Starting phenix.real_space_refine on Wed Jul 30 03:51:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ef5_28066/07_2025/8ef5_28066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ef5_28066/07_2025/8ef5_28066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2025/8ef5_28066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2025/8ef5_28066.map" model { file = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2025/8ef5_28066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ef5_28066/07_2025/8ef5_28066.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.81, per 1000 atoms: 0.58 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: 2.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.31 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: 3.41 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.430 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (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 TRP 0.027 0.002 TRP R 135 HIS 0.006 0.001 HIS B 225 PHE 0.020 0.002 PHE B 234 TYR 0.023 0.002 TYR M 151 ARG 0.007 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.26299 ( 653) hydrogen bonds : angle 7.44899 ( 1893) SS BOND : bond 0.00303 ( 3) SS BOND : angle 1.27502 ( 6) covalent geometry : bond 0.00443 (11984) covalent geometry : angle 0.88237 (16305) *********************** 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 : 1.267 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: 0.6913 (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: 0.7639 (mt) REVERT: A 8 GLU cc_start: 0.7435 (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: 0.8118 (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: 0.6615 (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: 0.7794 (p0) REVERT: A 273 LEU cc_start: 0.8792 (mt) cc_final: 0.8453 (tt) REVERT: A 274 PHE cc_start: 0.8509 (t80) cc_final: 0.7938 (t80) 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: 0.7677 (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: 0.7204 (mmm) cc_final: 0.6872 (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: 0.7867 (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: 0.7966 (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: 0.8134 (tttp) REVERT: F 349 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7719 (mtmm) outliers start: 0 outliers final: 0 residues processed: 508 average time/residue: 0.2743 time to fit residues: 188.0515 Evaluate side-chains 408 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0060 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 204 GLN A 322 HIS A 331 ASN B 91 HIS B 266 HIS E 180 GLN E 195 ASN E 232 GLN E 233 HIS ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.130179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113290 restraints weight = 20337.153| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.64 r_work: 0.3470 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11987 Z= 0.143 Angle : 0.588 11.422 16311 Z= 0.306 Chirality : 0.042 0.192 1905 Planarity : 0.004 0.057 1964 Dihedral : 5.915 88.975 2245 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.70 % Allowed : 13.10 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1423 helix: 2.15 (0.18), residues: 654 sheet: 0.42 (0.30), residues: 290 loop : -1.11 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 320 HIS 0.008 0.001 HIS A 322 PHE 0.025 0.001 PHE B 241 TYR 0.015 0.002 TYR M 93 ARG 0.010 0.001 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.05498 ( 653) hydrogen bonds : angle 4.75648 ( 1893) SS BOND : bond 0.00716 ( 3) SS BOND : angle 2.03428 ( 6) covalent geometry : bond 0.00304 (11984) covalent geometry : angle 0.58690 (16305) *********************** 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 440 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 406 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 72 THR cc_start: 0.8353 (t) cc_final: 0.8030 (p) REVERT: R 88 ASN cc_start: 0.7799 (m-40) cc_final: 0.7586 (m-40) REVERT: R 188 ILE cc_start: 0.7688 (mt) cc_final: 0.7482 (mt) REVERT: R 207 MET cc_start: 0.7946 (mtm) cc_final: 0.7742 (mtm) REVERT: R 209 THR cc_start: 0.8479 (p) cc_final: 0.8176 (p) REVERT: R 222 THR cc_start: 0.8133 (m) cc_final: 0.7918 (p) REVERT: R 266 MET cc_start: 0.7048 (tmm) cc_final: 0.6686 (tmm) REVERT: R 282 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.8274 (ttp-170) REVERT: R 301 TYR cc_start: 0.7502 (t80) cc_final: 0.6837 (t80) REVERT: A 14 GLU cc_start: 0.7758 (tt0) cc_final: 0.7433 (tt0) REVERT: A 17 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8059 (mmmt) REVERT: A 18 MET cc_start: 0.8020 (mmm) cc_final: 0.7723 (tpp) REVERT: A 21 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7482 (ttp80) REVERT: A 29 LYS cc_start: 0.8759 (tttt) cc_final: 0.8422 (tttt) REVERT: A 33 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 193 ASP cc_start: 0.7863 (t0) cc_final: 0.7630 (t0) REVERT: A 197 LYS cc_start: 0.8554 (mttt) cc_final: 0.8173 (mttt) REVERT: A 231 ASP cc_start: 0.7659 (t0) cc_final: 0.7378 (t0) REVERT: A 247 MET cc_start: 0.8326 (mtt) cc_final: 0.7942 (mtm) REVERT: A 272 ASP cc_start: 0.8048 (p0) cc_final: 0.7742 (p0) REVERT: A 273 LEU cc_start: 0.8784 (mt) cc_final: 0.8243 (tt) REVERT: A 274 PHE cc_start: 0.8586 (t80) cc_final: 0.8093 (t80) REVERT: A 275 GLU cc_start: 0.7602 (pt0) cc_final: 0.7145 (pt0) REVERT: A 276 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7675 (mp0) REVERT: A 308 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7996 (mt-10) REVERT: A 312 LYS cc_start: 0.8244 (mmtm) cc_final: 0.8002 (mttp) REVERT: A 316 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7916 (p) REVERT: A 317 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8465 (tttt) REVERT: A 350 ASP cc_start: 0.8520 (t0) cc_final: 0.8206 (t0) REVERT: B 17 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 38 ASP cc_start: 0.8522 (p0) cc_final: 0.7917 (p0) REVERT: B 50 THR cc_start: 0.8488 (m) cc_final: 0.8238 (t) REVERT: B 89 LYS cc_start: 0.8968 (mttp) cc_final: 0.8759 (mttp) REVERT: B 111 TYR cc_start: 0.8841 (m-80) cc_final: 0.8555 (m-80) REVERT: B 188 MET cc_start: 0.8213 (mmm) cc_final: 0.7390 (mmm) REVERT: B 221 THR cc_start: 0.8616 (m) cc_final: 0.8097 (p) REVERT: B 229 ILE cc_start: 0.8510 (mt) cc_final: 0.8177 (mp) REVERT: B 234 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.6838 (t80) REVERT: B 289 TYR cc_start: 0.7889 (m-80) cc_final: 0.7591 (m-80) REVERT: C 13 ARG cc_start: 0.8802 (ttp-110) cc_final: 0.8489 (mtm110) REVERT: C 44 HIS cc_start: 0.8209 (m90) cc_final: 0.7851 (m90) REVERT: E 34 MET cc_start: 0.7217 (mmm) cc_final: 0.7008 (mmt) REVERT: E 47 TRP cc_start: 0.8036 (t60) cc_final: 0.7800 (t60) REVERT: E 85 SER cc_start: 0.7816 (t) cc_final: 0.7541 (t) REVERT: E 218 SER cc_start: 0.8421 (m) cc_final: 0.8202 (p) REVERT: E 231 MET cc_start: 0.7919 (ttp) cc_final: 0.7633 (ttm) REVERT: E 232 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7817 (pp30) REVERT: M 101 MET cc_start: 0.6133 (tmm) cc_final: 0.5927 (mmm) REVERT: M 150 TYR cc_start: 0.8485 (m-80) cc_final: 0.8182 (m-80) REVERT: M 190 ASN cc_start: 0.7651 (m-40) cc_final: 0.7340 (m110) REVERT: M 222 THR cc_start: 0.8738 (t) cc_final: 0.8308 (p) REVERT: M 245 MET cc_start: 0.7813 (tpp) cc_final: 0.7523 (mpp) REVERT: M 283 MET cc_start: 0.8169 (tpp) cc_final: 0.7881 (tpp) REVERT: F 345 LYS cc_start: 0.8770 (tttt) cc_final: 0.8557 (tttp) REVERT: F 349 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7985 (mtmm) outliers start: 34 outliers final: 17 residues processed: 422 average time/residue: 0.2850 time to fit residues: 161.2337 Evaluate side-chains 415 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 395 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 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 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain M residue 285 LEU 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 101 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 ASN R 321 HIS B 110 ASN B 142 HIS ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 173 HIS ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.126304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109321 restraints weight = 20443.801| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.63 r_work: 0.3412 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11987 Z= 0.143 Angle : 0.558 10.759 16311 Z= 0.289 Chirality : 0.041 0.226 1905 Planarity : 0.004 0.046 1964 Dihedral : 5.757 76.922 2245 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.97 % Allowed : 15.40 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1423 helix: 2.42 (0.19), residues: 658 sheet: 0.25 (0.30), residues: 294 loop : -0.92 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.001 PHE B 241 TYR 0.024 0.002 TYR R 130 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 653) hydrogen bonds : angle 4.39696 ( 1893) SS BOND : bond 0.00855 ( 3) SS BOND : angle 1.18952 ( 6) covalent geometry : bond 0.00310 (11984) covalent geometry : angle 0.55773 (16305) *********************** 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 450 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 400 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7698 (mmm) cc_final: 0.7412 (mmm) REVERT: R 79 ILE cc_start: 0.8407 (mt) cc_final: 0.8132 (mt) REVERT: R 141 LEU cc_start: 0.7427 (tp) cc_final: 0.7213 (tp) REVERT: R 176 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8602 (mttp) REVERT: R 209 THR cc_start: 0.8532 (p) cc_final: 0.8223 (p) REVERT: R 221 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8529 (mp) REVERT: R 282 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.8293 (ttp-170) REVERT: A 14 GLU cc_start: 0.7719 (tt0) cc_final: 0.7398 (tt0) REVERT: A 17 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8079 (mmmt) REVERT: A 21 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7470 (ttp80) REVERT: A 25 GLU cc_start: 0.8396 (tt0) cc_final: 0.8109 (tt0) REVERT: A 29 LYS cc_start: 0.8709 (tttt) cc_final: 0.8430 (tttt) REVERT: A 193 ASP cc_start: 0.7967 (t0) cc_final: 0.7723 (t0) REVERT: A 231 ASP cc_start: 0.7857 (t0) cc_final: 0.7550 (t0) REVERT: A 247 MET cc_start: 0.8348 (mtt) cc_final: 0.7889 (mtm) REVERT: A 308 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 316 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7930 (p) REVERT: A 317 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8404 (tttt) REVERT: A 350 ASP cc_start: 0.8550 (t0) cc_final: 0.8211 (t0) REVERT: B 17 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 89 LYS cc_start: 0.8974 (mttp) cc_final: 0.8746 (mttp) REVERT: B 96 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7491 (mtt90) REVERT: B 111 TYR cc_start: 0.8824 (m-80) cc_final: 0.8526 (m-80) REVERT: B 130 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8129 (mt-10) REVERT: B 163 ASP cc_start: 0.7973 (p0) cc_final: 0.7619 (p0) REVERT: B 170 ASP cc_start: 0.7720 (t0) cc_final: 0.7349 (t0) REVERT: B 188 MET cc_start: 0.8196 (mmm) cc_final: 0.7334 (mmm) REVERT: B 198 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8969 (mp) REVERT: B 221 THR cc_start: 0.8653 (m) cc_final: 0.8295 (p) REVERT: B 229 ILE cc_start: 0.8602 (mt) cc_final: 0.8237 (mp) REVERT: B 234 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.6961 (t80) REVERT: B 254 ASP cc_start: 0.7435 (t0) cc_final: 0.7127 (t0) REVERT: B 258 ASP cc_start: 0.8054 (t0) cc_final: 0.7821 (t70) REVERT: B 261 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8359 (tt) REVERT: C 38 MET cc_start: 0.9064 (mtt) cc_final: 0.8678 (mpp) REVERT: E 85 SER cc_start: 0.8178 (t) cc_final: 0.7777 (p) REVERT: E 115 THR cc_start: 0.8137 (t) cc_final: 0.7773 (p) REVERT: E 232 GLN cc_start: 0.8183 (pp30) cc_final: 0.7725 (pp30) REVERT: E 240 PHE cc_start: 0.8223 (m-10) cc_final: 0.7777 (m-80) REVERT: M 150 TYR cc_start: 0.8425 (m-80) cc_final: 0.8184 (m-80) REVERT: M 153 MET cc_start: 0.7874 (tmm) cc_final: 0.7660 (ttt) REVERT: M 222 THR cc_start: 0.8772 (t) cc_final: 0.8395 (p) REVERT: M 236 ILE cc_start: 0.8720 (mm) cc_final: 0.8479 (mt) REVERT: M 245 MET cc_start: 0.7885 (tpp) cc_final: 0.7442 (mpp) REVERT: M 283 MET cc_start: 0.8157 (tpp) cc_final: 0.7882 (tpp) REVERT: F 349 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7957 (mtmm) outliers start: 50 outliers final: 27 residues processed: 419 average time/residue: 0.2813 time to fit residues: 158.6973 Evaluate side-chains 404 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 293 VAL 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 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 212 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 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 211 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 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 99 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS B 110 ASN ** M 106 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 = 0.3759 r_free = 0.3759 target = 0.124491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.107562 restraints weight = 20208.617| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.61 r_work: 0.3385 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11987 Z= 0.144 Angle : 0.556 10.843 16311 Z= 0.285 Chirality : 0.041 0.180 1905 Planarity : 0.004 0.044 1964 Dihedral : 5.770 72.651 2245 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.52 % Allowed : 17.38 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.22), residues: 1423 helix: 2.44 (0.19), residues: 657 sheet: 0.29 (0.30), residues: 286 loop : -0.80 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 111 HIS 0.003 0.001 HIS M 173 PHE 0.021 0.001 PHE A 334 TYR 0.017 0.002 TYR R 151 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 653) hydrogen bonds : angle 4.24531 ( 1893) SS BOND : bond 0.00484 ( 3) SS BOND : angle 1.00403 ( 6) covalent geometry : bond 0.00324 (11984) covalent geometry : angle 0.55571 (16305) *********************** 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 435 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 378 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7542 (mmm) cc_final: 0.7313 (mmm) REVERT: R 79 ILE cc_start: 0.8370 (mt) cc_final: 0.8114 (mt) REVERT: R 176 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8589 (mttm) REVERT: R 221 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 14 GLU cc_start: 0.7795 (tt0) cc_final: 0.7434 (tt0) REVERT: A 17 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8086 (mmmt) REVERT: A 21 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7473 (ttp80) REVERT: A 25 GLU cc_start: 0.8317 (tt0) cc_final: 0.8028 (tt0) REVERT: A 33 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 193 ASP cc_start: 0.8033 (t0) cc_final: 0.7707 (t0) REVERT: A 230 TYR cc_start: 0.7141 (p90) cc_final: 0.6705 (p90) REVERT: A 231 ASP cc_start: 0.7957 (t0) cc_final: 0.7496 (t0) REVERT: A 272 ASP cc_start: 0.8065 (p0) cc_final: 0.7553 (p0) REVERT: A 275 GLU cc_start: 0.7538 (pt0) cc_final: 0.7229 (pp20) REVERT: A 308 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 312 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8195 (mttp) REVERT: A 316 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7926 (p) REVERT: A 317 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8419 (tttt) REVERT: A 350 ASP cc_start: 0.8610 (t0) cc_final: 0.8327 (t0) REVERT: B 17 GLN cc_start: 0.8447 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 78 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8766 (mmtm) REVERT: B 96 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7617 (mtt90) REVERT: B 111 TYR cc_start: 0.8845 (m-80) cc_final: 0.8558 (m-80) REVERT: B 130 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 163 ASP cc_start: 0.8189 (p0) cc_final: 0.7903 (p0) REVERT: B 173 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8913 (p) REVERT: B 188 MET cc_start: 0.8195 (mmm) cc_final: 0.7979 (mmm) REVERT: B 198 LEU cc_start: 0.9186 (mt) cc_final: 0.8969 (mp) REVERT: B 200 VAL cc_start: 0.8927 (p) cc_final: 0.8653 (m) REVERT: B 221 THR cc_start: 0.8763 (m) cc_final: 0.8426 (p) REVERT: B 234 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.6961 (t80) REVERT: B 254 ASP cc_start: 0.7458 (t0) cc_final: 0.7165 (t0) REVERT: B 261 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8453 (tt) REVERT: B 277 SER cc_start: 0.8469 (t) cc_final: 0.8241 (t) REVERT: E 85 SER cc_start: 0.8320 (t) cc_final: 0.7828 (p) REVERT: E 115 THR cc_start: 0.8113 (t) cc_final: 0.7745 (p) REVERT: E 141 MET cc_start: 0.8419 (mmm) cc_final: 0.8216 (mmm) REVERT: E 191 TYR cc_start: 0.8605 (p90) cc_final: 0.8333 (p90) REVERT: E 202 ASP cc_start: 0.7688 (t70) cc_final: 0.7378 (t70) REVERT: E 232 GLN cc_start: 0.8368 (pp30) cc_final: 0.7946 (pp30) REVERT: M 150 TYR cc_start: 0.8420 (m-80) cc_final: 0.8094 (m-80) REVERT: M 181 ARG cc_start: 0.8395 (mtp-110) cc_final: 0.8057 (mtm180) REVERT: M 194 TRP cc_start: 0.8340 (m100) cc_final: 0.7836 (m100) REVERT: M 200 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7962 (tt) REVERT: M 222 THR cc_start: 0.8832 (t) cc_final: 0.8457 (p) REVERT: M 245 MET cc_start: 0.7857 (tpp) cc_final: 0.7521 (mpp) REVERT: M 275 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7312 (ttp80) REVERT: F 349 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7915 (mtmm) outliers start: 57 outliers final: 31 residues processed: 400 average time/residue: 0.2931 time to fit residues: 156.1900 Evaluate side-chains 400 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 363 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU 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 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 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 105 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 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 136 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 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 ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.125494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108635 restraints weight = 20132.700| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.61 r_work: 0.3368 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11987 Z= 0.122 Angle : 0.549 10.830 16311 Z= 0.282 Chirality : 0.041 0.207 1905 Planarity : 0.004 0.042 1964 Dihedral : 5.646 73.424 2245 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.65 % Allowed : 19.37 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1423 helix: 2.49 (0.19), residues: 659 sheet: 0.20 (0.29), residues: 308 loop : -0.59 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS M 173 PHE 0.014 0.001 PHE A 334 TYR 0.019 0.001 TYR R 130 ARG 0.007 0.001 ARG M 279 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 653) hydrogen bonds : angle 4.23756 ( 1893) SS BOND : bond 0.00564 ( 3) SS BOND : angle 2.89477 ( 6) covalent geometry : bond 0.00269 (11984) covalent geometry : angle 0.54639 (16305) *********************** 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 429 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 383 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7657 (mmm) cc_final: 0.7370 (mmm) REVERT: R 79 ILE cc_start: 0.8318 (mt) cc_final: 0.8053 (mt) REVERT: R 101 MET cc_start: 0.7191 (mtp) cc_final: 0.6990 (mtp) REVERT: R 176 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8608 (mttm) REVERT: R 221 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 14 GLU cc_start: 0.7734 (tt0) cc_final: 0.7382 (tt0) REVERT: A 17 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8011 (mtmm) REVERT: A 21 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7482 (ttp80) REVERT: A 25 GLU cc_start: 0.8305 (tt0) cc_final: 0.8012 (tt0) REVERT: A 29 LYS cc_start: 0.8721 (tttt) cc_final: 0.8329 (ttmm) REVERT: A 193 ASP cc_start: 0.8025 (t0) cc_final: 0.7681 (t0) REVERT: A 230 TYR cc_start: 0.7175 (p90) cc_final: 0.6803 (p90) REVERT: A 231 ASP cc_start: 0.7963 (t0) cc_final: 0.7541 (t0) REVERT: A 272 ASP cc_start: 0.8163 (p0) cc_final: 0.7646 (p0) REVERT: A 275 GLU cc_start: 0.7466 (pt0) cc_final: 0.7166 (pp20) REVERT: A 308 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7967 (mt-10) REVERT: A 312 LYS cc_start: 0.8512 (mmtp) cc_final: 0.8312 (mptt) REVERT: A 316 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 350 ASP cc_start: 0.8651 (t0) cc_final: 0.8340 (t0) REVERT: B 89 LYS cc_start: 0.8962 (mttp) cc_final: 0.8707 (mttp) REVERT: B 96 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7647 (mtt90) REVERT: B 111 TYR cc_start: 0.8836 (m-80) cc_final: 0.8535 (m-80) REVERT: B 130 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 132 ASN cc_start: 0.8172 (p0) cc_final: 0.7935 (p0) REVERT: B 163 ASP cc_start: 0.8263 (p0) cc_final: 0.7995 (p0) REVERT: B 198 LEU cc_start: 0.9160 (mt) cc_final: 0.8941 (mp) REVERT: B 200 VAL cc_start: 0.8924 (p) cc_final: 0.8697 (m) REVERT: B 221 THR cc_start: 0.8670 (m) cc_final: 0.8465 (p) REVERT: B 234 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7039 (t80) REVERT: B 254 ASP cc_start: 0.7455 (t0) cc_final: 0.7162 (t0) REVERT: B 277 SER cc_start: 0.8453 (t) cc_final: 0.8220 (t) REVERT: E 85 SER cc_start: 0.8440 (t) cc_final: 0.7963 (p) REVERT: E 115 THR cc_start: 0.8128 (t) cc_final: 0.7764 (p) REVERT: E 202 ASP cc_start: 0.7697 (t70) cc_final: 0.7401 (t70) REVERT: E 232 GLN cc_start: 0.8343 (pp30) cc_final: 0.7997 (pp30) REVERT: M 181 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.8041 (mtm180) REVERT: M 194 TRP cc_start: 0.8342 (m100) cc_final: 0.7772 (m100) REVERT: M 200 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7963 (tt) REVERT: M 222 THR cc_start: 0.9007 (t) cc_final: 0.8711 (p) REVERT: M 245 MET cc_start: 0.7745 (tpp) cc_final: 0.7491 (mpp) REVERT: M 275 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7391 (ttp80) REVERT: M 283 MET cc_start: 0.8093 (tpp) cc_final: 0.7820 (tpp) REVERT: F 349 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7919 (mtmm) outliers start: 46 outliers final: 31 residues processed: 399 average time/residue: 0.2968 time to fit residues: 158.6953 Evaluate side-chains 397 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 362 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR 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 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 254 CYS 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 154 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 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 193 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 121 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108334 restraints weight = 20415.205| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.62 r_work: 0.3359 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4893 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= 0.121 Angle : 0.553 10.694 16311 Z= 0.280 Chirality : 0.040 0.227 1905 Planarity : 0.004 0.042 1964 Dihedral : 5.607 73.802 2245 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.37 % Allowed : 19.29 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1423 helix: 2.52 (0.19), residues: 660 sheet: 0.16 (0.29), residues: 308 loop : -0.52 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 PHE 0.017 0.001 PHE A 334 TYR 0.016 0.001 TYR R 151 ARG 0.007 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 653) hydrogen bonds : angle 4.19034 ( 1893) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.78712 ( 6) covalent geometry : bond 0.00268 (11984) covalent geometry : angle 0.55165 (16305) *********************** 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 412 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7584 (mmm) cc_final: 0.7313 (mmm) REVERT: R 79 ILE cc_start: 0.8305 (mt) cc_final: 0.8037 (mt) REVERT: R 101 MET cc_start: 0.7216 (mtp) cc_final: 0.6999 (mtp) REVERT: R 176 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8611 (mttm) REVERT: R 221 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8653 (mp) REVERT: R 266 MET cc_start: 0.7450 (tmm) cc_final: 0.6817 (tmm) REVERT: A 14 GLU cc_start: 0.7741 (tt0) cc_final: 0.7396 (tt0) REVERT: A 17 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8051 (mttp) REVERT: A 18 MET cc_start: 0.7924 (mmm) cc_final: 0.7643 (mmm) REVERT: A 21 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7506 (ttp80) REVERT: A 25 GLU cc_start: 0.8288 (tt0) cc_final: 0.8008 (tt0) REVERT: A 29 LYS cc_start: 0.8729 (tttt) cc_final: 0.8339 (ttmm) REVERT: A 193 ASP cc_start: 0.8067 (t0) cc_final: 0.7693 (t0) REVERT: A 230 TYR cc_start: 0.7269 (p90) cc_final: 0.6891 (p90) REVERT: A 231 ASP cc_start: 0.7997 (t0) cc_final: 0.7576 (t0) REVERT: A 312 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8320 (mptt) REVERT: A 316 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7979 (p) REVERT: A 350 ASP cc_start: 0.8666 (t0) cc_final: 0.8369 (t0) REVERT: B 89 LYS cc_start: 0.8928 (mttp) cc_final: 0.8677 (mttp) REVERT: B 111 TYR cc_start: 0.8832 (m-80) cc_final: 0.8569 (m-80) REVERT: B 130 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 163 ASP cc_start: 0.8309 (p0) cc_final: 0.8036 (p0) REVERT: B 188 MET cc_start: 0.8296 (mmm) cc_final: 0.7800 (mmt) REVERT: B 200 VAL cc_start: 0.8962 (p) cc_final: 0.8698 (m) REVERT: B 214 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7799 (ttp80) REVERT: B 221 THR cc_start: 0.8661 (m) cc_final: 0.8324 (p) REVERT: B 234 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7075 (t80) REVERT: B 254 ASP cc_start: 0.7415 (t0) cc_final: 0.7175 (t0) REVERT: B 277 SER cc_start: 0.8465 (t) cc_final: 0.8233 (t) REVERT: C 38 MET cc_start: 0.9076 (mtt) cc_final: 0.8689 (mpp) REVERT: C 44 HIS cc_start: 0.8077 (m90) cc_final: 0.7603 (m90) REVERT: E 11 LEU cc_start: 0.8533 (mp) cc_final: 0.8328 (tt) REVERT: E 85 SER cc_start: 0.8470 (t) cc_final: 0.7989 (p) REVERT: E 115 THR cc_start: 0.8082 (t) cc_final: 0.7713 (p) REVERT: E 200 VAL cc_start: 0.9172 (t) cc_final: 0.8864 (m) REVERT: E 202 ASP cc_start: 0.7687 (t70) cc_final: 0.7378 (t70) REVERT: E 232 GLN cc_start: 0.8330 (pp30) cc_final: 0.7991 (pp30) REVERT: M 181 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8035 (mtm180) REVERT: M 194 TRP cc_start: 0.8340 (m100) cc_final: 0.7712 (m100) REVERT: M 200 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7938 (tt) REVERT: M 222 THR cc_start: 0.9021 (t) cc_final: 0.8689 (p) REVERT: M 245 MET cc_start: 0.7733 (tpp) cc_final: 0.7506 (mpp) REVERT: F 349 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7911 (mtmm) outliers start: 55 outliers final: 39 residues processed: 382 average time/residue: 0.2872 time to fit residues: 147.0553 Evaluate side-chains 396 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 353 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE 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 308 VAL Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 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 105 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 112 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 101 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 ASN A 188 HIS B 88 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.122306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105515 restraints weight = 20505.339| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.61 r_work: 0.3318 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11987 Z= 0.171 Angle : 0.591 10.436 16311 Z= 0.304 Chirality : 0.042 0.189 1905 Planarity : 0.004 0.042 1964 Dihedral : 5.957 77.037 2245 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.37 % Allowed : 20.16 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.22), residues: 1423 helix: 2.41 (0.19), residues: 661 sheet: 0.03 (0.28), residues: 314 loop : -0.53 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 320 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.002 PHE A 334 TYR 0.030 0.002 TYR R 130 ARG 0.014 0.001 ARG M 275 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 653) hydrogen bonds : angle 4.27937 ( 1893) SS BOND : bond 0.01070 ( 3) SS BOND : angle 1.93087 ( 6) covalent geometry : bond 0.00391 (11984) covalent geometry : angle 0.59027 (16305) *********************** 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 418 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 363 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7529 (mmm) cc_final: 0.7245 (mmm) REVERT: R 79 ILE cc_start: 0.8275 (mt) cc_final: 0.8040 (mt) REVERT: R 101 MET cc_start: 0.7363 (mtp) cc_final: 0.7087 (mtp) REVERT: R 176 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8750 (mttm) REVERT: R 198 SER cc_start: 0.8117 (t) cc_final: 0.7760 (t) REVERT: R 221 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8701 (mp) REVERT: R 266 MET cc_start: 0.7621 (tmm) cc_final: 0.7150 (tmm) REVERT: A 14 GLU cc_start: 0.7819 (tt0) cc_final: 0.7539 (tt0) REVERT: A 17 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8001 (mtmm) REVERT: A 18 MET cc_start: 0.7976 (mmm) cc_final: 0.7753 (mmm) REVERT: A 21 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7552 (ttp80) REVERT: A 25 GLU cc_start: 0.8316 (tt0) cc_final: 0.8034 (tt0) REVERT: A 29 LYS cc_start: 0.8679 (tttt) cc_final: 0.8315 (ttmm) REVERT: A 193 ASP cc_start: 0.8052 (t0) cc_final: 0.7671 (t0) REVERT: A 231 ASP cc_start: 0.8018 (t0) cc_final: 0.7704 (t0) REVERT: A 275 GLU cc_start: 0.7567 (pt0) cc_final: 0.7205 (pp20) REVERT: A 290 TYR cc_start: 0.8254 (t80) cc_final: 0.8053 (t80) REVERT: A 316 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8201 (p) REVERT: A 337 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8156 (t0) REVERT: A 350 ASP cc_start: 0.8643 (t0) cc_final: 0.8250 (t0) REVERT: B 111 TYR cc_start: 0.8829 (m-80) cc_final: 0.8547 (m-80) REVERT: B 130 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 132 ASN cc_start: 0.8164 (p0) cc_final: 0.7916 (p0) REVERT: B 163 ASP cc_start: 0.8374 (p0) cc_final: 0.8133 (p0) REVERT: B 200 VAL cc_start: 0.8972 (p) cc_final: 0.8708 (m) REVERT: B 214 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7863 (ttp80) REVERT: B 221 THR cc_start: 0.8592 (m) cc_final: 0.8382 (p) REVERT: B 254 ASP cc_start: 0.7514 (t0) cc_final: 0.7264 (t0) REVERT: B 277 SER cc_start: 0.8525 (t) cc_final: 0.8260 (m) REVERT: C 13 ARG cc_start: 0.8804 (ttp-110) cc_final: 0.8495 (mtm-85) REVERT: C 44 HIS cc_start: 0.8367 (m90) cc_final: 0.7890 (m90) REVERT: E 85 SER cc_start: 0.8558 (t) cc_final: 0.8076 (p) REVERT: E 115 THR cc_start: 0.8129 (t) cc_final: 0.7743 (p) REVERT: E 200 VAL cc_start: 0.9263 (t) cc_final: 0.8975 (m) REVERT: E 202 ASP cc_start: 0.7880 (t70) cc_final: 0.7566 (t70) REVERT: M 198 SER cc_start: 0.8082 (t) cc_final: 0.7744 (p) REVERT: M 200 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7937 (tt) REVERT: M 205 MET cc_start: 0.7108 (mmt) cc_final: 0.6874 (mmt) REVERT: M 222 THR cc_start: 0.8973 (t) cc_final: 0.8641 (p) REVERT: M 245 MET cc_start: 0.7734 (tpp) cc_final: 0.7530 (tpp) REVERT: F 349 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7926 (mtmm) outliers start: 55 outliers final: 44 residues processed: 385 average time/residue: 0.2829 time to fit residues: 147.1855 Evaluate side-chains 400 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 352 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 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 308 VAL 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 218 VAL 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 88 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 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 105 THR 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 280 ILE Chi-restraints excluded: chain M residue 300 ILE Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 24 optimal weight: 0.0060 chunk 4 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 96 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 110 ASN ** M 152 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 = 0.3766 r_free = 0.3766 target = 0.125437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108578 restraints weight = 20265.555| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.60 r_work: 0.3371 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11987 Z= 0.116 Angle : 0.575 10.701 16311 Z= 0.290 Chirality : 0.040 0.201 1905 Planarity : 0.004 0.053 1964 Dihedral : 5.661 77.867 2245 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.49 % Allowed : 21.43 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1423 helix: 2.49 (0.19), residues: 660 sheet: 0.11 (0.29), residues: 312 loop : -0.45 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.023 0.001 PHE A 334 TYR 0.020 0.001 TYR R 130 ARG 0.013 0.001 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 653) hydrogen bonds : angle 4.15624 ( 1893) SS BOND : bond 0.00326 ( 3) SS BOND : angle 1.28186 ( 6) covalent geometry : bond 0.00244 (11984) covalent geometry : angle 0.57464 (16305) *********************** 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 408 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 364 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8259 (mt) cc_final: 0.7977 (mt) REVERT: R 101 MET cc_start: 0.7261 (mtp) cc_final: 0.6988 (mtp) REVERT: R 176 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8744 (mttm) REVERT: R 221 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8686 (mp) REVERT: R 266 MET cc_start: 0.7646 (tmm) cc_final: 0.7224 (tmm) REVERT: A 14 GLU cc_start: 0.7773 (tt0) cc_final: 0.7478 (tt0) REVERT: A 17 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8040 (mttp) REVERT: A 18 MET cc_start: 0.7897 (mmm) cc_final: 0.7659 (mmm) REVERT: A 21 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7505 (ttp80) REVERT: A 25 GLU cc_start: 0.8285 (tt0) cc_final: 0.7996 (tt0) REVERT: A 29 LYS cc_start: 0.8680 (tttt) cc_final: 0.8284 (ttmm) REVERT: A 193 ASP cc_start: 0.8053 (t0) cc_final: 0.7679 (t0) REVERT: A 197 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8208 (mtmm) REVERT: A 231 ASP cc_start: 0.8030 (t0) cc_final: 0.7697 (t0) REVERT: A 312 LYS cc_start: 0.8575 (mmtp) cc_final: 0.8302 (mptt) REVERT: A 316 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 337 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8051 (t0) REVERT: A 350 ASP cc_start: 0.8640 (t0) cc_final: 0.8377 (t0) REVERT: B 78 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8629 (mmtp) REVERT: B 86 THR cc_start: 0.8980 (p) cc_final: 0.8668 (t) REVERT: B 89 LYS cc_start: 0.9008 (mttp) cc_final: 0.8772 (mttp) REVERT: B 96 ARG cc_start: 0.8089 (mtt90) cc_final: 0.7589 (mtt90) REVERT: B 111 TYR cc_start: 0.8766 (m-80) cc_final: 0.8484 (m-80) REVERT: B 119 ASN cc_start: 0.9124 (m-40) cc_final: 0.8829 (m110) REVERT: B 127 LYS cc_start: 0.9263 (mmtt) cc_final: 0.9036 (mttm) REVERT: B 130 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8201 (mt-10) REVERT: B 132 ASN cc_start: 0.8139 (p0) cc_final: 0.7891 (p0) REVERT: B 163 ASP cc_start: 0.8335 (p0) cc_final: 0.8094 (p0) REVERT: B 188 MET cc_start: 0.8153 (mmm) cc_final: 0.7859 (mmm) REVERT: B 198 LEU cc_start: 0.9061 (mp) cc_final: 0.8795 (mm) REVERT: B 200 VAL cc_start: 0.8926 (p) cc_final: 0.8652 (m) REVERT: B 214 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7884 (ttp80) REVERT: B 220 GLN cc_start: 0.8310 (mp10) cc_final: 0.7990 (mp10) REVERT: B 221 THR cc_start: 0.8588 (m) cc_final: 0.8363 (p) REVERT: B 234 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.6980 (t80) REVERT: B 254 ASP cc_start: 0.7393 (t0) cc_final: 0.7155 (t0) REVERT: B 277 SER cc_start: 0.8470 (t) cc_final: 0.8227 (t) REVERT: C 13 ARG cc_start: 0.8804 (ttp-110) cc_final: 0.8407 (mtm110) REVERT: C 44 HIS cc_start: 0.8100 (m90) cc_final: 0.7587 (m90) REVERT: E 85 SER cc_start: 0.8554 (t) cc_final: 0.8085 (p) REVERT: E 115 THR cc_start: 0.8141 (t) cc_final: 0.7628 (p) REVERT: E 200 VAL cc_start: 0.9267 (t) cc_final: 0.8969 (m) REVERT: E 202 ASP cc_start: 0.7778 (t70) cc_final: 0.7464 (t70) REVERT: M 181 ARG cc_start: 0.8315 (mtp-110) cc_final: 0.8039 (mtm180) REVERT: M 200 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7889 (tt) REVERT: F 349 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7878 (mtmm) outliers start: 44 outliers final: 35 residues processed: 380 average time/residue: 0.2798 time to fit residues: 143.2849 Evaluate side-chains 396 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 356 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 SER 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 B residue 88 ASN 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 212 ASP 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 55 SER Chi-restraints excluded: chain E residue 91 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 114 LEU 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 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 0.0000 chunk 123 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.107845 restraints weight = 20270.591| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.61 r_work: 0.3349 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11987 Z= 0.126 Angle : 0.590 10.950 16311 Z= 0.296 Chirality : 0.040 0.198 1905 Planarity : 0.004 0.041 1964 Dihedral : 5.667 76.905 2245 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.65 % Allowed : 22.06 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1423 helix: 2.43 (0.19), residues: 661 sheet: 0.15 (0.29), residues: 310 loop : -0.47 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 PHE 0.022 0.001 PHE A 334 TYR 0.018 0.002 TYR M 93 ARG 0.008 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 653) hydrogen bonds : angle 4.15399 ( 1893) SS BOND : bond 0.00527 ( 3) SS BOND : angle 1.56197 ( 6) covalent geometry : bond 0.00281 (11984) covalent geometry : angle 0.58958 (16305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 360 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8270 (mt) cc_final: 0.7980 (mt) REVERT: R 101 MET cc_start: 0.7206 (mtp) cc_final: 0.6941 (mtp) REVERT: R 198 SER cc_start: 0.8107 (t) cc_final: 0.7768 (t) REVERT: R 221 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8694 (mp) REVERT: R 266 MET cc_start: 0.7652 (tmm) cc_final: 0.7235 (tmm) REVERT: A 14 GLU cc_start: 0.7797 (tt0) cc_final: 0.7508 (tt0) REVERT: A 17 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8080 (mttp) REVERT: A 18 MET cc_start: 0.7942 (mmm) cc_final: 0.7692 (mmm) REVERT: A 21 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7544 (ttp80) REVERT: A 25 GLU cc_start: 0.8291 (tt0) cc_final: 0.8011 (tt0) REVERT: A 29 LYS cc_start: 0.8704 (tttt) cc_final: 0.8315 (ttmm) REVERT: A 197 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8129 (mtmm) REVERT: A 231 ASP cc_start: 0.8030 (t0) cc_final: 0.7696 (t0) REVERT: A 290 TYR cc_start: 0.8266 (t80) cc_final: 0.8023 (t80) REVERT: A 312 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8286 (mptt) REVERT: A 316 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8228 (p) REVERT: A 337 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8070 (t0) REVERT: A 350 ASP cc_start: 0.8675 (t0) cc_final: 0.8348 (t0) REVERT: B 78 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8672 (mmtp) REVERT: B 86 THR cc_start: 0.9039 (p) cc_final: 0.8814 (t) REVERT: B 89 LYS cc_start: 0.8883 (mttp) cc_final: 0.8608 (mttp) REVERT: B 111 TYR cc_start: 0.8775 (m-80) cc_final: 0.8493 (m-80) REVERT: B 119 ASN cc_start: 0.9097 (m-40) cc_final: 0.8808 (m110) REVERT: B 130 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 132 ASN cc_start: 0.8132 (p0) cc_final: 0.7890 (p0) REVERT: B 163 ASP cc_start: 0.8334 (p0) cc_final: 0.8097 (p0) REVERT: B 188 MET cc_start: 0.8284 (mmm) cc_final: 0.8053 (mmm) REVERT: B 198 LEU cc_start: 0.9069 (mp) cc_final: 0.8792 (mm) REVERT: B 200 VAL cc_start: 0.8935 (p) cc_final: 0.8679 (m) REVERT: B 214 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7860 (ttp80) REVERT: B 221 THR cc_start: 0.8546 (m) cc_final: 0.8306 (p) REVERT: B 234 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6994 (t80) REVERT: B 277 SER cc_start: 0.8472 (t) cc_final: 0.8243 (m) REVERT: C 13 ARG cc_start: 0.8767 (ttp-110) cc_final: 0.8364 (mtm110) REVERT: C 44 HIS cc_start: 0.8127 (m90) cc_final: 0.7609 (m90) REVERT: E 85 SER cc_start: 0.8584 (t) cc_final: 0.8108 (p) REVERT: E 115 THR cc_start: 0.8103 (t) cc_final: 0.7732 (p) REVERT: E 200 VAL cc_start: 0.9269 (t) cc_final: 0.8983 (m) REVERT: E 202 ASP cc_start: 0.7778 (t70) cc_final: 0.7461 (t70) REVERT: M 181 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.8054 (mtm180) REVERT: M 200 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7936 (tt) REVERT: F 349 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7897 (mtmm) outliers start: 46 outliers final: 34 residues processed: 379 average time/residue: 0.2931 time to fit residues: 151.7117 Evaluate side-chains 396 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 357 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 337 ASP 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 212 ASP Chi-restraints excluded: chain B residue 230 ASN 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 55 SER 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 114 LEU Chi-restraints excluded: chain M residue 121 SER 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 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 24 optimal weight: 0.4980 chunk 128 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.124868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108091 restraints weight = 20229.066| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.61 r_work: 0.3352 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11987 Z= 0.124 Angle : 0.606 12.483 16311 Z= 0.300 Chirality : 0.040 0.195 1905 Planarity : 0.004 0.041 1964 Dihedral : 5.611 75.949 2245 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.25 % Allowed : 22.62 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1423 helix: 2.45 (0.19), residues: 661 sheet: 0.12 (0.29), residues: 312 loop : -0.47 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 PHE 0.028 0.001 PHE A 334 TYR 0.018 0.001 TYR M 93 ARG 0.009 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 653) hydrogen bonds : angle 4.14648 ( 1893) SS BOND : bond 0.00531 ( 3) SS BOND : angle 1.51671 ( 6) covalent geometry : bond 0.00276 (11984) covalent geometry : angle 0.60501 (16305) ********************** 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 403 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 362 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8228 (mt) cc_final: 0.7941 (mt) REVERT: R 101 MET cc_start: 0.7282 (mtp) cc_final: 0.7012 (mtp) REVERT: R 168 TYR cc_start: 0.8287 (t80) cc_final: 0.7685 (t80) REVERT: R 220 THR cc_start: 0.8512 (t) cc_final: 0.8298 (p) REVERT: R 221 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8607 (mp) REVERT: A 14 GLU cc_start: 0.7801 (tt0) cc_final: 0.7517 (tt0) REVERT: A 17 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8059 (mttp) REVERT: A 18 MET cc_start: 0.7930 (mmm) cc_final: 0.7690 (mmm) REVERT: A 21 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7513 (ttp80) REVERT: A 25 GLU cc_start: 0.8270 (tt0) cc_final: 0.7983 (tt0) REVERT: A 29 LYS cc_start: 0.8724 (tttt) cc_final: 0.8319 (ttmm) REVERT: A 197 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8089 (mtmm) REVERT: A 231 ASP cc_start: 0.8049 (t0) cc_final: 0.7717 (t0) REVERT: A 240 MET cc_start: 0.7831 (tpp) cc_final: 0.7330 (mmp) REVERT: A 290 TYR cc_start: 0.8281 (t80) cc_final: 0.7968 (t80) REVERT: A 312 LYS cc_start: 0.8612 (mmtp) cc_final: 0.8288 (mptt) REVERT: A 316 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8228 (p) REVERT: A 337 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8051 (t0) REVERT: A 350 ASP cc_start: 0.8656 (t0) cc_final: 0.8304 (t0) REVERT: B 78 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8677 (mmtp) REVERT: B 89 LYS cc_start: 0.8914 (mttp) cc_final: 0.8653 (mttp) REVERT: B 111 TYR cc_start: 0.8767 (m-80) cc_final: 0.8453 (m-80) REVERT: B 119 ASN cc_start: 0.9069 (m-40) cc_final: 0.8815 (m110) REVERT: B 130 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 163 ASP cc_start: 0.8342 (p0) cc_final: 0.8114 (p0) REVERT: B 188 MET cc_start: 0.8274 (mmm) cc_final: 0.8055 (mmm) REVERT: B 198 LEU cc_start: 0.9062 (mp) cc_final: 0.8776 (mm) REVERT: B 200 VAL cc_start: 0.8916 (p) cc_final: 0.8663 (m) REVERT: B 221 THR cc_start: 0.8484 (m) cc_final: 0.8218 (p) REVERT: B 234 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.6964 (t80) REVERT: B 277 SER cc_start: 0.8453 (t) cc_final: 0.8222 (m) REVERT: C 13 ARG cc_start: 0.8775 (ttp-110) cc_final: 0.8357 (mtm110) REVERT: C 44 HIS cc_start: 0.8148 (m90) cc_final: 0.7627 (m90) REVERT: E 85 SER cc_start: 0.8576 (t) cc_final: 0.8111 (p) REVERT: E 115 THR cc_start: 0.8159 (t) cc_final: 0.7770 (p) REVERT: E 200 VAL cc_start: 0.9270 (t) cc_final: 0.9027 (m) REVERT: E 202 ASP cc_start: 0.7772 (t70) cc_final: 0.7467 (t70) REVERT: E 232 GLN cc_start: 0.8474 (pp30) cc_final: 0.8248 (pp30) REVERT: M 181 ARG cc_start: 0.8332 (mtp-110) cc_final: 0.8038 (mtm180) REVERT: M 200 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7906 (tt) REVERT: F 349 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7883 (mtmm) outliers start: 41 outliers final: 33 residues processed: 378 average time/residue: 0.2771 time to fit residues: 141.1973 Evaluate side-chains 388 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 350 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 337 ASP 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 212 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 193 MET Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR 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 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 74 optimal weight: 4.9990 chunk 118 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 101 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 138 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 110 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 = 0.3773 r_free = 0.3773 target = 0.125831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109144 restraints weight = 20123.264| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.61 r_work: 0.3401 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11987 Z= 0.119 Angle : 0.610 11.244 16311 Z= 0.304 Chirality : 0.040 0.198 1905 Planarity : 0.004 0.041 1964 Dihedral : 5.530 74.525 2245 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.25 % Allowed : 23.02 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1423 helix: 2.49 (0.19), residues: 661 sheet: 0.17 (0.29), residues: 310 loop : -0.49 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS M 173 PHE 0.032 0.001 PHE A 334 TYR 0.034 0.001 TYR R 130 ARG 0.009 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 653) hydrogen bonds : angle 4.11898 ( 1893) SS BOND : bond 0.00482 ( 3) SS BOND : angle 1.37287 ( 6) covalent geometry : bond 0.00259 (11984) covalent geometry : angle 0.60908 (16305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5981.24 seconds wall clock time: 103 minutes 26.07 seconds (6206.07 seconds total)