Starting phenix.real_space_refine on Fri Aug 22 22:36:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ikg_35511/08_2025/8ikg_35511_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ikg_35511/08_2025/8ikg_35511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ikg_35511/08_2025/8ikg_35511_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ikg_35511/08_2025/8ikg_35511_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ikg_35511/08_2025/8ikg_35511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ikg_35511/08_2025/8ikg_35511.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.083 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 60 5.16 5 C 5414 2.51 5 N 1445 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8456 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1675 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2474 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 318} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2167 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'Q2B': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.20 Number of scatterers: 8456 At special positions: 0 Unit cell: (94.34, 124.6, 126.38, 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 60 16.00 O 1537 8.00 N 1445 7.00 C 5414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 319.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.562A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 4.351A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.545A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.772A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 removed outlier: 3.885A pdb=" N SER A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.207A pdb=" N CYS A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.965A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 22 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.775A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'C' and resid 8 through 23 removed outlier: 4.251A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.698A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 142 Processing helix chain 'R' and resid 146 through 149 removed outlier: 3.612A pdb=" N CYS R 149 " --> pdb=" O SER R 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 146 through 149' Processing helix chain 'R' and resid 150 through 171 removed outlier: 3.656A pdb=" N HIS R 154 " --> pdb=" O ARG R 150 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY R 157 " --> pdb=" O TYR R 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER R 158 " --> pdb=" O HIS R 154 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU R 159 " --> pdb=" O PHE R 155 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL R 171 " --> pdb=" O SER R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.797A pdb=" N ILE R 175 " --> pdb=" O TYR R 172 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP R 176 " --> pdb=" O SER R 173 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE R 177 " --> pdb=" O PHE R 174 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS R 178 " --> pdb=" O ILE R 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 178' Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.995A pdb=" N PHE R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 220 removed outlier: 3.647A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 Processing helix chain 'R' and resid 229 through 254 removed outlier: 3.899A pdb=" N VAL R 235 " --> pdb=" O PRO R 231 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP R 241 " --> pdb=" O PHE R 237 " (cutoff:3.500A) Proline residue: R 251 - end of helix Processing helix chain 'R' and resid 272 through 312 removed outlier: 3.763A pdb=" N VAL R 285 " --> pdb=" O GLY R 281 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 356 removed outlier: 3.918A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 366 removed outlier: 3.908A pdb=" N LEU R 360 " --> pdb=" O TRP R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 388 removed outlier: 4.517A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 401 Proline residue: R 394 - end of helix removed outlier: 4.214A pdb=" N SER R 401 " --> pdb=" O TYR R 397 " (cutoff:3.500A) Processing helix chain 'R' and resid 401 through 408 removed outlier: 3.935A pdb=" N ARG R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.179A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.543A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.894A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.966A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.703A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.989A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.549A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.123A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.931A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.817A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.817A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 144 through 148 Processing sheet with id=AB4, first strand: chain 'S' and resid 166 through 167 376 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1337 1.27 - 1.41: 2216 1.41 - 1.54: 4952 1.54 - 1.68: 32 1.68 - 1.81: 87 Bond restraints: 8624 Sorted by residual: bond pdb=" N2 Q2B R 501 " pdb=" O25 Q2B R 501 " ideal model delta sigma weight residual 1.207 1.385 -0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C LYS B 78 " pdb=" O LYS B 78 " ideal model delta sigma weight residual 1.234 1.139 0.095 1.22e-02 6.72e+03 6.06e+01 bond pdb=" C GLY B 53 " pdb=" O GLY B 53 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.35e-02 5.49e+03 2.23e+01 bond pdb=" C LEU B 55 " pdb=" O LEU B 55 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.58e-02 4.01e+03 2.22e+01 bond pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 1.521 1.463 0.058 1.26e-02 6.30e+03 2.12e+01 ... (remaining 8619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11393 1.95 - 3.91: 235 3.91 - 5.86: 39 5.86 - 7.82: 9 7.82 - 9.77: 6 Bond angle restraints: 11682 Sorted by residual: angle pdb=" O ARG R 145 " pdb=" C ARG R 145 " pdb=" N SER R 146 " ideal model delta sigma weight residual 122.19 130.27 -8.08 1.31e+00 5.83e-01 3.80e+01 angle pdb=" CA ARG R 145 " pdb=" C ARG R 145 " pdb=" N SER R 146 " ideal model delta sigma weight residual 117.60 109.24 8.36 1.39e+00 5.18e-01 3.62e+01 angle pdb=" C ARG R 145 " pdb=" N SER R 146 " pdb=" CA SER R 146 " ideal model delta sigma weight residual 121.52 111.75 9.77 1.74e+00 3.30e-01 3.15e+01 angle pdb=" CA HIS B 54 " pdb=" C HIS B 54 " pdb=" N LEU B 55 " ideal model delta sigma weight residual 116.20 122.24 -6.04 1.25e+00 6.40e-01 2.34e+01 angle pdb=" C LYS B 78 " pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " ideal model delta sigma weight residual 109.68 101.72 7.96 1.98e+00 2.55e-01 1.62e+01 ... (remaining 11677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 4502 16.08 - 32.16: 441 32.16 - 48.24: 118 48.24 - 64.33: 21 64.33 - 80.41: 2 Dihedral angle restraints: 5084 sinusoidal: 1912 harmonic: 3172 Sorted by residual: dihedral pdb=" CB CYS R 257 " pdb=" SG CYS R 257 " pdb=" SG CYS R 264 " pdb=" CB CYS R 264 " ideal model delta sinusoidal sigma weight residual 93.00 152.60 -59.60 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" C LYS B 78 " pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " ideal model delta harmonic sigma weight residual -122.60 -109.77 -12.83 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" CA PHE S 27 " pdb=" C PHE S 27 " pdb=" N ALA S 28 " pdb=" CA ALA S 28 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1240 0.076 - 0.152: 113 0.152 - 0.228: 3 0.228 - 0.304: 0 0.304 - 0.380: 1 Chirality restraints: 1357 Sorted by residual: chirality pdb=" C4 Q2B R 501 " pdb=" C10 Q2B R 501 " pdb=" C3 Q2B R 501 " pdb=" C5 Q2B R 501 " both_signs ideal model delta sigma weight residual False -2.50 -2.88 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA PHE R 191 " pdb=" N PHE R 191 " pdb=" C PHE R 191 " pdb=" CB PHE R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE S 58 " pdb=" CA ILE S 58 " pdb=" CG1 ILE S 58 " pdb=" CG2 ILE S 58 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1354 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " -0.021 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C ARG B 52 " 0.077 2.00e-02 2.50e+03 pdb=" O ARG B 52 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY B 53 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO B 194 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 54 " -0.024 2.00e-02 2.50e+03 1.97e-02 5.84e+00 pdb=" CG HIS B 54 " 0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS B 54 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS B 54 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS B 54 " -0.025 2.00e-02 2.50e+03 pdb=" NE2 HIS B 54 " -0.004 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1273 2.76 - 3.29: 7837 3.29 - 3.83: 13215 3.83 - 4.36: 14620 4.36 - 4.90: 26285 Nonbonded interactions: 63230 Sorted by model distance: nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.229 3.040 nonbonded pdb=" NH2 ARG R 186 " pdb=" O PRO R 269 " model vdw 2.254 3.120 nonbonded pdb=" O GLY S 8 " pdb=" OG1 THR S 115 " model vdw 2.275 3.040 nonbonded pdb=" O SER S 149 " pdb=" OG1 THR S 198 " model vdw 2.280 3.040 ... (remaining 63225 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.080 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 : 0.005 0.178 8625 Z= 0.260 Angle : 0.705 9.771 11684 Z= 0.385 Chirality : 0.044 0.380 1357 Planarity : 0.005 0.070 1456 Dihedral : 13.858 80.408 3027 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.33 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.26), residues: 1062 helix: 1.45 (0.29), residues: 350 sheet: -0.38 (0.33), residues: 270 loop : -1.21 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.013 0.001 TYR S 161 PHE 0.022 0.001 PHE B 241 TRP 0.013 0.001 TRP B 339 HIS 0.013 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 8624) covalent geometry : angle 0.70517 (11682) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.49406 ( 2) hydrogen bonds : bond 0.14485 ( 368) hydrogen bonds : angle 5.22118 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.314 Fit side-chains REVERT: C 15 LEU cc_start: 0.8010 (mm) cc_final: 0.7681 (tp) REVERT: R 191 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.5224 (t80) outliers start: 3 outliers final: 2 residues processed: 154 average time/residue: 0.0847 time to fit residues: 17.7572 Evaluate side-chains 121 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain R residue 191 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 331 ASN B 13 GLN B 91 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN R 112 ASN R 270 HIS S 157 ASN S 159 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.189834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156314 restraints weight = 11990.948| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.93 r_work: 0.3797 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8625 Z= 0.138 Angle : 0.574 7.028 11684 Z= 0.300 Chirality : 0.042 0.154 1357 Planarity : 0.004 0.060 1456 Dihedral : 6.228 57.834 1198 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.90 % Allowed : 9.74 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.27), residues: 1062 helix: 1.39 (0.29), residues: 367 sheet: -0.27 (0.34), residues: 256 loop : -1.28 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 311 TYR 0.014 0.001 TYR S 161 PHE 0.020 0.001 PHE B 199 TRP 0.011 0.001 TRP B 339 HIS 0.007 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8624) covalent geometry : angle 0.57377 (11682) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.59195 ( 2) hydrogen bonds : bond 0.04147 ( 368) hydrogen bonds : angle 4.37117 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: C 15 LEU cc_start: 0.8148 (mm) cc_final: 0.7781 (tp) REVERT: R 191 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.5166 (t80) REVERT: R 277 MET cc_start: 0.7573 (tmm) cc_final: 0.6822 (tpp) outliers start: 17 outliers final: 7 residues processed: 132 average time/residue: 0.0926 time to fit residues: 16.6724 Evaluate side-chains 127 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 295 MET Chi-restraints excluded: chain R residue 306 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 48 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 91 HIS B 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.181081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146876 restraints weight = 11880.094| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.90 r_work: 0.3683 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8625 Z= 0.267 Angle : 0.711 8.501 11684 Z= 0.375 Chirality : 0.047 0.192 1357 Planarity : 0.005 0.062 1456 Dihedral : 6.200 47.183 1194 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.26 % Allowed : 13.89 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.26), residues: 1062 helix: 1.03 (0.29), residues: 373 sheet: -0.69 (0.32), residues: 263 loop : -1.58 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 87 TYR 0.023 0.002 TYR S 178 PHE 0.029 0.003 PHE B 199 TRP 0.019 0.002 TRP S 36 HIS 0.012 0.002 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 8624) covalent geometry : angle 0.71101 (11682) SS BOND : bond 0.00002 ( 1) SS BOND : angle 1.05219 ( 2) hydrogen bonds : bond 0.05369 ( 368) hydrogen bonds : angle 4.82888 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.329 Fit side-chains REVERT: A 24 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7227 (mtm110) REVERT: A 28 GLU cc_start: 0.7599 (pp20) cc_final: 0.7090 (tm-30) REVERT: A 32 ARG cc_start: 0.8826 (mtm110) cc_final: 0.8537 (mtp-110) REVERT: A 275 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6334 (tt0) REVERT: B 199 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7714 (t80) REVERT: C 18 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7728 (tp40) REVERT: R 191 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.5670 (t80) outliers start: 38 outliers final: 21 residues processed: 153 average time/residue: 0.0824 time to fit residues: 17.5789 Evaluate side-chains 143 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 21 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.187182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155106 restraints weight = 12101.182| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.16 r_work: 0.3723 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8625 Z= 0.113 Angle : 0.544 6.659 11684 Z= 0.286 Chirality : 0.041 0.141 1357 Planarity : 0.004 0.055 1456 Dihedral : 5.385 48.290 1194 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.58 % Allowed : 17.69 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.27), residues: 1062 helix: 1.28 (0.29), residues: 376 sheet: -0.64 (0.32), residues: 259 loop : -1.40 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 311 TYR 0.012 0.001 TYR S 216 PHE 0.016 0.001 PHE S 80 TRP 0.010 0.001 TRP B 339 HIS 0.006 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8624) covalent geometry : angle 0.54413 (11682) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.32253 ( 2) hydrogen bonds : bond 0.03695 ( 368) hydrogen bonds : angle 4.31954 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.289 Fit side-chains REVERT: B 273 ILE cc_start: 0.8889 (mp) cc_final: 0.8501 (mp) REVERT: B 280 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7845 (ttpp) REVERT: C 18 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7755 (tp40) REVERT: R 191 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.5429 (t80) REVERT: R 277 MET cc_start: 0.7468 (tmm) cc_final: 0.6708 (tpp) REVERT: R 379 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: S 27 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.7003 (m-10) outliers start: 23 outliers final: 14 residues processed: 144 average time/residue: 0.0859 time to fit residues: 16.8359 Evaluate side-chains 136 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 27 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.181268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147607 restraints weight = 12041.127| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.15 r_work: 0.3656 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8625 Z= 0.216 Angle : 0.640 8.317 11684 Z= 0.337 Chirality : 0.044 0.165 1357 Planarity : 0.004 0.054 1456 Dihedral : 5.543 47.410 1194 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.93 % Allowed : 18.03 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.27), residues: 1062 helix: 1.18 (0.29), residues: 375 sheet: -0.77 (0.32), residues: 263 loop : -1.58 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.019 0.002 TYR S 178 PHE 0.027 0.002 PHE B 199 TRP 0.016 0.002 TRP S 36 HIS 0.011 0.002 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 8624) covalent geometry : angle 0.63967 (11682) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.83260 ( 2) hydrogen bonds : bond 0.04707 ( 368) hydrogen bonds : angle 4.55804 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.325 Fit side-chains REVERT: B 81 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8312 (mm) REVERT: B 241 PHE cc_start: 0.8760 (p90) cc_final: 0.8553 (p90) REVERT: C 15 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7875 (tp) REVERT: C 18 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7709 (tp40) REVERT: R 191 PHE cc_start: 0.5814 (OUTLIER) cc_final: 0.5558 (t80) REVERT: R 277 MET cc_start: 0.7450 (tmm) cc_final: 0.6727 (tpp) REVERT: R 379 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: S 27 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7168 (m-10) REVERT: S 70 ILE cc_start: 0.6420 (OUTLIER) cc_final: 0.5909 (mm) outliers start: 44 outliers final: 23 residues processed: 150 average time/residue: 0.0942 time to fit residues: 19.6259 Evaluate side-chains 139 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 295 MET Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.185122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152722 restraints weight = 11844.698| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.02 r_work: 0.3726 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 8625 Z= 0.115 Angle : 0.538 6.195 11684 Z= 0.283 Chirality : 0.041 0.140 1357 Planarity : 0.004 0.053 1456 Dihedral : 4.911 48.204 1192 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.70 % Allowed : 19.26 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.27), residues: 1062 helix: 1.33 (0.29), residues: 376 sheet: -0.70 (0.32), residues: 258 loop : -1.46 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.011 0.001 TYR S 216 PHE 0.015 0.001 PHE B 199 TRP 0.009 0.001 TRP R 356 HIS 0.007 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8624) covalent geometry : angle 0.53791 (11682) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.38693 ( 2) hydrogen bonds : bond 0.03635 ( 368) hydrogen bonds : angle 4.25556 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.334 Fit side-chains REVERT: A 275 GLU cc_start: 0.6858 (tp30) cc_final: 0.6629 (tp30) REVERT: A 304 GLN cc_start: 0.7042 (tt0) cc_final: 0.6571 (tt0) REVERT: B 241 PHE cc_start: 0.8814 (p90) cc_final: 0.8602 (p90) REVERT: C 15 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7815 (tp) REVERT: C 18 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7712 (tp40) REVERT: R 191 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.5240 (t80) REVERT: R 277 MET cc_start: 0.7544 (tmm) cc_final: 0.6900 (tpp) REVERT: R 379 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: S 27 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7030 (m-10) REVERT: S 159 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8233 (p0) outliers start: 33 outliers final: 18 residues processed: 141 average time/residue: 0.0983 time to fit residues: 18.8990 Evaluate side-chains 137 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.0370 chunk 4 optimal weight: 2.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.190454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.156788 restraints weight = 12099.410| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.32 r_work: 0.3750 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 8625 Z= 0.098 Angle : 0.507 6.486 11684 Z= 0.265 Chirality : 0.040 0.131 1357 Planarity : 0.003 0.051 1456 Dihedral : 4.421 49.409 1192 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.14 % Allowed : 19.04 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.27), residues: 1062 helix: 1.46 (0.29), residues: 375 sheet: -0.63 (0.33), residues: 257 loop : -1.34 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.009 0.001 TYR S 59 PHE 0.013 0.001 PHE B 241 TRP 0.011 0.001 TRP R 356 HIS 0.005 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8624) covalent geometry : angle 0.50675 (11682) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.37942 ( 2) hydrogen bonds : bond 0.03050 ( 368) hydrogen bonds : angle 3.99169 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.220 Fit side-chains REVERT: A 275 GLU cc_start: 0.6863 (tp30) cc_final: 0.6649 (tp30) REVERT: A 304 GLN cc_start: 0.6954 (tt0) cc_final: 0.6461 (tt0) REVERT: B 241 PHE cc_start: 0.8716 (p90) cc_final: 0.8502 (p90) REVERT: C 15 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7832 (tp) REVERT: C 18 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7735 (tp40) REVERT: R 191 PHE cc_start: 0.5400 (OUTLIER) cc_final: 0.4919 (t80) REVERT: R 277 MET cc_start: 0.7364 (tmm) cc_final: 0.6729 (tpp) REVERT: R 379 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: S 151 LYS cc_start: 0.7665 (mmtt) cc_final: 0.6971 (tttt) REVERT: S 159 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (p0) outliers start: 28 outliers final: 20 residues processed: 145 average time/residue: 0.0960 time to fit residues: 18.7747 Evaluate side-chains 145 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 270 HIS Chi-restraints excluded: chain R residue 295 MET Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.186529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155259 restraints weight = 11808.917| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.14 r_work: 0.3736 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8625 Z= 0.116 Angle : 0.535 7.006 11684 Z= 0.279 Chirality : 0.040 0.132 1357 Planarity : 0.004 0.050 1456 Dihedral : 4.486 49.094 1192 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.58 % Allowed : 19.15 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.27), residues: 1062 helix: 1.43 (0.28), residues: 376 sheet: -0.52 (0.33), residues: 259 loop : -1.39 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 311 TYR 0.009 0.001 TYR S 178 PHE 0.016 0.001 PHE B 199 TRP 0.008 0.001 TRP B 339 HIS 0.007 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8624) covalent geometry : angle 0.53463 (11682) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.31898 ( 2) hydrogen bonds : bond 0.03339 ( 368) hydrogen bonds : angle 4.03684 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.328 Fit side-chains REVERT: A 304 GLN cc_start: 0.6932 (tt0) cc_final: 0.6528 (tt0) REVERT: B 241 PHE cc_start: 0.8786 (p90) cc_final: 0.8563 (p90) REVERT: C 15 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7864 (tp) REVERT: C 18 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7638 (tp40) REVERT: R 191 PHE cc_start: 0.5595 (OUTLIER) cc_final: 0.5141 (t80) REVERT: R 277 MET cc_start: 0.7491 (tmm) cc_final: 0.6884 (tpp) REVERT: R 379 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: S 159 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8161 (p0) outliers start: 32 outliers final: 23 residues processed: 145 average time/residue: 0.0910 time to fit residues: 18.2121 Evaluate side-chains 141 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 270 HIS Chi-restraints excluded: chain R residue 295 MET Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 79 optimal weight: 0.0030 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.186682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.154140 restraints weight = 11877.770| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.30 r_work: 0.3744 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8625 Z= 0.112 Angle : 0.539 7.708 11684 Z= 0.281 Chirality : 0.040 0.135 1357 Planarity : 0.004 0.050 1456 Dihedral : 4.470 49.468 1192 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.36 % Allowed : 19.93 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.27), residues: 1062 helix: 1.44 (0.28), residues: 376 sheet: -0.57 (0.33), residues: 257 loop : -1.39 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 311 TYR 0.009 0.001 TYR S 161 PHE 0.015 0.001 PHE B 199 TRP 0.008 0.001 TRP B 339 HIS 0.008 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8624) covalent geometry : angle 0.53952 (11682) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.34246 ( 2) hydrogen bonds : bond 0.03344 ( 368) hydrogen bonds : angle 4.04391 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.206 Fit side-chains REVERT: A 304 GLN cc_start: 0.7066 (tt0) cc_final: 0.6531 (tt0) REVERT: C 15 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7857 (tp) REVERT: C 18 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7591 (tp40) REVERT: R 191 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.5035 (t80) REVERT: R 379 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: S 159 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8116 (p0) outliers start: 30 outliers final: 23 residues processed: 137 average time/residue: 0.0760 time to fit residues: 14.4963 Evaluate side-chains 141 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 295 MET Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.186976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.156317 restraints weight = 11764.062| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.96 r_work: 0.3740 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8625 Z= 0.108 Angle : 0.540 7.416 11684 Z= 0.280 Chirality : 0.040 0.138 1357 Planarity : 0.004 0.050 1456 Dihedral : 4.424 49.143 1192 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.36 % Allowed : 20.27 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.27), residues: 1062 helix: 1.49 (0.28), residues: 376 sheet: -0.60 (0.33), residues: 257 loop : -1.39 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.009 0.001 TYR S 161 PHE 0.014 0.001 PHE B 199 TRP 0.008 0.001 TRP R 279 HIS 0.006 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8624) covalent geometry : angle 0.54027 (11682) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.33471 ( 2) hydrogen bonds : bond 0.03249 ( 368) hydrogen bonds : angle 4.01370 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.330 Fit side-chains REVERT: A 53 MET cc_start: 0.6911 (mtt) cc_final: 0.6708 (mtt) REVERT: A 290 TYR cc_start: 0.7058 (t80) cc_final: 0.6693 (t80) REVERT: A 304 GLN cc_start: 0.6971 (tt0) cc_final: 0.6564 (tt0) REVERT: B 241 PHE cc_start: 0.8745 (p90) cc_final: 0.8528 (p90) REVERT: C 15 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7895 (tp) REVERT: C 18 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7710 (tp40) REVERT: R 191 PHE cc_start: 0.5518 (OUTLIER) cc_final: 0.5232 (t80) REVERT: R 277 MET cc_start: 0.7296 (tmm) cc_final: 0.6561 (tpp) REVERT: R 379 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7414 (m-80) outliers start: 30 outliers final: 25 residues processed: 142 average time/residue: 0.0896 time to fit residues: 17.5641 Evaluate side-chains 147 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 295 MET Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 102 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.188578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.152721 restraints weight = 11875.802| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.32 r_work: 0.3728 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 8625 Z= 0.199 Angle : 0.986 59.186 11684 Z= 0.558 Chirality : 0.044 0.695 1357 Planarity : 0.004 0.050 1456 Dihedral : 4.441 49.105 1192 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.25 % Allowed : 20.49 % Favored : 76.26 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.26), residues: 1062 helix: 1.45 (0.28), residues: 376 sheet: -0.60 (0.33), residues: 257 loop : -1.39 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.008 0.001 TYR S 161 PHE 0.014 0.001 PHE B 199 TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8624) covalent geometry : angle 0.98589 (11682) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.32084 ( 2) hydrogen bonds : bond 0.03229 ( 368) hydrogen bonds : angle 4.02047 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.69 seconds wall clock time: 36 minutes 3.12 seconds (2163.12 seconds total)