Starting phenix.real_space_refine on Wed Mar 4 07:47:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ef5_28066/03_2026/8ef5_28066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ef5_28066/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ef5_28066/03_2026/8ef5_28066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ef5_28066/03_2026/8ef5_28066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ef5_28066/03_2026/8ef5_28066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ef5_28066/03_2026/8ef5_28066.map" } 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-5986/lib/python3.9/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: 2.80, per 1000 atoms: 0.24 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: 0.96 Conformation dependent library (CDL) restraints added in 488.2 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: 0.42 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: 1.91 Time building geometry restraints manager: 1.23 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: 7330 16.39 - 32.78: 226 32.78 - 49.18: 20 49.18 - 65.57: 3 65.57 - 81.96: 2 Dihedral angle restraints: 7581 sinusoidal: 3368 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 7578 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: 0.710 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 8.234 81.961 4848 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 covalent geometry : bond 0.00443 (11984) covalent geometry : angle 0.88237 (16305) SS BOND : bond 0.00303 ( 3) SS BOND : angle 1.27502 ( 6) hydrogen bonds : bond 0.26299 ( 653) hydrogen bonds : angle 7.44899 ( 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 : 0.426 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: 0.1320 time to fit residues: 91.4227 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 : 0.345 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 173 HIS R 190 ASN R 321 HIS A 188 HIS A 204 GLN A 322 HIS A 331 ASN B 91 HIS B 266 HIS E 180 GLN E 233 HIS M 106 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 ASN M 299 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.126805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.109777 restraints weight = 20444.371| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.65 r_work: 0.3421 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11987 Z= 0.183 Angle : 0.623 11.158 16311 Z= 0.326 Chirality : 0.043 0.196 1905 Planarity : 0.005 0.059 1964 Dihedral : 6.013 85.833 2245 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.33 % Allowed : 12.54 % Favored : 84.13 % 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: 0.99 (0.21), residues: 1423 helix: 2.07 (0.18), residues: 652 sheet: 0.24 (0.29), residues: 297 loop : -1.06 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 13 TYR 0.018 0.002 TYR M 93 PHE 0.026 0.002 PHE B 241 TRP 0.018 0.002 TRP R 320 HIS 0.009 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00412 (11984) covalent geometry : angle 0.62132 (16305) SS BOND : bond 0.00983 ( 3) SS BOND : angle 2.21772 ( 6) hydrogen bonds : bond 0.05399 ( 653) hydrogen bonds : angle 4.76046 ( 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 464 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 422 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 72 THR cc_start: 0.8358 (t) cc_final: 0.8051 (p) REVERT: R 130 TYR cc_start: 0.8194 (t80) cc_final: 0.7991 (t80) REVERT: R 188 ILE cc_start: 0.7664 (mt) cc_final: 0.7459 (mt) REVERT: R 222 THR cc_start: 0.8288 (m) cc_final: 0.7948 (p) REVERT: R 266 MET cc_start: 0.7233 (tmm) cc_final: 0.6889 (tmm) REVERT: R 282 ARG cc_start: 0.8513 (ttp-170) cc_final: 0.8233 (ttp-170) REVERT: R 301 TYR cc_start: 0.7872 (t80) cc_final: 0.6931 (t80) REVERT: R 304 ILE cc_start: 0.8351 (mt) cc_final: 0.8147 (tt) REVERT: A 14 GLU cc_start: 0.7783 (tt0) cc_final: 0.7516 (tt0) REVERT: A 17 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8077 (mmmt) REVERT: A 21 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7475 (ttp80) REVERT: A 25 GLU cc_start: 0.8345 (tt0) cc_final: 0.8042 (tt0) REVERT: A 29 LYS cc_start: 0.8760 (tttt) cc_final: 0.8473 (tttt) REVERT: A 33 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 193 ASP cc_start: 0.7908 (t0) cc_final: 0.7653 (t0) REVERT: A 197 LYS cc_start: 0.8639 (mttt) cc_final: 0.7870 (mttt) REVERT: A 231 ASP cc_start: 0.7724 (t0) cc_final: 0.7435 (t0) REVERT: A 247 MET cc_start: 0.8393 (mtt) cc_final: 0.8022 (mtm) REVERT: A 273 LEU cc_start: 0.8862 (mt) cc_final: 0.8388 (tt) REVERT: A 274 PHE cc_start: 0.8603 (t80) cc_final: 0.8112 (t80) REVERT: A 308 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 312 LYS cc_start: 0.8374 (mmtm) cc_final: 0.7981 (mttp) REVERT: A 316 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7966 (p) REVERT: A 317 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8509 (tttt) REVERT: A 350 ASP cc_start: 0.8540 (t0) cc_final: 0.8258 (t0) REVERT: B 17 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 38 ASP cc_start: 0.8526 (p0) cc_final: 0.7930 (p0) REVERT: B 50 THR cc_start: 0.8515 (m) cc_final: 0.8274 (t) REVERT: B 89 LYS cc_start: 0.8956 (mttp) cc_final: 0.8735 (mttp) REVERT: B 96 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7322 (mtt90) REVERT: B 111 TYR cc_start: 0.8842 (m-80) cc_final: 0.8552 (m-80) REVERT: B 130 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 170 ASP cc_start: 0.7799 (t0) cc_final: 0.7302 (t0) REVERT: B 173 THR cc_start: 0.8715 (m) cc_final: 0.8494 (t) REVERT: B 188 MET cc_start: 0.8351 (mmm) cc_final: 0.7609 (mmm) REVERT: B 221 THR cc_start: 0.8653 (m) cc_final: 0.8261 (p) REVERT: B 234 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.6767 (t80) REVERT: B 254 ASP cc_start: 0.7454 (t0) cc_final: 0.7151 (t0) REVERT: C 44 HIS cc_start: 0.8360 (m90) cc_final: 0.7875 (m90) REVERT: E 48 VAL cc_start: 0.7568 (t) cc_final: 0.7190 (t) REVERT: E 115 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7835 (p) REVERT: E 195 ASN cc_start: 0.6679 (m-40) cc_final: 0.6427 (m-40) REVERT: E 202 ASP cc_start: 0.7635 (t70) cc_final: 0.7381 (t70) REVERT: E 231 MET cc_start: 0.8069 (ttp) cc_final: 0.7818 (ttm) REVERT: M 150 TYR cc_start: 0.8480 (m-80) cc_final: 0.8199 (m-80) REVERT: M 190 ASN cc_start: 0.7709 (m-40) cc_final: 0.7396 (m110) REVERT: M 222 THR cc_start: 0.8771 (t) cc_final: 0.8376 (p) REVERT: M 245 MET cc_start: 0.7874 (tpp) cc_final: 0.7533 (mpp) REVERT: F 345 LYS cc_start: 0.8763 (tttt) cc_final: 0.8551 (tttp) REVERT: F 349 LYS cc_start: 0.8277 (mtpt) cc_final: 0.7976 (mtmm) outliers start: 42 outliers final: 23 residues processed: 444 average time/residue: 0.1239 time to fit residues: 74.5003 Evaluate side-chains 412 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 386 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 ILE 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 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: 0.9980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 104 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 ASN B 110 ASN B 142 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 = 0.3781 r_free = 0.3781 target = 0.126450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109503 restraints weight = 20412.354| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.67 r_work: 0.3405 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3947 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= 0.129 Angle : 0.556 10.983 16311 Z= 0.288 Chirality : 0.041 0.200 1905 Planarity : 0.004 0.049 1964 Dihedral : 5.757 73.514 2245 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 4.05 % Allowed : 16.59 % Favored : 79.37 % 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: 1.30 (0.21), residues: 1423 helix: 2.36 (0.19), residues: 657 sheet: 0.27 (0.30), residues: 288 loop : -0.91 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 275 TYR 0.017 0.002 TYR R 151 PHE 0.020 0.001 PHE A 334 TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00279 (11984) covalent geometry : angle 0.55498 (16305) SS BOND : bond 0.00563 ( 3) SS BOND : angle 1.39900 ( 6) hydrogen bonds : bond 0.04488 ( 653) hydrogen bonds : angle 4.37720 ( 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 434 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 383 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7665 (mmm) cc_final: 0.7372 (mmm) REVERT: R 79 ILE cc_start: 0.8382 (mt) cc_final: 0.8113 (mt) REVERT: R 221 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8519 (mp) REVERT: R 222 THR cc_start: 0.8272 (m) cc_final: 0.7930 (p) REVERT: R 304 ILE cc_start: 0.8260 (mt) cc_final: 0.8044 (tt) REVERT: A 14 GLU cc_start: 0.7738 (tt0) cc_final: 0.7400 (tt0) REVERT: A 17 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7927 (mtmm) REVERT: A 21 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7473 (ttp80) REVERT: A 25 GLU cc_start: 0.8403 (tt0) cc_final: 0.8109 (tt0) REVERT: A 29 LYS cc_start: 0.8703 (tttt) cc_final: 0.8476 (ttmm) REVERT: A 193 ASP cc_start: 0.7992 (t0) cc_final: 0.7678 (t0) REVERT: A 231 ASP cc_start: 0.7911 (t0) cc_final: 0.7554 (t0) REVERT: A 247 MET cc_start: 0.8375 (mtt) cc_final: 0.7917 (mtm) REVERT: A 272 ASP cc_start: 0.8139 (p0) cc_final: 0.7725 (p0) REVERT: A 308 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8020 (mt-10) REVERT: A 316 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7971 (p) REVERT: A 350 ASP cc_start: 0.8589 (t0) cc_final: 0.8265 (t0) REVERT: B 17 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 89 LYS cc_start: 0.8990 (mttp) cc_final: 0.8765 (mttp) REVERT: B 111 TYR cc_start: 0.8858 (m-80) cc_final: 0.8547 (m-80) REVERT: B 130 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 163 ASP cc_start: 0.8101 (p0) cc_final: 0.7489 (p0) REVERT: B 165 THR cc_start: 0.8199 (m) cc_final: 0.7859 (p) REVERT: B 170 ASP cc_start: 0.7737 (t0) cc_final: 0.7295 (t0) REVERT: B 173 THR cc_start: 0.8741 (m) cc_final: 0.8530 (t) REVERT: B 198 LEU cc_start: 0.9139 (mp) cc_final: 0.8798 (mp) REVERT: B 212 ASP cc_start: 0.7688 (p0) cc_final: 0.6940 (p0) REVERT: B 221 THR cc_start: 0.8656 (m) cc_final: 0.8274 (p) REVERT: B 229 ILE cc_start: 0.8597 (mt) cc_final: 0.8246 (mp) REVERT: B 234 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.6950 (t80) REVERT: B 254 ASP cc_start: 0.7502 (t0) cc_final: 0.7190 (t0) REVERT: B 261 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8363 (tt) REVERT: B 267 ASP cc_start: 0.8006 (m-30) cc_final: 0.7751 (t0) REVERT: C 38 MET cc_start: 0.9082 (mtt) cc_final: 0.8682 (mpp) REVERT: E 48 VAL cc_start: 0.7566 (t) cc_final: 0.7363 (t) REVERT: E 111 TRP cc_start: 0.8135 (m100) cc_final: 0.7910 (m-10) REVERT: E 115 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7723 (p) REVERT: E 195 ASN cc_start: 0.6920 (m-40) cc_final: 0.6665 (m-40) REVERT: E 202 ASP cc_start: 0.7656 (t70) cc_final: 0.7356 (t70) REVERT: E 232 GLN cc_start: 0.8405 (pp30) cc_final: 0.8204 (pp30) REVERT: M 150 TYR cc_start: 0.8409 (m-80) cc_final: 0.8124 (m-80) REVERT: M 222 THR cc_start: 0.8756 (t) cc_final: 0.8397 (p) REVERT: M 236 ILE cc_start: 0.8723 (mm) cc_final: 0.8495 (mt) REVERT: M 245 MET cc_start: 0.7844 (tpp) cc_final: 0.7427 (mpp) REVERT: F 349 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7943 (mtmm) outliers start: 51 outliers final: 27 residues processed: 400 average time/residue: 0.1241 time to fit residues: 67.2582 Evaluate side-chains 408 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 376 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 285 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 330 ASN 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 128 THR 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 12 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 264 VAL 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: 8.9990 chunk 5 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3708 r_free = 0.3708 target = 0.120989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104244 restraints weight = 20506.339| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.59 r_work: 0.3331 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11987 Z= 0.189 Angle : 0.601 11.068 16311 Z= 0.309 Chirality : 0.042 0.193 1905 Planarity : 0.004 0.048 1964 Dihedral : 6.032 68.414 2245 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.29 % Allowed : 17.86 % Favored : 77.86 % 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: 1.19 (0.21), residues: 1423 helix: 2.20 (0.19), residues: 659 sheet: 0.12 (0.30), residues: 292 loop : -0.79 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 97 TYR 0.028 0.002 TYR R 130 PHE 0.020 0.002 PHE A 334 TRP 0.017 0.002 TRP R 320 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00434 (11984) covalent geometry : angle 0.59948 (16305) SS BOND : bond 0.00820 ( 3) SS BOND : angle 1.99358 ( 6) hydrogen bonds : bond 0.04598 ( 653) hydrogen bonds : angle 4.38385 ( 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 434 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 380 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7602 (mmm) cc_final: 0.7323 (mmm) REVERT: R 79 ILE cc_start: 0.8393 (mt) cc_final: 0.8144 (mt) REVERT: R 101 MET cc_start: 0.7461 (mtm) cc_final: 0.7223 (mtp) REVERT: R 141 LEU cc_start: 0.7310 (tp) cc_final: 0.7106 (tp) REVERT: R 198 SER cc_start: 0.8139 (t) cc_final: 0.7758 (t) REVERT: R 221 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8660 (mp) REVERT: R 222 THR cc_start: 0.8403 (m) cc_final: 0.8039 (p) REVERT: R 304 ILE cc_start: 0.8386 (mt) cc_final: 0.8086 (tt) REVERT: R 330 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8509 (p0) REVERT: A 14 GLU cc_start: 0.7806 (tt0) cc_final: 0.7468 (tt0) REVERT: A 17 LYS cc_start: 0.8482 (mmmt) cc_final: 0.7998 (mtmm) REVERT: A 21 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7537 (ttp80) REVERT: A 25 GLU cc_start: 0.8361 (tt0) cc_final: 0.8065 (tt0) REVERT: A 29 LYS cc_start: 0.8686 (tttt) cc_final: 0.8479 (ttmm) REVERT: A 33 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 193 ASP cc_start: 0.8037 (t0) cc_final: 0.7675 (t0) REVERT: A 231 ASP cc_start: 0.8005 (t0) cc_final: 0.7684 (t0) REVERT: A 276 GLU cc_start: 0.7952 (mp0) cc_final: 0.7724 (mp0) REVERT: A 308 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 316 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 350 ASP cc_start: 0.8648 (t0) cc_final: 0.8236 (t0) REVERT: B 17 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 74 SER cc_start: 0.8738 (t) cc_final: 0.8343 (p) REVERT: B 78 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8568 (mmtm) REVERT: B 96 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7612 (mtt90) REVERT: B 111 TYR cc_start: 0.8815 (m-80) cc_final: 0.8564 (m-80) REVERT: B 130 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8172 (mt-10) REVERT: B 170 ASP cc_start: 0.7828 (t0) cc_final: 0.7431 (t0) REVERT: B 198 LEU cc_start: 0.9151 (mp) cc_final: 0.8871 (mp) REVERT: B 200 VAL cc_start: 0.8990 (p) cc_final: 0.8736 (m) REVERT: B 221 THR cc_start: 0.8655 (m) cc_final: 0.8424 (p) REVERT: B 229 ILE cc_start: 0.8713 (mt) cc_final: 0.8491 (mm) REVERT: B 254 ASP cc_start: 0.7607 (t0) cc_final: 0.7304 (t0) REVERT: B 261 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8482 (tt) REVERT: B 277 SER cc_start: 0.8541 (t) cc_final: 0.8301 (m) REVERT: C 13 ARG cc_start: 0.8833 (ptp-110) cc_final: 0.8362 (ptt-90) REVERT: E 111 TRP cc_start: 0.8180 (m100) cc_final: 0.7830 (m-10) REVERT: E 115 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7708 (p) REVERT: E 141 MET cc_start: 0.8522 (mmm) cc_final: 0.8248 (mmm) REVERT: E 202 ASP cc_start: 0.7845 (t70) cc_final: 0.7519 (t70) REVERT: M 150 TYR cc_start: 0.8447 (m-80) cc_final: 0.8088 (m-80) REVERT: M 153 MET cc_start: 0.7899 (tmm) cc_final: 0.7687 (ttt) REVERT: M 222 THR cc_start: 0.8874 (t) cc_final: 0.8550 (p) REVERT: M 245 MET cc_start: 0.7876 (tpp) cc_final: 0.7525 (mpp) REVERT: F 349 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7920 (mtmm) outliers start: 54 outliers final: 36 residues processed: 397 average time/residue: 0.1258 time to fit residues: 67.5399 Evaluate side-chains 417 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 95 ILE 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 308 VAL Chi-restraints excluded: chain R residue 330 ASN 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 218 VAL Chi-restraints excluded: chain A residue 277 LYS 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 154 ASP 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 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 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: 0.6980 chunk 88 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 35 optimal weight: 0.0020 chunk 120 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN E 195 ASN M 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.107893 restraints weight = 20267.741| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.61 r_work: 0.3382 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11987 Z= 0.112 Angle : 0.541 10.803 16311 Z= 0.277 Chirality : 0.040 0.181 1905 Planarity : 0.004 0.045 1964 Dihedral : 5.646 67.486 2245 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.89 % Allowed : 19.21 % Favored : 76.90 % 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: 1.37 (0.22), residues: 1423 helix: 2.39 (0.19), residues: 661 sheet: 0.13 (0.30), residues: 288 loop : -0.73 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.020 0.001 TYR M 93 PHE 0.024 0.001 PHE A 334 TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS M 173 Details of bonding type rmsd covalent geometry : bond 0.00239 (11984) covalent geometry : angle 0.54061 (16305) SS BOND : bond 0.00398 ( 3) SS BOND : angle 1.61163 ( 6) hydrogen bonds : bond 0.03816 ( 653) hydrogen bonds : angle 4.20186 ( 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 443 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 394 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7631 (mmm) cc_final: 0.7280 (mmm) REVERT: R 79 ILE cc_start: 0.8328 (mt) cc_final: 0.8079 (mt) REVERT: R 198 SER cc_start: 0.8061 (t) cc_final: 0.7728 (t) REVERT: R 221 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8603 (mp) REVERT: R 222 THR cc_start: 0.8338 (m) cc_final: 0.7973 (p) REVERT: R 304 ILE cc_start: 0.8326 (mt) cc_final: 0.8056 (tt) REVERT: R 330 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8536 (p0) REVERT: A 14 GLU cc_start: 0.7748 (tt0) cc_final: 0.7429 (tt0) REVERT: A 17 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8015 (mttp) REVERT: A 21 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7507 (ttp80) REVERT: A 25 GLU cc_start: 0.8312 (tt0) cc_final: 0.8023 (tt0) REVERT: A 29 LYS cc_start: 0.8683 (tttt) cc_final: 0.8408 (ttmm) REVERT: A 193 ASP cc_start: 0.8045 (t0) cc_final: 0.7688 (t0) REVERT: A 230 TYR cc_start: 0.7212 (p90) cc_final: 0.6845 (p90) REVERT: A 231 ASP cc_start: 0.8006 (t0) cc_final: 0.7563 (t0) REVERT: A 275 GLU cc_start: 0.7571 (pt0) cc_final: 0.7365 (pt0) REVERT: A 308 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7982 (mt-10) REVERT: A 316 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7981 (p) REVERT: B 111 TYR cc_start: 0.8806 (m-80) cc_final: 0.8533 (m-80) REVERT: B 130 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 173 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8866 (p) REVERT: B 197 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8254 (mmm-85) REVERT: B 198 LEU cc_start: 0.9111 (mp) cc_final: 0.8849 (mp) REVERT: B 200 VAL cc_start: 0.8950 (p) cc_final: 0.8679 (m) REVERT: B 221 THR cc_start: 0.8631 (m) cc_final: 0.8376 (p) REVERT: B 234 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.6954 (t80) REVERT: B 254 ASP cc_start: 0.7479 (t0) cc_final: 0.7194 (t0) REVERT: B 277 SER cc_start: 0.8505 (t) cc_final: 0.8286 (m) REVERT: C 13 ARG cc_start: 0.8695 (ptp-110) cc_final: 0.8320 (ptt-90) REVERT: C 44 HIS cc_start: 0.8124 (m90) cc_final: 0.7739 (m90) REVERT: E 111 TRP cc_start: 0.8110 (m100) cc_final: 0.7810 (m-10) REVERT: E 115 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7668 (p) REVERT: E 202 ASP cc_start: 0.7743 (t70) cc_final: 0.7426 (t70) REVERT: E 232 GLN cc_start: 0.8518 (pp30) cc_final: 0.8072 (pp30) REVERT: M 150 TYR cc_start: 0.8338 (m-80) cc_final: 0.7908 (m-80) REVERT: M 200 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7913 (tt) REVERT: M 222 THR cc_start: 0.8867 (t) cc_final: 0.8536 (p) REVERT: M 245 MET cc_start: 0.7718 (tpp) cc_final: 0.7472 (mpp) REVERT: F 349 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7886 (mtmm) outliers start: 49 outliers final: 30 residues processed: 410 average time/residue: 0.1224 time to fit residues: 68.6958 Evaluate side-chains 410 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 330 ASN 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 138 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER 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 28 ILE 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 200 ILE 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: 0.5980 chunk 118 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 110 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN M 232 ASN M 344 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.124673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.107879 restraints weight = 20311.463| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.62 r_work: 0.3346 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11987 Z= 0.125 Angle : 0.570 10.750 16311 Z= 0.288 Chirality : 0.041 0.191 1905 Planarity : 0.004 0.052 1964 Dihedral : 5.627 62.307 2245 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.13 % Allowed : 20.16 % Favored : 75.71 % 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: 2.42 (0.19), residues: 661 sheet: 0.14 (0.30), residues: 288 loop : -0.63 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 181 TYR 0.018 0.001 TYR M 93 PHE 0.015 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 covalent geometry : bond 0.00277 (11984) covalent geometry : angle 0.56973 (16305) SS BOND : bond 0.00448 ( 3) SS BOND : angle 1.40260 ( 6) hydrogen bonds : bond 0.03811 ( 653) hydrogen bonds : angle 4.17028 ( 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 431 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 379 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7570 (mmm) cc_final: 0.7251 (mmm) REVERT: R 79 ILE cc_start: 0.8301 (mt) cc_final: 0.8021 (mt) REVERT: R 168 TYR cc_start: 0.8304 (t80) cc_final: 0.7896 (t80) REVERT: R 221 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8618 (mp) REVERT: R 222 THR cc_start: 0.8290 (m) cc_final: 0.7952 (p) REVERT: R 266 MET cc_start: 0.7536 (tmm) cc_final: 0.6890 (tmm) REVERT: A 14 GLU cc_start: 0.7761 (tt0) cc_final: 0.7446 (tt0) REVERT: A 17 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8012 (mttp) REVERT: A 21 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7494 (ttp80) REVERT: A 25 GLU cc_start: 0.8308 (tt0) cc_final: 0.8016 (tt0) REVERT: A 29 LYS cc_start: 0.8655 (tttt) cc_final: 0.8368 (ttmm) REVERT: A 193 ASP cc_start: 0.8041 (t0) cc_final: 0.7668 (t0) REVERT: A 231 ASP cc_start: 0.8030 (t0) cc_final: 0.7686 (t0) REVERT: A 308 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 316 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8030 (p) REVERT: B 78 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8654 (mmtt) REVERT: B 111 TYR cc_start: 0.8777 (m-80) cc_final: 0.8512 (m-80) REVERT: B 130 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8204 (mt-10) REVERT: B 161 SER cc_start: 0.8476 (m) cc_final: 0.8245 (p) REVERT: B 198 LEU cc_start: 0.9137 (mp) cc_final: 0.8865 (mp) REVERT: B 200 VAL cc_start: 0.8950 (p) cc_final: 0.8674 (m) REVERT: B 221 THR cc_start: 0.8607 (m) cc_final: 0.8350 (p) REVERT: B 234 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.6923 (t80) REVERT: B 254 ASP cc_start: 0.7466 (t0) cc_final: 0.7194 (t0) REVERT: B 277 SER cc_start: 0.8506 (t) cc_final: 0.8273 (m) REVERT: C 44 HIS cc_start: 0.8139 (m90) cc_final: 0.7909 (m90) REVERT: E 34 MET cc_start: 0.7504 (mmm) cc_final: 0.7277 (mmt) REVERT: E 85 SER cc_start: 0.8389 (t) cc_final: 0.8010 (p) REVERT: E 111 TRP cc_start: 0.8131 (m100) cc_final: 0.7754 (m-10) REVERT: E 115 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7669 (p) REVERT: E 202 ASP cc_start: 0.7780 (t70) cc_final: 0.7469 (t70) REVERT: M 200 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7909 (tt) REVERT: M 205 MET cc_start: 0.7054 (mmt) cc_final: 0.6798 (mmt) REVERT: M 222 THR cc_start: 0.8888 (t) cc_final: 0.8560 (p) REVERT: M 245 MET cc_start: 0.7708 (tpp) cc_final: 0.7495 (mpp) REVERT: F 349 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7871 (mtmm) outliers start: 52 outliers final: 35 residues processed: 400 average time/residue: 0.1240 time to fit residues: 67.7152 Evaluate side-chains 412 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 372 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 214 ARG 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 28 ILE 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 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 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: 1.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS 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 = 0.3732 r_free = 0.3732 target = 0.123015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106165 restraints weight = 20202.699| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.62 r_work: 0.3357 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5185 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= 0.144 Angle : 0.575 10.519 16311 Z= 0.291 Chirality : 0.041 0.189 1905 Planarity : 0.004 0.057 1964 Dihedral : 5.677 60.302 2245 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.05 % Allowed : 20.79 % 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: 1.39 (0.22), residues: 1423 helix: 2.40 (0.19), residues: 660 sheet: 0.09 (0.30), residues: 287 loop : -0.64 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 181 TYR 0.019 0.002 TYR M 93 PHE 0.022 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 covalent geometry : bond 0.00329 (11984) covalent geometry : angle 0.57407 (16305) SS BOND : bond 0.00493 ( 3) SS BOND : angle 1.48358 ( 6) hydrogen bonds : bond 0.03902 ( 653) hydrogen bonds : angle 4.17613 ( 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 427 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 376 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7549 (mmm) cc_final: 0.7246 (mmm) REVERT: R 79 ILE cc_start: 0.8294 (mt) cc_final: 0.8013 (mt) REVERT: R 168 TYR cc_start: 0.8327 (t80) cc_final: 0.7941 (t80) REVERT: R 198 SER cc_start: 0.8086 (t) cc_final: 0.7758 (t) REVERT: R 221 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8580 (mp) REVERT: R 222 THR cc_start: 0.8352 (m) cc_final: 0.8017 (p) REVERT: R 266 MET cc_start: 0.7627 (tmm) cc_final: 0.7114 (tmm) REVERT: A 14 GLU cc_start: 0.7806 (tt0) cc_final: 0.7512 (tt0) REVERT: A 17 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8035 (mttp) REVERT: A 21 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7523 (ttp80) REVERT: A 25 GLU cc_start: 0.8302 (tt0) cc_final: 0.8022 (tt0) REVERT: A 29 LYS cc_start: 0.8675 (tttt) cc_final: 0.8420 (ttmm) REVERT: A 193 ASP cc_start: 0.8035 (t0) cc_final: 0.7656 (t0) REVERT: A 231 ASP cc_start: 0.7931 (t0) cc_final: 0.7581 (t0) REVERT: A 308 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 316 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8086 (p) REVERT: B 111 TYR cc_start: 0.8783 (m-80) cc_final: 0.8558 (m-80) REVERT: B 130 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8208 (mt-10) REVERT: B 132 ASN cc_start: 0.8193 (p0) cc_final: 0.7983 (p0) REVERT: B 198 LEU cc_start: 0.9116 (mp) cc_final: 0.8734 (mp) REVERT: B 200 VAL cc_start: 0.8980 (p) cc_final: 0.8702 (m) REVERT: B 221 THR cc_start: 0.8585 (m) cc_final: 0.8341 (p) REVERT: B 254 ASP cc_start: 0.7499 (t0) cc_final: 0.7249 (t0) REVERT: B 277 SER cc_start: 0.8526 (t) cc_final: 0.8286 (m) REVERT: E 85 SER cc_start: 0.8432 (t) cc_final: 0.8072 (p) REVERT: E 98 ARG cc_start: 0.8504 (ptt-90) cc_final: 0.8215 (ptt180) REVERT: E 111 TRP cc_start: 0.8139 (m100) cc_final: 0.7697 (m-10) REVERT: E 115 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7720 (p) REVERT: E 200 VAL cc_start: 0.9245 (t) cc_final: 0.8952 (m) REVERT: E 202 ASP cc_start: 0.7860 (t70) cc_final: 0.7546 (t70) REVERT: E 232 GLN cc_start: 0.8522 (pp30) cc_final: 0.8307 (pp30) REVERT: E 234 LEU cc_start: 0.9030 (tp) cc_final: 0.8717 (mt) REVERT: M 200 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7940 (tt) REVERT: M 222 THR cc_start: 0.8922 (t) cc_final: 0.8622 (p) REVERT: F 349 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7879 (mtmm) outliers start: 51 outliers final: 39 residues processed: 399 average time/residue: 0.1275 time to fit residues: 69.6915 Evaluate side-chains 413 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 370 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 330 ASN Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN 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 52 ARG Chi-restraints excluded: chain B residue 138 GLU 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 28 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 13 GLN B 110 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107629 restraints weight = 20117.559| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.60 r_work: 0.3374 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5310 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= 0.119 Angle : 0.565 10.850 16311 Z= 0.285 Chirality : 0.040 0.193 1905 Planarity : 0.004 0.051 1964 Dihedral : 5.579 63.353 2245 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.13 % Allowed : 21.35 % Favored : 74.52 % 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: 2.38 (0.19), residues: 662 sheet: 0.17 (0.30), residues: 281 loop : -0.58 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 279 TYR 0.027 0.002 TYR A 290 PHE 0.026 0.001 PHE A 334 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd covalent geometry : bond 0.00264 (11984) covalent geometry : angle 0.56502 (16305) SS BOND : bond 0.00414 ( 3) SS BOND : angle 1.31217 ( 6) hydrogen bonds : bond 0.03680 ( 653) hydrogen bonds : angle 4.09750 ( 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 430 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 378 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8289 (mt) cc_final: 0.8005 (mt) REVERT: R 168 TYR cc_start: 0.8342 (t80) cc_final: 0.7997 (t80) REVERT: R 221 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8573 (mp) REVERT: R 222 THR cc_start: 0.8338 (m) cc_final: 0.8005 (p) REVERT: R 266 MET cc_start: 0.7684 (tmm) cc_final: 0.7240 (tmm) REVERT: A 14 GLU cc_start: 0.7811 (tt0) cc_final: 0.7524 (tt0) REVERT: A 17 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8046 (mttp) REVERT: A 21 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7524 (ttp80) REVERT: A 25 GLU cc_start: 0.8321 (tt0) cc_final: 0.8031 (tt0) REVERT: A 29 LYS cc_start: 0.8648 (tttt) cc_final: 0.8357 (ttmm) REVERT: A 231 ASP cc_start: 0.8034 (t0) cc_final: 0.7678 (t0) REVERT: A 316 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 78 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8653 (mmtt) REVERT: B 96 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7615 (mtt90) REVERT: B 111 TYR cc_start: 0.8777 (m-80) cc_final: 0.8502 (m-80) REVERT: B 127 LYS cc_start: 0.9263 (mmtt) cc_final: 0.9057 (mttm) REVERT: B 130 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8255 (mt-10) REVERT: B 132 ASN cc_start: 0.8150 (p0) cc_final: 0.7894 (p0) REVERT: B 198 LEU cc_start: 0.9110 (mp) cc_final: 0.8842 (mp) REVERT: B 200 VAL cc_start: 0.8960 (p) cc_final: 0.8734 (m) REVERT: B 221 THR cc_start: 0.8529 (m) cc_final: 0.8310 (p) REVERT: B 234 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.6954 (t80) REVERT: B 254 ASP cc_start: 0.7448 (t0) cc_final: 0.7202 (t0) REVERT: B 277 SER cc_start: 0.8511 (t) cc_final: 0.8272 (m) REVERT: C 44 HIS cc_start: 0.8132 (m90) cc_final: 0.7660 (m90) REVERT: E 34 MET cc_start: 0.7452 (mmm) cc_final: 0.7104 (mmt) REVERT: E 85 SER cc_start: 0.8410 (t) cc_final: 0.8106 (p) REVERT: E 98 ARG cc_start: 0.8468 (ptt-90) cc_final: 0.8042 (ptt180) REVERT: E 115 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7708 (p) REVERT: E 200 VAL cc_start: 0.9233 (t) cc_final: 0.8943 (m) REVERT: E 202 ASP cc_start: 0.7820 (t70) cc_final: 0.7515 (t70) REVERT: E 234 LEU cc_start: 0.9000 (tp) cc_final: 0.8719 (mt) REVERT: M 200 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7899 (tt) REVERT: M 222 THR cc_start: 0.8928 (t) cc_final: 0.8624 (p) REVERT: F 349 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7853 (mtmm) outliers start: 52 outliers final: 39 residues processed: 399 average time/residue: 0.1287 time to fit residues: 70.1418 Evaluate side-chains 414 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 370 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 285 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 33 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 138 GLU 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 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 28 ILE 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 121 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 146 ILE 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 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: 3.9990 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 75 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** 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 = 0.3762 r_free = 0.3762 target = 0.125083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108445 restraints weight = 19978.320| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.59 r_work: 0.3387 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11987 Z= 0.119 Angle : 0.586 11.038 16311 Z= 0.294 Chirality : 0.040 0.194 1905 Planarity : 0.004 0.053 1964 Dihedral : 5.510 65.562 2245 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.65 % Allowed : 22.38 % Favored : 73.97 % 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: 1.47 (0.22), residues: 1423 helix: 2.39 (0.19), residues: 661 sheet: 0.24 (0.30), residues: 281 loop : -0.56 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 87 TYR 0.019 0.001 TYR M 93 PHE 0.029 0.001 PHE A 334 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd covalent geometry : bond 0.00263 (11984) covalent geometry : angle 0.58594 (16305) SS BOND : bond 0.00489 ( 3) SS BOND : angle 1.34468 ( 6) hydrogen bonds : bond 0.03610 ( 653) hydrogen bonds : angle 4.08511 ( 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 416 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 370 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8265 (mt) cc_final: 0.7980 (mt) REVERT: R 168 TYR cc_start: 0.8327 (t80) cc_final: 0.7998 (t80) REVERT: R 221 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8593 (mp) REVERT: R 222 THR cc_start: 0.8338 (m) cc_final: 0.8005 (p) REVERT: R 266 MET cc_start: 0.7729 (tmm) cc_final: 0.7306 (tmm) REVERT: A 14 GLU cc_start: 0.7819 (tt0) cc_final: 0.7529 (tt0) REVERT: A 17 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8049 (mttp) REVERT: A 21 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7515 (ttp80) REVERT: A 25 GLU cc_start: 0.8291 (tt0) cc_final: 0.8001 (tt0) REVERT: A 29 LYS cc_start: 0.8657 (tttt) cc_final: 0.8318 (ttmm) REVERT: A 231 ASP cc_start: 0.7995 (t0) cc_final: 0.7634 (t0) REVERT: A 316 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 78 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8633 (mmtt) REVERT: B 89 LYS cc_start: 0.9084 (mttp) cc_final: 0.8857 (mttp) REVERT: B 96 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7618 (mtt90) REVERT: B 111 TYR cc_start: 0.8749 (m-80) cc_final: 0.8502 (m-80) REVERT: B 120 ILE cc_start: 0.8506 (mm) cc_final: 0.8301 (mm) REVERT: B 130 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8247 (mt-10) REVERT: B 132 ASN cc_start: 0.8156 (p0) cc_final: 0.7899 (p0) REVERT: B 198 LEU cc_start: 0.9101 (mp) cc_final: 0.8672 (mp) REVERT: B 200 VAL cc_start: 0.8938 (p) cc_final: 0.8705 (m) REVERT: B 221 THR cc_start: 0.8485 (m) cc_final: 0.8243 (p) REVERT: B 234 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.6991 (t80) REVERT: B 254 ASP cc_start: 0.7395 (t0) cc_final: 0.7177 (t0) REVERT: B 277 SER cc_start: 0.8505 (t) cc_final: 0.8278 (m) REVERT: C 44 HIS cc_start: 0.8092 (m90) cc_final: 0.7800 (m90) REVERT: E 34 MET cc_start: 0.7429 (mmm) cc_final: 0.7127 (mmt) REVERT: E 85 SER cc_start: 0.8413 (t) cc_final: 0.8108 (p) REVERT: E 98 ARG cc_start: 0.8469 (ptt-90) cc_final: 0.8073 (ptt180) REVERT: E 115 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7830 (p) REVERT: E 200 VAL cc_start: 0.9242 (t) cc_final: 0.8957 (m) REVERT: E 202 ASP cc_start: 0.7788 (t70) cc_final: 0.7469 (t70) REVERT: M 190 ASN cc_start: 0.7731 (m-40) cc_final: 0.7487 (m-40) REVERT: M 200 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7865 (tt) REVERT: M 222 THR cc_start: 0.8919 (t) cc_final: 0.8610 (p) REVERT: F 349 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7856 (mtmm) outliers start: 46 outliers final: 37 residues processed: 385 average time/residue: 0.1301 time to fit residues: 68.2603 Evaluate side-chains 409 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 367 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN 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 A residue 337 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 138 GLU 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 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 28 ILE 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 121 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 146 ILE 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: 4.9990 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 105 optimal weight: 0.0050 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** 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 = 0.3750 r_free = 0.3750 target = 0.124066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107429 restraints weight = 20332.737| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.62 r_work: 0.3374 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5533 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= 0.127 Angle : 0.603 11.356 16311 Z= 0.302 Chirality : 0.040 0.189 1905 Planarity : 0.004 0.056 1964 Dihedral : 5.527 66.301 2245 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.49 % Allowed : 22.70 % Favored : 73.81 % 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: 1.45 (0.22), residues: 1423 helix: 2.40 (0.19), residues: 661 sheet: 0.21 (0.30), residues: 286 loop : -0.61 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 87 TYR 0.030 0.002 TYR R 130 PHE 0.038 0.001 PHE A 334 TRP 0.024 0.001 TRP E 111 HIS 0.003 0.001 HIS M 173 Details of bonding type rmsd covalent geometry : bond 0.00287 (11984) covalent geometry : angle 0.60221 (16305) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.42832 ( 6) hydrogen bonds : bond 0.03635 ( 653) hydrogen bonds : angle 4.10950 ( 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 415 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 371 time to evaluate : 0.442 Fit side-chains 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 168 TYR cc_start: 0.8331 (t80) cc_final: 0.8010 (t80) REVERT: R 221 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8608 (mp) REVERT: R 222 THR cc_start: 0.8357 (m) cc_final: 0.8027 (p) REVERT: A 14 GLU cc_start: 0.7820 (tt0) cc_final: 0.7537 (tt0) REVERT: A 17 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8048 (mttp) REVERT: A 21 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7542 (ttp80) REVERT: A 25 GLU cc_start: 0.8273 (tt0) cc_final: 0.7986 (tt0) REVERT: A 29 LYS cc_start: 0.8682 (tttt) cc_final: 0.8338 (ttmm) REVERT: A 231 ASP cc_start: 0.7931 (t0) cc_final: 0.7574 (t0) REVERT: A 240 MET cc_start: 0.7799 (tpp) cc_final: 0.7337 (mmp) REVERT: A 308 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7995 (mt-10) REVERT: A 316 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 78 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8649 (mmtt) REVERT: B 89 LYS cc_start: 0.9002 (mttp) cc_final: 0.8760 (mttp) REVERT: B 96 ARG cc_start: 0.8117 (mtt90) cc_final: 0.7630 (mtt90) REVERT: B 111 TYR cc_start: 0.8758 (m-80) cc_final: 0.8528 (m-80) REVERT: B 119 ASN cc_start: 0.9112 (m-40) cc_final: 0.8807 (m110) REVERT: B 130 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8225 (mt-10) REVERT: B 198 LEU cc_start: 0.9096 (mp) cc_final: 0.8740 (mp) REVERT: B 200 VAL cc_start: 0.8952 (p) cc_final: 0.8724 (m) REVERT: B 221 THR cc_start: 0.8432 (m) cc_final: 0.8193 (p) REVERT: B 234 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6989 (t80) REVERT: B 277 SER cc_start: 0.8491 (t) cc_final: 0.8269 (m) REVERT: C 44 HIS cc_start: 0.8069 (m90) cc_final: 0.7790 (m90) REVERT: E 34 MET cc_start: 0.7449 (mmm) cc_final: 0.7152 (mmt) REVERT: E 85 SER cc_start: 0.8420 (t) cc_final: 0.8129 (p) REVERT: E 98 ARG cc_start: 0.8456 (ptt-90) cc_final: 0.8017 (ptt180) REVERT: E 115 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7877 (p) REVERT: E 200 VAL cc_start: 0.9252 (t) cc_final: 0.9018 (m) REVERT: E 202 ASP cc_start: 0.7771 (t70) cc_final: 0.7458 (t70) REVERT: M 200 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7886 (tt) REVERT: M 222 THR cc_start: 0.8924 (t) cc_final: 0.8633 (p) REVERT: F 349 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7866 (mtmm) outliers start: 44 outliers final: 35 residues processed: 388 average time/residue: 0.1300 time to fit residues: 68.7663 Evaluate side-chains 401 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 361 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 340 THR 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 28 ILE 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 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: 10.0000 chunk 92 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 110 ASN B 155 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107465 restraints weight = 20195.594| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.62 r_work: 0.3377 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5642 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= 0.133 Angle : 0.612 11.239 16311 Z= 0.309 Chirality : 0.041 0.289 1905 Planarity : 0.004 0.057 1964 Dihedral : 5.562 65.826 2245 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.73 % Allowed : 22.78 % 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: 1.45 (0.22), residues: 1423 helix: 2.37 (0.19), residues: 663 sheet: 0.25 (0.30), residues: 282 loop : -0.61 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 260 TYR 0.019 0.002 TYR M 93 PHE 0.036 0.001 PHE A 334 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00300 (11984) covalent geometry : angle 0.61156 (16305) SS BOND : bond 0.00565 ( 3) SS BOND : angle 1.57715 ( 6) hydrogen bonds : bond 0.03679 ( 653) hydrogen bonds : angle 4.18335 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2715.76 seconds wall clock time: 47 minutes 23.49 seconds (2843.49 seconds total)