " pdb=" C15 CLR M 504 " pdb=" C8 CLR M 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 1902 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 7V7 R 501 " 0.031 2.00e-02 2.50e+03 3.11e-01 1.45e+03 pdb=" C03 7V7 R 501 " -0.394 2.00e-02 2.50e+03 pdb=" C06 7V7 R 501 " -0.374 2.00e-02 2.50e+03 pdb=" C20 7V7 R 501 " 0.330 2.00e-02 2.50e+03 pdb=" N05 7V7 R 501 " -0.010 2.00e-02 2.50e+03 pdb=" O01 7V7 R 501 " 0.417 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 7V7 M 501 " -0.032 2.00e-02 2.50e+03 3.09e-01 1.44e+03 pdb=" C03 7V7 M 501 " 0.392 2.00e-02 2.50e+03 pdb=" C06 7V7 M 501 " 0.374 2.00e-02 2.50e+03 pdb=" C20 7V7 M 501 " -0.327 2.00e-02 2.50e+03 pdb=" N05 7V7 M 501 " 0.009 2.00e-02 2.50e+03 pdb=" O01 7V7 M 501 " -0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO B 236 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.046 5.00e-02 4.00e+02 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2745 2.81 - 3.33: 10503 3.33 - 3.85: 18654 3.85 - 4.38: 21263 4.38 - 4.90: 37885 Nonbonded interactions: 91050 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.284 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.291 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.309 3.040 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.319 3.040 nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.324 3.040 ... (remaining 91045 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 'M' and (resid 66 through 352 or resid 501 through 506)) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.630 Find NCS groups from input model: 0.140 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.004 0.077 11987 Z= 0.230 Angle : 0.883 12.130 16311 Z= 0.474 Chirality : 0.066 0.424 1905 Planarity : 0.012 0.311 1964 Dihedral : 7.981 81.961 4272 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1423 helix: 0.88 (0.18), residues: 638 sheet: 0.35 (0.30), residues: 274 loop : -1.23 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 68 TYR 0.023 0.002 TYR M 151 PHE 0.020 0.002 PHE B 234 TRP 0.027 0.002 TRP R 135 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.23 (11984) covalent geometry : angle 0.88237 / 0.47 (16305) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 1.27502 / 0.75 ( 6) hydrogen bonds : bond 0.26299 / 17.64 ( 653) hydrogen bonds : angle 7.44899 / 5.35 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7583 (m-80) cc_final: 0.7367 (m-80) REVERT: R 145 VAL cc_start: 0.7276 (t) cc_final: 0.6910 (t) REVERT: R 185 ASN cc_start: 0.8093 (t0) cc_final: 0.7866 (t0) REVERT: R 282 ARG cc_start: 0.8319 (ttp-170) cc_final: 0.8103 (ttp-170) REVERT: R 303 ILE cc_start: 0.8080 (mm) cc_final: 0.7640 (mt) REVERT: A 8 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7226 (mt-10) REVERT: A 10 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7602 (mtmt) REVERT: A 14 GLU cc_start: 0.7450 (tt0) cc_final: 0.7173 (tt0) REVERT: A 17 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7929 (mmmt) REVERT: A 29 LYS cc_start: 0.8317 (tttt) cc_final: 0.8050 (tttt) REVERT: A 49 ILE cc_start: 0.8119 (tt) cc_final: 0.7448 (mm) REVERT: A 193 ASP cc_start: 0.7383 (t0) cc_final: 0.7174 (t0) REVERT: A 197 LYS cc_start: 0.8113 (mttt) cc_final: 0.7883 (mttt) REVERT: A 231 ASP cc_start: 0.7032 (t0) cc_final: 0.6612 (t0) REVERT: A 247 MET cc_start: 0.7933 (mtt) cc_final: 0.7522 (mtm) REVERT: A 251 ASP cc_start: 0.7409 (t0) cc_final: 0.7183 (t0) REVERT: A 272 ASP cc_start: 0.8085 (p0) cc_final: 0.7793 (p0) REVERT: A 273 LEU cc_start: 0.8792 (mt) cc_final: 0.8447 (tt) REVERT: A 274 PHE cc_start: 0.8509 (t80) cc_final: 0.7937 (t80) REVERT: A 276 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6966 (mt-10) REVERT: A 304 GLN cc_start: 0.7986 (tt0) cc_final: 0.7637 (tt0) REVERT: A 308 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 316 THR cc_start: 0.8027 (m) cc_final: 0.7731 (p) REVERT: B 17 GLN cc_start: 0.8256 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 38 ASP cc_start: 0.8507 (p0) cc_final: 0.7848 (p0) REVERT: B 50 THR cc_start: 0.8217 (m) cc_final: 0.7604 (t) REVERT: B 52 ARG cc_start: 0.7676 (mtt90) cc_final: 0.7453 (mtt90) REVERT: B 87 THR cc_start: 0.8521 (m) cc_final: 0.8221 (t) REVERT: B 171 ILE cc_start: 0.8617 (mt) cc_final: 0.8375 (mm) REVERT: B 188 MET cc_start: 0.7203 (mmm) cc_final: 0.6871 (mmt) REVERT: B 221 THR cc_start: 0.8391 (m) cc_final: 0.7998 (p) REVERT: B 258 ASP cc_start: 0.7980 (t0) cc_final: 0.7664 (t70) REVERT: E 231 MET cc_start: 0.7554 (ttp) cc_final: 0.7347 (ttm) REVERT: E 232 GLN cc_start: 0.7868 (pp30) cc_final: 0.7531 (pp30) REVERT: M 145 VAL cc_start: 0.7598 (t) cc_final: 0.7307 (p) REVERT: M 283 MET cc_start: 0.8220 (tpp) cc_final: 0.7965 (tpp) REVERT: F 341 ASP cc_start: 0.7697 (t0) cc_final: 0.7353 (t0) REVERT: F 345 LYS cc_start: 0.8415 (tttt) cc_final: 0.8132 (tttp) REVERT: F 349 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7697 (mtmm) outliers start: 0 outliers final: 0 residues processed: 508 average time/residue: 0.1282 time to fit residues: 89.5333 Evaluate side-chains 407 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 129 ASN R 173 HIS R 190 ASN R 321 HIS R 330 ASN A 188 HIS A 204 GLN A 322 HIS A 331 ASN B 91 HIS B 266 HIS C 18 GLN E 180 GLN E 233 HIS ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 ASN M 299 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109214 restraints weight = 20451.574| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.62 r_work: 0.3416 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11987 Z= 0.183 Angle : 0.626 11.403 16311 Z= 0.326 Chirality : 0.043 0.195 1905 Planarity : 0.005 0.058 1964 Dihedral : 5.537 85.373 1669 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.49 % Allowed : 12.46 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1423 helix: 2.00 (0.18), residues: 653 sheet: 0.22 (0.29), residues: 297 loop : -1.04 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 13 TYR 0.018 0.002 TYR M 93 PHE 0.026 0.002 PHE B 241 TRP 0.019 0.002 TRP R 320 HIS 0.009 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (11984) covalent geometry : angle 0.62449 / 0.33 (16305) SS BOND : bond 0.00868 / 0.43 ( 3) SS BOND : angle 2.19351 / 1.18 ( 6) hydrogen bonds : bond 0.05211 / 3.46 ( 653) hydrogen bonds : angle 4.72794 / 3.38 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 419 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 72 THR cc_start: 0.8392 (t) cc_final: 0.8099 (p) REVERT: R 188 ILE cc_start: 0.7650 (mt) cc_final: 0.7450 (mt) REVERT: R 222 THR cc_start: 0.8335 (m) cc_final: 0.7991 (p) REVERT: R 266 MET cc_start: 0.7210 (tmm) cc_final: 0.6823 (tmm) REVERT: R 282 ARG cc_start: 0.8521 (ttp-170) cc_final: 0.8248 (ttp-170) REVERT: R 301 TYR cc_start: 0.7905 (t80) cc_final: 0.7036 (t80) REVERT: R 304 ILE cc_start: 0.8390 (mt) cc_final: 0.8187 (tt) REVERT: A 14 GLU cc_start: 0.7771 (tt0) cc_final: 0.7510 (tt0) REVERT: A 17 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8101 (mmmt) REVERT: A 21 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7472 (ttp80) REVERT: A 25 GLU cc_start: 0.8356 (tt0) cc_final: 0.8052 (tt0) REVERT: A 29 LYS cc_start: 0.8764 (tttt) cc_final: 0.8478 (tttt) REVERT: A 33 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 193 ASP cc_start: 0.7910 (t0) cc_final: 0.7659 (t0) REVERT: A 197 LYS cc_start: 0.8604 (mttt) cc_final: 0.7821 (mttt) REVERT: A 231 ASP cc_start: 0.7709 (t0) cc_final: 0.7423 (t0) REVERT: A 247 MET cc_start: 0.8402 (mtt) cc_final: 0.8039 (mtm) REVERT: A 272 ASP cc_start: 0.8153 (p0) cc_final: 0.7793 (p0) REVERT: A 274 PHE cc_start: 0.8600 (t80) cc_final: 0.8136 (t80) REVERT: A 289 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7846 (tp30) REVERT: A 308 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 312 LYS cc_start: 0.8364 (mmtm) cc_final: 0.7974 (mttp) REVERT: A 316 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.7990 (p) REVERT: A 317 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8545 (tttt) REVERT: A 330 LYS cc_start: 0.8513 (mttt) cc_final: 0.8052 (mttt) REVERT: A 350 ASP cc_start: 0.8542 (t0) cc_final: 0.8242 (t0) REVERT: B 17 GLN cc_start: 0.8311 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 50 THR cc_start: 0.8524 (m) cc_final: 0.8290 (t) REVERT: B 89 LYS cc_start: 0.8953 (mttp) cc_final: 0.8733 (mttp) REVERT: B 96 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7337 (mtt90) REVERT: B 111 TYR cc_start: 0.8852 (m-80) cc_final: 0.8575 (m-80) REVERT: B 130 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8064 (mt-10) REVERT: B 170 ASP cc_start: 0.7777 (t0) cc_final: 0.7290 (t0) REVERT: B 173 THR cc_start: 0.8720 (m) cc_final: 0.8515 (t) REVERT: B 188 MET cc_start: 0.8418 (mmm) cc_final: 0.7681 (mmm) REVERT: B 221 THR cc_start: 0.8647 (m) cc_final: 0.8247 (p) REVERT: B 229 ILE cc_start: 0.8582 (mt) cc_final: 0.8276 (mp) REVERT: B 234 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.6892 (t80) REVERT: B 254 ASP cc_start: 0.7440 (t0) cc_final: 0.7146 (t0) REVERT: C 44 HIS cc_start: 0.8298 (m90) cc_final: 0.7858 (m90) REVERT: E 115 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7821 (p) REVERT: E 195 ASN cc_start: 0.6721 (m-40) cc_final: 0.6448 (m-40) REVERT: E 202 ASP cc_start: 0.7636 (t70) cc_final: 0.7379 (t70) REVERT: E 231 MET cc_start: 0.8077 (ttp) cc_final: 0.7847 (ttm) REVERT: M 150 TYR cc_start: 0.8475 (m-80) cc_final: 0.8200 (m-80) REVERT: M 190 ASN cc_start: 0.7706 (m-40) cc_final: 0.7388 (m110) REVERT: M 222 THR cc_start: 0.8755 (t) cc_final: 0.8362 (p) REVERT: M 245 MET cc_start: 0.7900 (tpp) cc_final: 0.7535 (mpp) REVERT: F 345 LYS cc_start: 0.8773 (tttt) cc_final: 0.8568 (tttp) REVERT: F 349 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7978 (mtmm) outliers start: 44 outliers final: 25 residues processed: 443 average time/residue: 0.1299 time to fit residues: 78.5326 Evaluate side-chains 422 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 394 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 104 optimal weight: 0.0000 chunk 122 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 190 ASN R 299 HIS B 110 ASN B 142 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110169 restraints weight = 20430.016| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.66 r_work: 0.3420 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11987 Z= 0.120 Angle : 0.549 10.786 16311 Z= 0.284 Chirality : 0.040 0.186 1905 Planarity : 0.004 0.049 1964 Dihedral : 5.210 73.337 1669 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.89 % Allowed : 17.30 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.21), residues: 1423 helix: 2.32 (0.19), residues: 656 sheet: 0.24 (0.30), residues: 293 loop : -0.85 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 275 TYR 0.022 0.001 TYR R 130 PHE 0.016 0.001 PHE B 241 TRP 0.019 0.002 TRP B 82 HIS 0.002 0.001 HIS R 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11984) covalent geometry : angle 0.54873 / 0.28 (16305) SS BOND : bond 0.00597 / 0.29 ( 3) SS BOND : angle 1.31792 / 0.72 ( 6) hydrogen bonds : bond 0.04411 / 2.91 ( 653) hydrogen bonds : angle 4.41076 / 3.15 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 395 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7627 (mmm) cc_final: 0.7357 (mmm) REVERT: R 79 ILE cc_start: 0.8387 (mt) cc_final: 0.8119 (mt) REVERT: R 221 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8510 (mp) REVERT: R 222 THR cc_start: 0.8338 (m) cc_final: 0.7946 (p) REVERT: A 14 GLU cc_start: 0.7686 (tt0) cc_final: 0.7348 (tt0) REVERT: A 17 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8067 (mmmt) REVERT: A 21 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7475 (ttp80) REVERT: A 25 GLU cc_start: 0.8410 (tt0) cc_final: 0.8128 (tt0) REVERT: A 193 ASP cc_start: 0.7966 (t0) cc_final: 0.7708 (t0) REVERT: A 231 ASP cc_start: 0.7885 (t0) cc_final: 0.7680 (t0) REVERT: A 247 MET cc_start: 0.8360 (mtt) cc_final: 0.7911 (mtm) REVERT: A 274 PHE cc_start: 0.8569 (t80) cc_final: 0.8048 (t80) REVERT: A 289 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7918 (tp30) REVERT: A 308 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7960 (mt-10) REVERT: A 316 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 317 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8424 (tttt) REVERT: A 330 LYS cc_start: 0.8493 (mttt) cc_final: 0.8056 (mttt) REVERT: A 350 ASP cc_start: 0.8579 (t0) cc_final: 0.8198 (t0) REVERT: B 17 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 111 TYR cc_start: 0.8858 (m-80) cc_final: 0.8580 (m-80) REVERT: B 130 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 170 ASP cc_start: 0.7722 (t0) cc_final: 0.7299 (t0) REVERT: B 188 MET cc_start: 0.8178 (mmm) cc_final: 0.7740 (mmm) REVERT: B 198 LEU cc_start: 0.9129 (mp) cc_final: 0.8893 (mp) REVERT: B 212 ASP cc_start: 0.7671 (p0) cc_final: 0.6895 (p0) REVERT: B 221 THR cc_start: 0.8655 (m) cc_final: 0.8262 (p) REVERT: B 229 ILE cc_start: 0.8620 (mt) cc_final: 0.8254 (mp) REVERT: B 234 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.6997 (t80) REVERT: B 254 ASP cc_start: 0.7495 (t0) cc_final: 0.7190 (t0) REVERT: B 261 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8350 (tt) REVERT: B 267 ASP cc_start: 0.7997 (m-30) cc_final: 0.7720 (t0) REVERT: C 38 MET cc_start: 0.9062 (mtt) cc_final: 0.8664 (mpp) REVERT: E 32 PHE cc_start: 0.9144 (m-80) cc_final: 0.8780 (m-80) REVERT: E 111 TRP cc_start: 0.8115 (m100) cc_final: 0.7885 (m-10) REVERT: E 115 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7728 (p) REVERT: E 141 MET cc_start: 0.8340 (mmm) cc_final: 0.8034 (mmm) REVERT: E 195 ASN cc_start: 0.6855 (m-40) cc_final: 0.6556 (m-40) REVERT: E 231 MET cc_start: 0.8069 (ttp) cc_final: 0.7863 (ttt) REVERT: E 232 GLN cc_start: 0.8353 (pp30) cc_final: 0.8120 (pp30) REVERT: M 150 TYR cc_start: 0.8418 (m-80) cc_final: 0.8176 (m-80) REVERT: M 200 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7961 (tt) REVERT: M 222 THR cc_start: 0.8774 (t) cc_final: 0.8420 (p) REVERT: M 236 ILE cc_start: 0.8719 (mm) cc_final: 0.8486 (mt) REVERT: M 245 MET cc_start: 0.7810 (tpp) cc_final: 0.7396 (mpp) REVERT: F 349 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7955 (mtmm) outliers start: 49 outliers final: 22 residues processed: 414 average time/residue: 0.1355 time to fit residues: 75.5784 Evaluate side-chains 401 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 373 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LYS Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 95 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN M 152 ASN M 173 HIS ** M 190 ASN ** 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 = 0.3732 r_free = 0.3732 target = 0.122613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.105676 restraints weight = 20467.850| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.62 r_work: 0.3352 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11987 Z= 0.170 Angle : 0.584 11.015 16311 Z= 0.300 Chirality : 0.041 0.191 1905 Planarity : 0.004 0.047 1964 Dihedral : 5.339 68.452 1669 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.21 % Allowed : 18.65 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.21), residues: 1423 helix: 2.27 (0.19), residues: 656 sheet: 0.28 (0.30), residues: 287 loop : -0.77 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 97 TYR 0.019 0.002 TYR R 151 PHE 0.014 0.002 PHE B 241 TRP 0.016 0.002 TRP R 320 HIS 0.003 0.001 HIS R 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (11984) covalent geometry : angle 0.58253 / 0.30 (16305) SS BOND : bond 0.00817 / 0.41 ( 3) SS BOND : angle 2.20261 / 1.24 ( 6) hydrogen bonds : bond 0.04407 / 2.92 ( 653) hydrogen bonds : angle 4.32842 / 3.09 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 379 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7588 (mmm) cc_final: 0.7329 (mmm) REVERT: R 79 ILE cc_start: 0.8346 (mt) cc_final: 0.8087 (mt) REVERT: R 141 LEU cc_start: 0.7258 (tp) cc_final: 0.7056 (tp) REVERT: R 198 SER cc_start: 0.8066 (t) cc_final: 0.7739 (t) REVERT: R 221 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8612 (mp) REVERT: R 222 THR cc_start: 0.8345 (m) cc_final: 0.7996 (p) REVERT: A 14 GLU cc_start: 0.7774 (tt0) cc_final: 0.7421 (tt0) REVERT: A 17 LYS cc_start: 0.8453 (mmmt) cc_final: 0.7978 (mtmm) REVERT: A 21 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7535 (ttp80) REVERT: A 25 GLU cc_start: 0.8416 (tt0) cc_final: 0.8119 (tt0) REVERT: A 29 LYS cc_start: 0.8747 (tttt) cc_final: 0.8411 (ttmm) REVERT: A 33 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 193 ASP cc_start: 0.8040 (t0) cc_final: 0.7700 (t0) REVERT: A 197 LYS cc_start: 0.8542 (mttt) cc_final: 0.8258 (mttt) REVERT: A 231 ASP cc_start: 0.8048 (t0) cc_final: 0.7700 (t0) REVERT: A 275 GLU cc_start: 0.7562 (pt0) cc_final: 0.7303 (pt0) REVERT: A 276 GLU cc_start: 0.7964 (mp0) cc_final: 0.7693 (mp0) REVERT: A 289 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7897 (tp30) REVERT: A 308 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 316 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8003 (p) REVERT: B 17 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 78 LYS cc_start: 0.9057 (mmtm) cc_final: 0.8713 (mptt) REVERT: B 96 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7617 (mtt90) REVERT: B 111 TYR cc_start: 0.8816 (m-80) cc_final: 0.8521 (m-80) REVERT: B 130 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 173 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8916 (p) REVERT: B 188 MET cc_start: 0.8312 (mmm) cc_final: 0.7965 (mmm) REVERT: B 198 LEU cc_start: 0.9129 (mp) cc_final: 0.8769 (mp) REVERT: B 200 VAL cc_start: 0.8944 (p) cc_final: 0.8682 (m) REVERT: B 221 THR cc_start: 0.8666 (m) cc_final: 0.8433 (p) REVERT: B 229 ILE cc_start: 0.8674 (mt) cc_final: 0.8460 (mm) REVERT: B 254 ASP cc_start: 0.7579 (t0) cc_final: 0.7272 (t0) REVERT: B 261 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8466 (tt) REVERT: B 277 SER cc_start: 0.8521 (t) cc_final: 0.8262 (t) REVERT: C 13 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.8344 (ptt-90) REVERT: E 111 TRP cc_start: 0.8160 (m100) cc_final: 0.7778 (m-10) REVERT: E 115 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7678 (p) REVERT: E 141 MET cc_start: 0.8334 (mmm) cc_final: 0.7975 (mmm) REVERT: E 202 ASP cc_start: 0.7773 (t70) cc_final: 0.7451 (t70) REVERT: E 232 GLN cc_start: 0.8476 (pp30) cc_final: 0.8248 (pp30) REVERT: E 240 PHE cc_start: 0.8576 (m-10) cc_final: 0.8256 (m-80) REVERT: M 150 TYR cc_start: 0.8450 (m-80) cc_final: 0.8127 (m-80) REVERT: M 194 TRP cc_start: 0.8344 (m100) cc_final: 0.7808 (m100) REVERT: M 222 THR cc_start: 0.8849 (t) cc_final: 0.8497 (p) REVERT: M 245 MET cc_start: 0.7824 (tpp) cc_final: 0.7473 (mpp) REVERT: F 349 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7927 (mtmm) outliers start: 53 outliers final: 35 residues processed: 401 average time/residue: 0.1353 time to fit residues: 73.7532 Evaluate side-chains 411 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 371 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 176 LYS Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 129 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN M 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107755 restraints weight = 20308.608| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.62 r_work: 0.3381 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11987 Z= 0.123 Angle : 0.550 10.673 16311 Z= 0.281 Chirality : 0.040 0.182 1905 Planarity : 0.004 0.045 1964 Dihedral : 5.191 66.178 1669 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.73 % Allowed : 20.24 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.22), residues: 1423 helix: 2.38 (0.19), residues: 659 sheet: 0.18 (0.30), residues: 289 loop : -0.69 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 260 TYR 0.021 0.002 TYR M 93 PHE 0.016 0.001 PHE A 334 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11984) covalent geometry : angle 0.54919 / 0.28 (16305) SS BOND : bond 0.00391 / 0.19 ( 3) SS BOND : angle 1.70702 / 1.00 ( 6) hydrogen bonds : bond 0.03916 / 2.60 ( 653) hydrogen bonds : angle 4.22402 / 3.01 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 384 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7633 (mmm) cc_final: 0.7307 (mmm) REVERT: R 79 ILE cc_start: 0.8302 (mt) cc_final: 0.8055 (mt) REVERT: R 110 PHE cc_start: 0.8073 (t80) cc_final: 0.7739 (t80) REVERT: R 141 LEU cc_start: 0.7102 (tp) cc_final: 0.6896 (tp) REVERT: R 168 TYR cc_start: 0.8339 (t80) cc_final: 0.7816 (t80) REVERT: R 221 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8586 (mp) REVERT: R 222 THR cc_start: 0.8349 (m) cc_final: 0.7994 (p) REVERT: A 14 GLU cc_start: 0.7735 (tt0) cc_final: 0.7390 (tt0) REVERT: A 17 LYS cc_start: 0.8423 (mmmt) cc_final: 0.7937 (mtmm) REVERT: A 21 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7509 (ttp80) REVERT: A 25 GLU cc_start: 0.8347 (tt0) cc_final: 0.8053 (tt0) REVERT: A 29 LYS cc_start: 0.8717 (tttt) cc_final: 0.8344 (ttmm) REVERT: A 33 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 193 ASP cc_start: 0.8021 (t0) cc_final: 0.7663 (t0) REVERT: A 197 LYS cc_start: 0.8523 (mttt) cc_final: 0.8246 (mttt) REVERT: A 231 ASP cc_start: 0.8031 (t0) cc_final: 0.7687 (t0) REVERT: A 275 GLU cc_start: 0.7534 (pt0) cc_final: 0.7308 (pt0) REVERT: A 289 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7881 (tp30) REVERT: A 308 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 316 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8034 (p) REVERT: B 111 TYR cc_start: 0.8803 (m-80) cc_final: 0.8528 (m-80) REVERT: B 130 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 173 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 188 MET cc_start: 0.8401 (mmm) cc_final: 0.8077 (mmt) REVERT: B 191 SER cc_start: 0.9061 (p) cc_final: 0.8818 (m) REVERT: B 198 LEU cc_start: 0.9121 (mp) cc_final: 0.8765 (mp) REVERT: B 200 VAL cc_start: 0.8937 (p) cc_final: 0.8690 (m) REVERT: B 221 THR cc_start: 0.8610 (m) cc_final: 0.8355 (p) REVERT: B 234 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6947 (t80) REVERT: B 254 ASP cc_start: 0.7502 (t0) cc_final: 0.7217 (t0) REVERT: B 277 SER cc_start: 0.8514 (t) cc_final: 0.8283 (m) REVERT: C 13 ARG cc_start: 0.8741 (ptp-110) cc_final: 0.8343 (ptt-90) REVERT: C 44 HIS cc_start: 0.8211 (m90) cc_final: 0.7757 (m90) REVERT: E 111 TRP cc_start: 0.8134 (m100) cc_final: 0.7770 (m-10) REVERT: E 115 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7686 (p) REVERT: E 141 MET cc_start: 0.8278 (mmm) cc_final: 0.7969 (mmm) REVERT: E 202 ASP cc_start: 0.7758 (t70) cc_final: 0.7449 (t70) REVERT: E 232 GLN cc_start: 0.8455 (pp30) cc_final: 0.8238 (pp30) REVERT: M 150 TYR cc_start: 0.8407 (m-80) cc_final: 0.8002 (m-80) REVERT: M 181 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.8060 (mtm180) REVERT: M 200 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7959 (tt) REVERT: M 222 THR cc_start: 0.8851 (t) cc_final: 0.8525 (p) REVERT: M 245 MET cc_start: 0.7776 (tpp) cc_final: 0.7502 (mpp) REVERT: F 349 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7898 (mtmm) outliers start: 47 outliers final: 29 residues processed: 399 average time/residue: 0.1333 time to fit residues: 72.4507 Evaluate side-chains 411 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 376 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 128 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN E 195 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.124457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107683 restraints weight = 20290.944| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.63 r_work: 0.3345 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11987 Z= 0.124 Angle : 0.566 10.841 16311 Z= 0.286 Chirality : 0.040 0.192 1905 Planarity : 0.004 0.044 1964 Dihedral : 5.135 60.943 1669 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.81 % Allowed : 20.71 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.22), residues: 1423 helix: 2.40 (0.19), residues: 660 sheet: 0.19 (0.30), residues: 288 loop : -0.63 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 260 TYR 0.018 0.001 TYR M 93 PHE 0.014 0.001 PHE A 334 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (11984) covalent geometry : angle 0.56519 / 0.29 (16305) SS BOND : bond 0.00447 / 0.22 ( 3) SS BOND : angle 1.57580 / 0.90 ( 6) hydrogen bonds : bond 0.03831 / 2.54 ( 653) hydrogen bonds : angle 4.17628 / 2.99 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 376 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7607 (mmm) cc_final: 0.7280 (mmm) REVERT: R 79 ILE cc_start: 0.8299 (mt) cc_final: 0.8028 (mt) REVERT: R 110 PHE cc_start: 0.7955 (t80) cc_final: 0.7689 (t80) REVERT: R 141 LEU cc_start: 0.7109 (tp) cc_final: 0.6890 (tp) REVERT: R 168 TYR cc_start: 0.8351 (t80) cc_final: 0.7848 (t80) REVERT: R 221 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8630 (mp) REVERT: R 222 THR cc_start: 0.8367 (m) cc_final: 0.8017 (p) REVERT: R 266 MET cc_start: 0.7536 (tmm) cc_final: 0.6886 (tmm) REVERT: A 14 GLU cc_start: 0.7712 (tt0) cc_final: 0.7390 (tt0) REVERT: A 17 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8007 (mttp) REVERT: A 21 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7507 (ttp80) REVERT: A 25 GLU cc_start: 0.8332 (tt0) cc_final: 0.8049 (tt0) REVERT: A 29 LYS cc_start: 0.8741 (tttt) cc_final: 0.8349 (ttmm) REVERT: A 33 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 193 ASP cc_start: 0.8031 (t0) cc_final: 0.7662 (t0) REVERT: A 197 LYS cc_start: 0.8500 (mttt) cc_final: 0.8121 (mttt) REVERT: A 230 TYR cc_start: 0.7448 (p90) cc_final: 0.6993 (p90) REVERT: A 231 ASP cc_start: 0.7965 (t0) cc_final: 0.7534 (t0) REVERT: A 275 GLU cc_start: 0.7530 (pt0) cc_final: 0.7321 (pt0) REVERT: A 289 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7876 (tp30) REVERT: A 308 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 312 LYS cc_start: 0.8560 (mmtp) cc_final: 0.8259 (mptt) REVERT: A 316 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 96 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7653 (mtt90) REVERT: B 111 TYR cc_start: 0.8792 (m-80) cc_final: 0.8551 (m-80) REVERT: B 130 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 188 MET cc_start: 0.8374 (mmm) cc_final: 0.8044 (mmt) REVERT: B 191 SER cc_start: 0.9063 (p) cc_final: 0.8859 (m) REVERT: B 198 LEU cc_start: 0.9094 (mp) cc_final: 0.8741 (mp) REVERT: B 221 THR cc_start: 0.8565 (m) cc_final: 0.8343 (p) REVERT: B 234 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.6924 (t80) REVERT: B 254 ASP cc_start: 0.7486 (t0) cc_final: 0.7206 (t0) REVERT: B 277 SER cc_start: 0.8501 (t) cc_final: 0.8265 (m) REVERT: C 44 HIS cc_start: 0.8162 (m90) cc_final: 0.7854 (m90) REVERT: E 32 PHE cc_start: 0.8798 (m-80) cc_final: 0.8452 (m-80) REVERT: E 34 MET cc_start: 0.7524 (mmm) cc_final: 0.7292 (mmt) REVERT: E 82 GLN cc_start: 0.7962 (tp40) cc_final: 0.7410 (mm-40) REVERT: E 111 TRP cc_start: 0.8128 (m100) cc_final: 0.7735 (m-10) REVERT: E 115 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7685 (p) REVERT: E 202 ASP cc_start: 0.7749 (t70) cc_final: 0.7442 (t70) REVERT: M 181 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.8061 (mtm180) REVERT: M 200 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7964 (tt) REVERT: M 222 THR cc_start: 0.8878 (t) cc_final: 0.8550 (p) REVERT: M 245 MET cc_start: 0.7706 (tpp) cc_final: 0.7479 (mpp) REVERT: F 349 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7884 (mtmm) outliers start: 48 outliers final: 35 residues processed: 395 average time/residue: 0.1315 time to fit residues: 71.1888 Evaluate side-chains 404 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 364 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 37 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 190 ASN ** 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 = 0.3726 r_free = 0.3726 target = 0.122638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105793 restraints weight = 20205.671| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.62 r_work: 0.3349 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11987 Z= 0.148 Angle : 0.580 10.595 16311 Z= 0.293 Chirality : 0.041 0.199 1905 Planarity : 0.004 0.044 1964 Dihedral : 5.222 59.212 1669 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.44 % Allowed : 20.40 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1423 helix: 2.35 (0.19), residues: 663 sheet: 0.05 (0.29), residues: 289 loop : -0.59 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 260 TYR 0.024 0.002 TYR R 130 PHE 0.020 0.001 PHE A 334 TRP 0.014 0.001 TRP R 320 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11984) covalent geometry : angle 0.57891 / 0.29 (16305) SS BOND : bond 0.00815 / 0.39 ( 3) SS BOND : angle 1.61924 / 0.95 ( 6) hydrogen bonds : bond 0.03975 / 2.65 ( 653) hydrogen bonds : angle 4.21107 / 3.01 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 361 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8288 (mt) cc_final: 0.8019 (mt) REVERT: R 110 PHE cc_start: 0.7911 (t80) cc_final: 0.7688 (t80) REVERT: R 141 LEU cc_start: 0.7223 (tp) cc_final: 0.6993 (tp) REVERT: R 168 TYR cc_start: 0.8331 (t80) cc_final: 0.7889 (t80) REVERT: R 198 SER cc_start: 0.8064 (t) cc_final: 0.7757 (t) REVERT: R 221 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8604 (mp) REVERT: R 222 THR cc_start: 0.8374 (m) cc_final: 0.8042 (p) REVERT: A 14 GLU cc_start: 0.7748 (tt0) cc_final: 0.7462 (tt0) REVERT: A 17 LYS cc_start: 0.8436 (mmmt) cc_final: 0.7928 (mtmm) REVERT: A 21 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7533 (ttp80) REVERT: A 25 GLU cc_start: 0.8329 (tt0) cc_final: 0.8039 (tt0) REVERT: A 29 LYS cc_start: 0.8720 (tttt) cc_final: 0.8346 (ttmm) REVERT: A 33 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7924 (mt-10) REVERT: A 197 LYS cc_start: 0.8546 (mttt) cc_final: 0.8225 (mttt) REVERT: A 230 TYR cc_start: 0.7527 (p90) cc_final: 0.7085 (p90) REVERT: A 231 ASP cc_start: 0.7985 (t0) cc_final: 0.7569 (t0) REVERT: A 275 GLU cc_start: 0.7510 (pt0) cc_final: 0.7302 (pt0) REVERT: A 289 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7805 (tp30) REVERT: A 308 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7988 (mt-10) REVERT: A 312 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8307 (mptt) REVERT: A 316 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8115 (p) REVERT: B 78 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8697 (mmtp) REVERT: B 86 THR cc_start: 0.8876 (p) cc_final: 0.8587 (t) REVERT: B 96 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7666 (mtt90) REVERT: B 111 TYR cc_start: 0.8797 (m-80) cc_final: 0.8559 (m-80) REVERT: B 130 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8193 (mt-10) REVERT: B 132 ASN cc_start: 0.8166 (p0) cc_final: 0.7909 (p0) REVERT: B 188 MET cc_start: 0.8457 (mmm) cc_final: 0.8142 (mmt) REVERT: B 198 LEU cc_start: 0.9139 (mp) cc_final: 0.8875 (mp) REVERT: B 200 VAL cc_start: 0.8950 (p) cc_final: 0.8711 (m) REVERT: B 219 ARG cc_start: 0.8399 (tpp80) cc_final: 0.8002 (ttm110) REVERT: B 221 THR cc_start: 0.8524 (m) cc_final: 0.8314 (p) REVERT: B 254 ASP cc_start: 0.7511 (t0) cc_final: 0.7237 (t0) REVERT: B 277 SER cc_start: 0.8536 (t) cc_final: 0.8290 (m) REVERT: C 44 HIS cc_start: 0.8195 (m90) cc_final: 0.7916 (m90) REVERT: E 32 PHE cc_start: 0.9010 (m-80) cc_final: 0.8347 (m-80) REVERT: E 111 TRP cc_start: 0.8148 (m100) cc_final: 0.7738 (m-10) REVERT: E 115 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7715 (p) REVERT: E 141 MET cc_start: 0.8502 (mmm) cc_final: 0.8252 (mmm) REVERT: E 200 VAL cc_start: 0.9244 (t) cc_final: 0.8959 (m) REVERT: E 202 ASP cc_start: 0.7849 (t70) cc_final: 0.7530 (t70) REVERT: E 232 GLN cc_start: 0.8518 (pp30) cc_final: 0.8281 (pp30) REVERT: M 181 ARG cc_start: 0.8347 (mtp-110) cc_final: 0.8021 (mtm180) REVERT: M 200 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7964 (tt) REVERT: M 205 MET cc_start: 0.7140 (mmt) cc_final: 0.6921 (mmt) REVERT: M 222 THR cc_start: 0.8914 (t) cc_final: 0.8602 (p) REVERT: M 245 MET cc_start: 0.7728 (tpp) cc_final: 0.7492 (tpp) REVERT: F 349 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7895 (mtmm) outliers start: 56 outliers final: 41 residues processed: 386 average time/residue: 0.1314 time to fit residues: 69.5263 Evaluate side-chains 408 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.123690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106892 restraints weight = 20121.161| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.61 r_work: 0.3369 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11987 Z= 0.123 Angle : 0.576 10.648 16311 Z= 0.290 Chirality : 0.040 0.202 1905 Planarity : 0.004 0.043 1964 Dihedral : 5.124 62.433 1669 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.65 % Allowed : 21.27 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.22), residues: 1423 helix: 2.37 (0.19), residues: 665 sheet: 0.12 (0.30), residues: 288 loop : -0.52 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 87 TYR 0.022 0.001 TYR R 130 PHE 0.023 0.001 PHE A 334 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11984) covalent geometry : angle 0.57520 / 0.29 (16305) SS BOND : bond 0.00407 / 0.20 ( 3) SS BOND : angle 1.47610 / 0.85 ( 6) hydrogen bonds : bond 0.03723 / 2.47 ( 653) hydrogen bonds : angle 4.13521 / 2.95 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 366 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8273 (mt) cc_final: 0.7992 (mt) REVERT: R 110 PHE cc_start: 0.7759 (t80) cc_final: 0.7501 (t80) REVERT: R 141 LEU cc_start: 0.7142 (tp) cc_final: 0.6921 (tp) REVERT: R 168 TYR cc_start: 0.8351 (t80) cc_final: 0.7951 (t80) REVERT: R 221 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8578 (mp) REVERT: R 222 THR cc_start: 0.8349 (m) cc_final: 0.8022 (p) REVERT: A 14 GLU cc_start: 0.7743 (tt0) cc_final: 0.7446 (tt0) REVERT: A 17 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8015 (mttp) REVERT: A 21 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7556 (ttp80) REVERT: A 25 GLU cc_start: 0.8326 (tt0) cc_final: 0.8027 (tt0) REVERT: A 29 LYS cc_start: 0.8729 (tttt) cc_final: 0.8337 (ttmm) REVERT: A 33 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 197 LYS cc_start: 0.8495 (mttt) cc_final: 0.8124 (mttt) REVERT: A 230 TYR cc_start: 0.7472 (p90) cc_final: 0.7028 (p90) REVERT: A 231 ASP cc_start: 0.7963 (t0) cc_final: 0.7533 (t0) REVERT: A 289 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7781 (tp30) REVERT: A 308 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8030 (mt-10) REVERT: A 312 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8308 (mptt) REVERT: A 316 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8186 (p) REVERT: B 78 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8698 (mmtp) REVERT: B 111 TYR cc_start: 0.8768 (m-80) cc_final: 0.8476 (m-80) REVERT: B 130 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 132 ASN cc_start: 0.8116 (p0) cc_final: 0.7853 (p0) REVERT: B 188 MET cc_start: 0.8432 (mmm) cc_final: 0.8097 (mmt) REVERT: B 198 LEU cc_start: 0.9105 (mp) cc_final: 0.8861 (mp) REVERT: B 221 THR cc_start: 0.8518 (m) cc_final: 0.8277 (p) REVERT: B 234 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.6930 (t80) REVERT: B 254 ASP cc_start: 0.7451 (t0) cc_final: 0.7192 (t0) REVERT: B 277 SER cc_start: 0.8507 (t) cc_final: 0.8266 (m) REVERT: E 32 PHE cc_start: 0.9017 (m-80) cc_final: 0.8392 (m-80) REVERT: E 34 MET cc_start: 0.7461 (mmm) cc_final: 0.6958 (mmt) REVERT: E 111 TRP cc_start: 0.8086 (m100) cc_final: 0.7767 (m-10) REVERT: E 115 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7720 (p) REVERT: E 200 VAL cc_start: 0.9235 (t) cc_final: 0.8946 (m) REVERT: E 202 ASP cc_start: 0.7810 (t70) cc_final: 0.7499 (t70) REVERT: E 232 GLN cc_start: 0.8446 (pp30) cc_final: 0.8186 (pp30) REVERT: M 181 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.8007 (mtm180) REVERT: M 200 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7898 (tt) REVERT: M 222 THR cc_start: 0.8927 (t) cc_final: 0.8621 (p) REVERT: M 245 MET cc_start: 0.7709 (tpp) cc_final: 0.7508 (tpp) REVERT: F 349 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7868 (mtmm) outliers start: 46 outliers final: 36 residues processed: 387 average time/residue: 0.1313 time to fit residues: 69.5815 Evaluate side-chains 403 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 362 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 0.5980 chunk 26 optimal weight: 0.0370 chunk 69 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 HIS A 213 HIS M 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106570 restraints weight = 20046.764| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.59 r_work: 0.3333 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11987 Z= 0.128 Angle : 0.600 11.061 16311 Z= 0.299 Chirality : 0.040 0.196 1905 Planarity : 0.004 0.043 1964 Dihedral : 5.060 63.495 1669 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.25 % Allowed : 22.62 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.22), residues: 1423 helix: 2.40 (0.19), residues: 665 sheet: 0.13 (0.30), residues: 282 loop : -0.50 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 87 TYR 0.019 0.002 TYR M 93 PHE 0.025 0.001 PHE A 334 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11984) covalent geometry : angle 0.59966 / 0.30 (16305) SS BOND : bond 0.00528 / 0.25 ( 3) SS BOND : angle 1.42474 / 0.83 ( 6) hydrogen bonds : bond 0.03727 / 2.47 ( 653) hydrogen bonds : angle 4.12226 / 2.94 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 365 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8258 (mt) cc_final: 0.7971 (mt) REVERT: R 110 PHE cc_start: 0.7761 (t80) cc_final: 0.7534 (t80) REVERT: R 141 LEU cc_start: 0.7142 (tp) cc_final: 0.6910 (tp) REVERT: R 168 TYR cc_start: 0.8334 (t80) cc_final: 0.7947 (t80) REVERT: R 220 THR cc_start: 0.8555 (t) cc_final: 0.8217 (m) REVERT: R 221 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8607 (mp) REVERT: R 222 THR cc_start: 0.8373 (m) cc_final: 0.8038 (p) REVERT: A 14 GLU cc_start: 0.7757 (tt0) cc_final: 0.7479 (tt0) REVERT: A 17 LYS cc_start: 0.8412 (mmmt) cc_final: 0.7994 (mttp) REVERT: A 21 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7536 (ttp80) REVERT: A 25 GLU cc_start: 0.8304 (tt0) cc_final: 0.7995 (tt0) REVERT: A 29 LYS cc_start: 0.8715 (tttt) cc_final: 0.8319 (ttmm) REVERT: A 33 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 197 LYS cc_start: 0.8485 (mttt) cc_final: 0.8149 (mttt) REVERT: A 230 TYR cc_start: 0.7528 (p90) cc_final: 0.7091 (p90) REVERT: A 231 ASP cc_start: 0.7982 (t0) cc_final: 0.7536 (t0) REVERT: A 312 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8316 (mptt) REVERT: A 316 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8239 (p) REVERT: B 78 LYS cc_start: 0.8921 (mmtm) cc_final: 0.8669 (mmtp) REVERT: B 111 TYR cc_start: 0.8776 (m-80) cc_final: 0.8487 (m-80) REVERT: B 130 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 132 ASN cc_start: 0.8115 (p0) cc_final: 0.7862 (p0) REVERT: B 163 ASP cc_start: 0.8183 (p0) cc_final: 0.7841 (p0) REVERT: B 188 MET cc_start: 0.8445 (mmm) cc_final: 0.8166 (mmt) REVERT: B 198 LEU cc_start: 0.9112 (mp) cc_final: 0.8863 (mp) REVERT: B 221 THR cc_start: 0.8508 (m) cc_final: 0.8261 (p) REVERT: B 234 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.6929 (t80) REVERT: B 254 ASP cc_start: 0.7457 (t0) cc_final: 0.7239 (t0) REVERT: B 277 SER cc_start: 0.8498 (t) cc_final: 0.8241 (m) REVERT: E 34 MET cc_start: 0.7483 (mmm) cc_final: 0.6989 (mmt) REVERT: E 111 TRP cc_start: 0.8087 (m100) cc_final: 0.7711 (m-10) REVERT: E 115 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7808 (p) REVERT: E 200 VAL cc_start: 0.9254 (t) cc_final: 0.8977 (m) REVERT: E 202 ASP cc_start: 0.7807 (t70) cc_final: 0.7478 (t70) REVERT: E 232 GLN cc_start: 0.8418 (pp30) cc_final: 0.8213 (pp30) REVERT: E 234 LEU cc_start: 0.9007 (tp) cc_final: 0.8720 (mt) REVERT: M 181 ARG cc_start: 0.8334 (mtp-110) cc_final: 0.8011 (mtm180) REVERT: M 200 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7910 (tt) REVERT: M 205 MET cc_start: 0.7120 (mmt) cc_final: 0.6887 (mmt) REVERT: M 222 THR cc_start: 0.8921 (t) cc_final: 0.8613 (p) REVERT: F 349 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7864 (mtmm) outliers start: 41 outliers final: 34 residues processed: 381 average time/residue: 0.1216 time to fit residues: 63.4034 Evaluate side-chains 397 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 358 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 110 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 190 ASN ** 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 = 0.3749 r_free = 0.3749 target = 0.124118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107478 restraints weight = 20338.623| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.63 r_work: 0.3373 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11987 Z= 0.122 Angle : 0.598 11.245 16311 Z= 0.302 Chirality : 0.040 0.207 1905 Planarity : 0.004 0.043 1964 Dihedral : 4.968 64.671 1669 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.65 % Allowed : 22.86 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.22), residues: 1423 helix: 2.43 (0.19), residues: 665 sheet: 0.18 (0.30), residues: 283 loop : -0.47 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 87 TYR 0.034 0.002 TYR R 130 PHE 0.030 0.001 PHE A 334 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (11984) covalent geometry : angle 0.59784 / 0.30 (16305) SS BOND : bond 0.00479 / 0.23 ( 3) SS BOND : angle 1.34865 / 0.78 ( 6) hydrogen bonds : bond 0.03612 / 2.39 ( 653) hydrogen bonds : angle 4.09663 / 2.93 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 370 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8186 (mt) cc_final: 0.7899 (mt) REVERT: R 141 LEU cc_start: 0.7157 (tp) cc_final: 0.6937 (tp) REVERT: R 168 TYR cc_start: 0.8336 (t80) cc_final: 0.7968 (t80) REVERT: R 220 THR cc_start: 0.8551 (t) cc_final: 0.8194 (m) REVERT: R 221 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8587 (mp) REVERT: R 222 THR cc_start: 0.8358 (m) cc_final: 0.8032 (p) REVERT: A 14 GLU cc_start: 0.7746 (tt0) cc_final: 0.7468 (tt0) REVERT: A 17 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8020 (mttp) REVERT: A 21 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7547 (ttp80) REVERT: A 25 GLU cc_start: 0.8315 (tt0) cc_final: 0.8019 (tt0) REVERT: A 29 LYS cc_start: 0.8726 (tttt) cc_final: 0.8330 (ttmm) REVERT: A 33 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 197 LYS cc_start: 0.8487 (mttt) cc_final: 0.8105 (mttt) REVERT: A 230 TYR cc_start: 0.7519 (p90) cc_final: 0.7104 (p90) REVERT: A 231 ASP cc_start: 0.7944 (t0) cc_final: 0.7503 (t0) REVERT: A 240 MET cc_start: 0.7793 (tpp) cc_final: 0.7313 (mmp) REVERT: A 312 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8320 (mptt) REVERT: A 316 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 78 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8664 (mmtp) REVERT: B 111 TYR cc_start: 0.8770 (m-80) cc_final: 0.8500 (m-80) REVERT: B 132 ASN cc_start: 0.8137 (p0) cc_final: 0.7889 (p0) REVERT: B 188 MET cc_start: 0.8464 (mmm) cc_final: 0.8169 (mmt) REVERT: B 198 LEU cc_start: 0.9096 (mp) cc_final: 0.8837 (mp) REVERT: B 214 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7929 (ttm110) REVERT: B 221 THR cc_start: 0.8436 (m) cc_final: 0.8181 (p) REVERT: B 234 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6928 (t80) REVERT: B 254 ASP cc_start: 0.7413 (t0) cc_final: 0.7192 (t0) REVERT: B 277 SER cc_start: 0.8503 (t) cc_final: 0.8265 (m) REVERT: E 34 MET cc_start: 0.7496 (mmm) cc_final: 0.7033 (mmt) REVERT: E 111 TRP cc_start: 0.8055 (m100) cc_final: 0.7762 (m-10) REVERT: E 115 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7864 (p) REVERT: E 191 TYR cc_start: 0.8488 (p90) cc_final: 0.8206 (p90) REVERT: E 200 VAL cc_start: 0.9262 (t) cc_final: 0.8986 (m) REVERT: E 202 ASP cc_start: 0.7795 (t70) cc_final: 0.7465 (t70) REVERT: E 232 GLN cc_start: 0.8412 (pp30) cc_final: 0.8178 (pp30) REVERT: E 234 LEU cc_start: 0.8983 (tp) cc_final: 0.8705 (mt) REVERT: M 181 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.7998 (mtm180) REVERT: M 190 ASN cc_start: 0.7720 (m-40) cc_final: 0.7498 (m-40) REVERT: M 200 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7891 (tt) REVERT: M 205 MET cc_start: 0.7150 (mmt) cc_final: 0.6933 (mmt) REVERT: M 222 THR cc_start: 0.8927 (t) cc_final: 0.8624 (p) REVERT: F 349 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7882 (mtmm) outliers start: 46 outliers final: 35 residues processed: 388 average time/residue: 0.1152 time to fit residues: 61.1336 Evaluate side-chains 404 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 364 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 85 optimal weight: 0.0270 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 101 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 110 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 190 ASN ** 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 = 0.3751 r_free = 0.3751 target = 0.124233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.107565 restraints weight = 20103.081| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.59 r_work: 0.3369 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11987 Z= 0.136 Angle : 0.615 11.355 16311 Z= 0.309 Chirality : 0.040 0.193 1905 Planarity : 0.004 0.043 1964 Dihedral : 5.007 64.049 1669 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.33 % Allowed : 23.41 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.22), residues: 1423 helix: 2.39 (0.19), residues: 665 sheet: 0.24 (0.30), residues: 287 loop : -0.52 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 219 TYR 0.018 0.002 TYR M 93 PHE 0.035 0.001 PHE A 334 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11984) covalent geometry : angle 0.61420 / 0.31 (16305) SS BOND : bond 0.00668 / 0.32 ( 3) SS BOND : angle 1.45404 / 0.85 ( 6) hydrogen bonds : bond 0.03748 / 2.49 ( 653) hydrogen bonds : angle 4.13644 / 2.95 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.15 seconds wall clock time: 50 minutes 51.45 seconds (3051.45 seconds total)