Starting phenix.real_space_refine on Wed Mar 12 22:33:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ikg_35511/03_2025/8ikg_35511_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ikg_35511/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ikg_35511/03_2025/8ikg_35511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ikg_35511/03_2025/8ikg_35511.map" model { file = "/net/cci-nas-00/data/ceres_data/8ikg_35511/03_2025/8ikg_35511_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ikg_35511/03_2025/8ikg_35511_neut.cif" } resolution = 3.4 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} 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: {'GLU:plan': 2, 'ASN:plan1': 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: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} 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: 5.44, per 1000 atoms: 0.64 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 2.29 Time building geometry restraints manager: 2.67 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: 0.700 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- 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 8624 Z= 0.320 Angle : 0.705 9.771 11682 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 : 11.28 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 (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: -0.19 (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 TRP 0.013 0.001 TRP B 339 HIS 0.013 0.001 HIS B 54 PHE 0.022 0.001 PHE B 241 TYR 0.013 0.001 TYR S 161 ARG 0.008 0.000 ARG A 32 *********************** 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 : 1.040 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: 0.2136 time to fit residues: 44.7451 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 : 0.913 ------------------------------------------------------------------------------- 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 90 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.0470 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.186574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.152383 restraints weight = 11697.998| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.18 r_work: 0.3734 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8624 Z= 0.287 Angle : 0.622 6.948 11682 Z= 0.326 Chirality : 0.044 0.157 1357 Planarity : 0.004 0.062 1456 Dihedral : 6.424 57.773 1198 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.46 % Allowed : 10.41 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.27), residues: 1062 helix: 1.25 (0.29), residues: 373 sheet: -0.42 (0.33), residues: 256 loop : -1.35 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 36 HIS 0.009 0.001 HIS S 220 PHE 0.025 0.002 PHE B 199 TYR 0.016 0.002 TYR S 161 ARG 0.007 0.001 ARG R 311 *********************** 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 148 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6397 (tt0) REVERT: C 15 LEU cc_start: 0.8172 (mm) cc_final: 0.7943 (mm) REVERT: R 191 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.5187 (t80) REVERT: R 277 MET cc_start: 0.7652 (tmm) cc_final: 0.6886 (tpp) outliers start: 22 outliers final: 13 residues processed: 134 average time/residue: 0.2130 time to fit residues: 38.7132 Evaluate side-chains 131 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 263 THR 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 112 ASN 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 339 ILE Chi-restraints excluded: chain R residue 383 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** 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 = 0.4298 r_free = 0.4298 target = 0.191074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.156341 restraints weight = 11844.247| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.19 r_work: 0.3760 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 8624 Z= 0.158 Angle : 0.533 6.995 11682 Z= 0.279 Chirality : 0.040 0.142 1357 Planarity : 0.004 0.056 1456 Dihedral : 5.858 50.176 1198 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.58 % Allowed : 13.33 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.27), residues: 1062 helix: 1.41 (0.29), residues: 367 sheet: -0.41 (0.33), residues: 258 loop : -1.29 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.006 0.001 HIS R 154 PHE 0.015 0.001 PHE S 80 TYR 0.011 0.001 TYR S 161 ARG 0.005 0.000 ARG S 87 *********************** 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 147 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.913 Fit side-chains REVERT: A 28 GLU cc_start: 0.7375 (pp20) cc_final: 0.6963 (tm-30) REVERT: B 45 MET cc_start: 0.8074 (mtm) cc_final: 0.7585 (ptp) REVERT: B 325 MET cc_start: 0.8692 (tpp) cc_final: 0.8485 (tpp) REVERT: R 191 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5372 (t80) REVERT: S 70 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.5925 (mm) outliers start: 23 outliers final: 14 residues processed: 136 average time/residue: 0.2086 time to fit residues: 38.8000 Evaluate side-chains 128 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 307 PHE Chi-restraints excluded: chain B residue 55 LEU 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 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 S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 28 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.190609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.157282 restraints weight = 11754.062| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.10 r_work: 0.3804 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 8624 Z= 0.149 Angle : 0.510 6.864 11682 Z= 0.265 Chirality : 0.040 0.138 1357 Planarity : 0.004 0.053 1456 Dihedral : 5.042 48.310 1194 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.24 % Allowed : 15.45 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.27), residues: 1062 helix: 1.44 (0.29), residues: 373 sheet: -0.47 (0.33), residues: 256 loop : -1.30 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.006 0.001 HIS R 154 PHE 0.013 0.001 PHE B 241 TYR 0.010 0.001 TYR S 161 ARG 0.006 0.000 ARG S 87 *********************** 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 151 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.175 Fit side-chains REVERT: B 32 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7775 (tt0) REVERT: B 45 MET cc_start: 0.8264 (mtm) cc_final: 0.7738 (ptp) REVERT: C 18 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7756 (tp40) REVERT: R 191 PHE cc_start: 0.5570 (OUTLIER) cc_final: 0.5208 (t80) REVERT: R 277 MET cc_start: 0.7519 (tmm) cc_final: 0.6825 (tpp) outliers start: 20 outliers final: 12 residues processed: 138 average time/residue: 0.2415 time to fit residues: 45.8737 Evaluate side-chains 129 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 307 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 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 383 SER Chi-restraints excluded: chain S residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 94 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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** B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.191442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158495 restraints weight = 11779.644| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.13 r_work: 0.3769 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 8624 Z= 0.155 Angle : 0.506 6.706 11682 Z= 0.263 Chirality : 0.040 0.135 1357 Planarity : 0.004 0.052 1456 Dihedral : 4.579 46.995 1192 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.91 % Allowed : 17.69 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.27), residues: 1062 helix: 1.45 (0.29), residues: 376 sheet: -0.48 (0.33), residues: 256 loop : -1.29 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.006 0.001 HIS R 154 PHE 0.013 0.001 PHE B 199 TYR 0.009 0.001 TYR S 161 ARG 0.006 0.000 ARG S 87 *********************** 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 147 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.065 Fit side-chains REVERT: B 32 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7759 (tt0) REVERT: B 45 MET cc_start: 0.8153 (mtm) cc_final: 0.7793 (ptp) REVERT: C 18 GLN cc_start: 0.8204 (tp-100) cc_final: 0.7768 (tp40) REVERT: R 191 PHE cc_start: 0.5593 (OUTLIER) cc_final: 0.5279 (t80) REVERT: R 277 MET cc_start: 0.7400 (tmm) cc_final: 0.6670 (tpp) REVERT: R 379 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: S 70 ILE cc_start: 0.6213 (OUTLIER) cc_final: 0.5943 (mm) REVERT: S 157 ASN cc_start: 0.5891 (m-40) cc_final: 0.5498 (m-40) outliers start: 26 outliers final: 15 residues processed: 134 average time/residue: 0.2874 time to fit residues: 53.6070 Evaluate side-chains 135 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 172 GLU 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 218 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** B 91 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.190561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.157668 restraints weight = 11708.255| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.04 r_work: 0.3765 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8624 Z= 0.164 Angle : 0.508 6.667 11682 Z= 0.265 Chirality : 0.040 0.134 1357 Planarity : 0.003 0.051 1456 Dihedral : 4.426 46.614 1192 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.25 % Allowed : 17.92 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.27), residues: 1062 helix: 1.51 (0.28), residues: 376 sheet: -0.44 (0.33), residues: 254 loop : -1.30 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS S 220 PHE 0.015 0.001 PHE B 199 TYR 0.009 0.001 TYR S 161 ARG 0.002 0.000 ARG B 137 *********************** 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: 29 poor density : 121 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7713 (tt0) REVERT: B 45 MET cc_start: 0.8149 (mtm) cc_final: 0.7812 (ptp) REVERT: C 18 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7798 (tp40) REVERT: R 191 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.5450 (t80) REVERT: R 277 MET cc_start: 0.7395 (tmm) cc_final: 0.6650 (tpp) REVERT: R 379 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: S 70 ILE cc_start: 0.6185 (OUTLIER) cc_final: 0.5860 (mm) outliers start: 29 outliers final: 18 residues processed: 138 average time/residue: 0.2135 time to fit residues: 40.0886 Evaluate side-chains 136 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 307 PHE 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 B residue 318 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 218 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 B 91 HIS B 259 GLN ** B 295 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 = 0.4291 r_free = 0.4291 target = 0.190502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.157217 restraints weight = 11890.575| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.25 r_work: 0.3757 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8624 Z= 0.164 Angle : 0.511 6.606 11682 Z= 0.266 Chirality : 0.040 0.197 1357 Planarity : 0.004 0.052 1456 Dihedral : 4.378 46.544 1192 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.14 % Allowed : 18.70 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.27), residues: 1062 helix: 1.54 (0.28), residues: 376 sheet: -0.44 (0.34), residues: 254 loop : -1.29 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS S 220 PHE 0.015 0.001 PHE B 199 TYR 0.009 0.001 TYR S 161 ARG 0.005 0.000 ARG R 311 *********************** 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 154 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6902 (tp30) cc_final: 0.6690 (tp30) REVERT: B 32 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7717 (tt0) REVERT: B 45 MET cc_start: 0.8218 (mtm) cc_final: 0.7887 (ptp) REVERT: B 280 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7617 (ttpt) REVERT: C 18 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7849 (tp40) REVERT: R 277 MET cc_start: 0.7463 (tmm) cc_final: 0.6719 (tpp) REVERT: R 379 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: S 70 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5898 (mm) outliers start: 28 outliers final: 19 residues processed: 140 average time/residue: 0.2185 time to fit residues: 41.3785 Evaluate side-chains 139 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 PHE 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 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 133 GLU Chi-restraints excluded: chain R residue 218 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 B 91 HIS B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.182212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149306 restraints weight = 11936.802| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.16 r_work: 0.3670 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8624 Z= 0.371 Angle : 0.645 7.592 11682 Z= 0.340 Chirality : 0.045 0.212 1357 Planarity : 0.004 0.052 1456 Dihedral : 4.933 26.964 1190 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.36 % Allowed : 19.37 % 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 (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: -0.47 (0.26), residues: 1062 helix: 1.29 (0.28), residues: 377 sheet: -0.66 (0.32), residues: 262 loop : -1.53 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.011 0.002 HIS S 220 PHE 0.029 0.002 PHE B 199 TYR 0.020 0.002 TYR S 178 ARG 0.008 0.001 ARG B 19 *********************** 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 155 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6931 (tp30) cc_final: 0.6703 (tp30) REVERT: A 304 GLN cc_start: 0.7158 (tt0) cc_final: 0.6705 (tt0) REVERT: B 32 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7816 (tt0) REVERT: B 45 MET cc_start: 0.8201 (mtm) cc_final: 0.7883 (ptp) REVERT: B 81 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8454 (mt) REVERT: C 18 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7964 (tp40) REVERT: R 191 PHE cc_start: 0.5989 (OUTLIER) cc_final: 0.5728 (t80) REVERT: R 379 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: S 70 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5968 (mm) outliers start: 30 outliers final: 22 residues processed: 144 average time/residue: 0.2140 time to fit residues: 42.2590 Evaluate side-chains 140 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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 C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 218 ILE 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 379 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 384 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 B 91 HIS B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.184618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151322 restraints weight = 12034.510| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.93 r_work: 0.3710 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8624 Z= 0.276 Angle : 0.610 8.061 11682 Z= 0.322 Chirality : 0.043 0.200 1357 Planarity : 0.004 0.053 1456 Dihedral : 4.818 26.899 1190 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.70 % Allowed : 20.16 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.26), residues: 1062 helix: 1.26 (0.28), residues: 376 sheet: -0.73 (0.32), residues: 263 loop : -1.57 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 36 HIS 0.010 0.001 HIS S 220 PHE 0.022 0.002 PHE B 199 TYR 0.015 0.001 TYR S 178 ARG 0.007 0.001 ARG A 24 *********************** 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 151 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7807 (tt0) REVERT: B 45 MET cc_start: 0.8309 (mtm) cc_final: 0.7898 (ptp) REVERT: B 81 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8489 (mt) REVERT: C 18 GLN cc_start: 0.8274 (tp-100) cc_final: 0.7940 (tp40) REVERT: R 277 MET cc_start: 0.7393 (tmm) cc_final: 0.6592 (tpp) REVERT: R 379 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: S 70 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5983 (mm) outliers start: 33 outliers final: 22 residues processed: 136 average time/residue: 0.2079 time to fit residues: 39.2855 Evaluate side-chains 140 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 218 ILE 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 360 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.188437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155518 restraints weight = 11914.074| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.08 r_work: 0.3735 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 8624 Z= 0.166 Angle : 0.552 8.366 11682 Z= 0.288 Chirality : 0.041 0.207 1357 Planarity : 0.004 0.052 1456 Dihedral : 4.419 25.815 1190 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.58 % Allowed : 21.95 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.27), residues: 1062 helix: 1.39 (0.28), residues: 377 sheet: -0.70 (0.32), residues: 261 loop : -1.40 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 356 HIS 0.007 0.001 HIS S 220 PHE 0.014 0.001 PHE B 241 TYR 0.011 0.001 TYR A 302 ARG 0.009 0.000 ARG A 32 ********************** 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 145 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6961 (tp30) cc_final: 0.6728 (tp30) REVERT: A 304 GLN cc_start: 0.7375 (tt0) cc_final: 0.6793 (tt0) REVERT: B 45 MET cc_start: 0.8211 (mtm) cc_final: 0.7825 (ptp) REVERT: B 241 PHE cc_start: 0.8739 (p90) cc_final: 0.8488 (p90) REVERT: C 18 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7875 (tp40) REVERT: R 277 MET cc_start: 0.7247 (tmm) cc_final: 0.6492 (tpp) REVERT: R 379 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: S 70 ILE cc_start: 0.6147 (OUTLIER) cc_final: 0.5833 (mm) outliers start: 23 outliers final: 18 residues processed: 136 average time/residue: 0.2172 time to fit residues: 40.3182 Evaluate side-chains 135 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 308 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.188404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153097 restraints weight = 12068.414| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.23 r_work: 0.3736 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8624 Z= 0.172 Angle : 0.551 7.714 11682 Z= 0.288 Chirality : 0.041 0.217 1357 Planarity : 0.004 0.052 1456 Dihedral : 4.315 23.677 1190 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.91 % Allowed : 21.39 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.27), residues: 1062 helix: 1.48 (0.28), residues: 376 sheet: -0.72 (0.32), residues: 262 loop : -1.34 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 356 HIS 0.006 0.001 HIS S 220 PHE 0.015 0.001 PHE B 199 TYR 0.008 0.001 TYR S 216 ARG 0.007 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.19 seconds wall clock time: 78 minutes 48.60 seconds (4728.60 seconds total)