Starting phenix.real_space_refine on Tue Apr 29 21:24:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hcx_34667/04_2025/8hcx_34667_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hcx_34667/04_2025/8hcx_34667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hcx_34667/04_2025/8hcx_34667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hcx_34667/04_2025/8hcx_34667.map" model { file = "/net/cci-nas-00/data/ceres_data/8hcx_34667/04_2025/8hcx_34667_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hcx_34667/04_2025/8hcx_34667_neut.cif" } resolution = 3.5 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= 0.026 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 63 5.16 5 C 5695 2.51 5 N 1505 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8933 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1780 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2190 Classifications: {'peptide': 292} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1770 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 5.50, per 1000 atoms: 0.62 Number of scatterers: 8933 At special positions: 0 Unit cell: (136.24, 100.88, 120.64, 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 63 16.00 O 1670 8.00 N 1505 7.00 C 5695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS D 1 " - pdb=" SG CYS D 15 " 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 39.3% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.585A pdb=" N LYS A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.701A pdb=" N CYS A 212 " --> pdb=" O TRP A 209 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 214 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 215 " --> pdb=" O CYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 296 through 317 removed outlier: 4.482A pdb=" N SER A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.821A pdb=" N ARG B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 4.097A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 129 removed outlier: 3.534A pdb=" N LEU C 122 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 164 removed outlier: 3.580A pdb=" N LEU C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Proline residue: C 156 - end of helix removed outlier: 3.808A pdb=" N LEU C 162 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 4.288A pdb=" N MET C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 204 removed outlier: 3.514A pdb=" N PHE C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 238 removed outlier: 3.521A pdb=" N VAL C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.667A pdb=" N ILE C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 272 removed outlier: 3.516A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 282 Processing helix chain 'C' and resid 282 through 302 removed outlier: 3.820A pdb=" N TYR C 293 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 350 Proline residue: C 338 - end of helix removed outlier: 3.843A pdb=" N ARG C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 390 removed outlier: 3.522A pdb=" N CYS C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) Proline residue: C 383 - end of helix removed outlier: 3.539A pdb=" N TYR C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.001A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.670A pdb=" N LYS E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.988A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.574A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 189 removed outlier: 3.717A pdb=" N MET A 196 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 187 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG A 35 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 37 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 222 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU A 39 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ASP A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 219 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE A 255 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 221 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 257 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 223 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 256 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.752A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 7.119A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 77 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.101A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.577A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.833A pdb=" N SER B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.973A pdb=" N ALA B 236 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 257 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.192A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 240 through 245 removed outlier: 3.630A pdb=" N LEU C 256 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 252 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.511A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 116 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.511A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 116 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.504A pdb=" N VAL E 226 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1227 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: 2.55 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2889 1.34 - 1.46: 2199 1.46 - 1.58: 3944 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 9118 Sorted by residual: bond pdb=" N ILE A 273 " pdb=" CA ILE A 273 " ideal model delta sigma weight residual 1.459 1.513 -0.054 1.25e-02 6.40e+03 1.90e+01 bond pdb=" N ILE C 96 " pdb=" CA ILE C 96 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" N ILE C 94 " pdb=" CA ILE C 94 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.60e+00 bond pdb=" N GLU E 234 " pdb=" CA GLU E 234 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.81e+00 bond pdb=" C LYS A 272 " pdb=" N ILE A 273 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.36e-02 5.41e+03 2.68e+00 ... (remaining 9113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 12204 2.34 - 4.68: 152 4.68 - 7.02: 16 7.02 - 9.37: 7 9.37 - 11.71: 2 Bond angle restraints: 12381 Sorted by residual: angle pdb=" CA LEU C 149 " pdb=" CB LEU C 149 " pdb=" CG LEU C 149 " ideal model delta sigma weight residual 116.30 128.01 -11.71 3.50e+00 8.16e-02 1.12e+01 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 109.81 117.10 -7.29 2.21e+00 2.05e-01 1.09e+01 angle pdb=" CB MET C 245 " pdb=" CG MET C 245 " pdb=" SD MET C 245 " ideal model delta sigma weight residual 112.70 121.96 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" CA LEU E 219 " pdb=" CB LEU E 219 " pdb=" CG LEU E 219 " ideal model delta sigma weight residual 116.30 126.68 -10.38 3.50e+00 8.16e-02 8.79e+00 angle pdb=" CA MET C 245 " pdb=" CB MET C 245 " pdb=" CG MET C 245 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.62e+00 ... (remaining 12376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 4553 15.66 - 31.33: 591 31.33 - 46.99: 192 46.99 - 62.66: 50 62.66 - 78.32: 9 Dihedral angle restraints: 5395 sinusoidal: 2034 harmonic: 3361 Sorted by residual: dihedral pdb=" CB CYS D 1 " pdb=" SG CYS D 1 " pdb=" SG CYS D 15 " pdb=" CB CYS D 15 " ideal model delta sinusoidal sigma weight residual -86.00 -119.46 33.46 1 1.00e+01 1.00e-02 1.59e+01 dihedral pdb=" CA THR B 91 " pdb=" C THR B 91 " pdb=" N THR B 92 " pdb=" CA THR B 92 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG B 319 " pdb=" CD ARG B 319 " pdb=" NE ARG B 319 " pdb=" CZ ARG B 319 " ideal model delta sinusoidal sigma weight residual 180.00 137.63 42.37 2 1.50e+01 4.44e-03 9.69e+00 ... (remaining 5392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 987 0.034 - 0.068: 306 0.068 - 0.102: 83 0.102 - 0.136: 44 0.136 - 0.170: 3 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CB ILE B 23 " pdb=" CA ILE B 23 " pdb=" CG1 ILE B 23 " pdb=" CG2 ILE B 23 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA LYS C 97 " pdb=" N LYS C 97 " pdb=" C LYS C 97 " pdb=" CB LYS C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1420 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO B 241 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 233 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C LEU E 233 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU E 233 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU E 234 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 190 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ASP A 190 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A 190 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 191 " -0.013 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 196 2.67 - 3.23: 8654 3.23 - 3.79: 14361 3.79 - 4.34: 18863 4.34 - 4.90: 30471 Nonbonded interactions: 72545 Sorted by model distance: nonbonded pdb=" OG1 THR B 91 " pdb=" OD1 ASN B 93 " model vdw 2.117 3.040 nonbonded pdb=" O ASP E 89 " pdb=" OH TYR E 93 " model vdw 2.168 3.040 nonbonded pdb=" OD1 ASN B 318 " pdb=" N ARG B 319 " model vdw 2.224 3.120 nonbonded pdb=" O GLY E 7 " pdb=" OG1 THR E 114 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.286 3.040 ... (remaining 72540 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 group one per residue 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: 1.560 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.770 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 : 0.003 0.054 9120 Z= 0.134 Angle : 0.624 11.707 12385 Z= 0.311 Chirality : 0.040 0.170 1423 Planarity : 0.005 0.106 1570 Dihedral : 16.427 78.322 3217 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.46 % Favored : 97.19 % Rotamer: Outliers : 0.31 % Allowed : 31.37 % Favored : 68.31 % 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: 0.14 (0.26), residues: 1137 helix: 0.61 (0.27), residues: 392 sheet: 0.58 (0.34), residues: 264 loop : -0.52 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 87 HIS 0.004 0.001 HIS C 150 PHE 0.024 0.001 PHE C 280 TYR 0.014 0.001 TYR B 150 ARG 0.009 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.24598 ( 436) hydrogen bonds : angle 8.25104 ( 1227) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.35229 ( 4) covalent geometry : bond 0.00254 ( 9118) covalent geometry : angle 0.62434 (12381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 0.857 Fit side-chains REVERT: A 18 MET cc_start: 0.7394 (tpp) cc_final: 0.7081 (tpp) REVERT: A 210 ILE cc_start: 0.7749 (tp) cc_final: 0.7363 (tp) REVERT: B 85 ILE cc_start: 0.7937 (tt) cc_final: 0.7578 (pt) REVERT: B 256 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7157 (mtt180) REVERT: C 96 ILE cc_start: 0.5610 (OUTLIER) cc_final: 0.5343 (tt) REVERT: C 180 ILE cc_start: 0.8200 (mt) cc_final: 0.7871 (mt) REVERT: C 346 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7880 (ttmm) REVERT: E 44 LEU cc_start: 0.7788 (mt) cc_final: 0.7476 (mt) REVERT: E 228 TYR cc_start: 0.7424 (m-10) cc_final: 0.7135 (m-10) outliers start: 3 outliers final: 0 residues processed: 281 average time/residue: 0.2360 time to fit residues: 88.4102 Evaluate side-chains 285 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** 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 = 0.3817 r_free = 0.3817 target = 0.135987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122668 restraints weight = 14767.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126538 restraints weight = 6371.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128929 restraints weight = 3348.322| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9120 Z= 0.199 Angle : 0.648 8.662 12385 Z= 0.340 Chirality : 0.044 0.169 1423 Planarity : 0.005 0.072 1570 Dihedral : 4.078 22.183 1247 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.46 % Favored : 97.27 % Rotamer: Outliers : 5.25 % Allowed : 26.02 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.25), residues: 1137 helix: 1.10 (0.26), residues: 391 sheet: 0.44 (0.32), residues: 280 loop : -0.50 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 216 HIS 0.005 0.001 HIS B 59 PHE 0.024 0.002 PHE C 280 TYR 0.014 0.002 TYR E 101 ARG 0.008 0.001 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 436) hydrogen bonds : angle 5.22470 ( 1227) SS BOND : bond 0.00302 ( 2) SS BOND : angle 1.13011 ( 4) covalent geometry : bond 0.00417 ( 9118) covalent geometry : angle 0.64814 (12381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7362 (tt0) cc_final: 0.7099 (tt0) REVERT: A 17 LYS cc_start: 0.7673 (mttt) cc_final: 0.7432 (mttt) REVERT: A 25 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6409 (tm-30) REVERT: A 190 ASP cc_start: 0.7869 (t0) cc_final: 0.7645 (t0) REVERT: A 195 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7018 (t-90) REVERT: A 215 ASP cc_start: 0.7057 (t0) cc_final: 0.6634 (t0) REVERT: A 257 ASN cc_start: 0.7954 (m-40) cc_final: 0.7671 (m-40) REVERT: A 261 LEU cc_start: 0.8066 (mp) cc_final: 0.7849 (mp) REVERT: A 350 GLN cc_start: 0.8276 (tp-100) cc_final: 0.7990 (tp-100) REVERT: B 115 ASN cc_start: 0.7701 (m-40) cc_final: 0.7426 (m-40) REVERT: B 202 ARG cc_start: 0.7621 (tpp80) cc_final: 0.7394 (tpp80) REVERT: B 313 LEU cc_start: 0.8281 (mp) cc_final: 0.8038 (mt) REVERT: C 112 PHE cc_start: 0.7359 (t80) cc_final: 0.7013 (t80) REVERT: C 148 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7867 (mm) REVERT: C 167 TRP cc_start: 0.6260 (m100) cc_final: 0.5888 (m100) REVERT: C 180 ILE cc_start: 0.8195 (mt) cc_final: 0.7791 (mt) REVERT: C 369 TYR cc_start: 0.7414 (m-80) cc_final: 0.7113 (m-80) REVERT: E 10 LEU cc_start: 0.8278 (tp) cc_final: 0.8041 (tt) REVERT: E 102 TYR cc_start: 0.7836 (t80) cc_final: 0.7362 (t80) REVERT: E 176 TRP cc_start: 0.8170 (m100) cc_final: 0.7901 (m100) REVERT: E 226 VAL cc_start: 0.8374 (t) cc_final: 0.7903 (p) outliers start: 50 outliers final: 26 residues processed: 341 average time/residue: 0.2269 time to fit residues: 104.0759 Evaluate side-chains 342 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 314 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 61 optimal weight: 0.0470 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** 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 = 0.3850 r_free = 0.3850 target = 0.138372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124540 restraints weight = 15175.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128665 restraints weight = 6340.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131150 restraints weight = 3269.156| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9120 Z= 0.119 Angle : 0.605 8.701 12385 Z= 0.310 Chirality : 0.041 0.141 1423 Planarity : 0.004 0.061 1570 Dihedral : 3.906 16.146 1245 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.64 % Favored : 97.10 % Rotamer: Outliers : 4.30 % Allowed : 28.12 % Favored : 67.58 % 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: 0.49 (0.26), residues: 1137 helix: 1.25 (0.26), residues: 392 sheet: 0.28 (0.32), residues: 285 loop : -0.35 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 216 HIS 0.004 0.001 HIS C 150 PHE 0.031 0.001 PHE C 280 TYR 0.015 0.001 TYR C 281 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 436) hydrogen bonds : angle 5.02004 ( 1227) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.58933 ( 4) covalent geometry : bond 0.00255 ( 9118) covalent geometry : angle 0.60469 (12381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 316 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7683 (mttt) cc_final: 0.7452 (mttt) REVERT: A 18 MET cc_start: 0.7245 (tpp) cc_final: 0.6874 (tpp) REVERT: A 190 ASP cc_start: 0.7968 (t0) cc_final: 0.7757 (t0) REVERT: A 195 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.6956 (t-90) REVERT: A 215 ASP cc_start: 0.7039 (t0) cc_final: 0.6618 (t0) REVERT: A 257 ASN cc_start: 0.7986 (m-40) cc_final: 0.7667 (m-40) REVERT: A 261 LEU cc_start: 0.8066 (mp) cc_final: 0.7861 (mp) REVERT: A 350 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7968 (tp-100) REVERT: B 115 ASN cc_start: 0.7543 (m-40) cc_final: 0.7198 (m-40) REVERT: B 202 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7213 (tpp80) REVERT: B 259 ASP cc_start: 0.7326 (t0) cc_final: 0.7050 (t0) REVERT: B 294 TYR cc_start: 0.7382 (m-80) cc_final: 0.6728 (m-80) REVERT: B 313 LEU cc_start: 0.8295 (mp) cc_final: 0.8079 (mt) REVERT: B 318 ASN cc_start: 0.8190 (t0) cc_final: 0.7919 (t0) REVERT: C 112 PHE cc_start: 0.7470 (t80) cc_final: 0.7077 (t80) REVERT: C 129 ASN cc_start: 0.7953 (t0) cc_final: 0.7680 (t0) REVERT: C 148 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7711 (mm) REVERT: C 149 LEU cc_start: 0.8430 (tt) cc_final: 0.8227 (tt) REVERT: C 180 ILE cc_start: 0.8195 (mt) cc_final: 0.7813 (mt) REVERT: C 346 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7916 (ttmm) REVERT: C 369 TYR cc_start: 0.7455 (m-80) cc_final: 0.7162 (m-80) REVERT: E 10 LEU cc_start: 0.8318 (tp) cc_final: 0.8075 (tt) REVERT: E 102 TYR cc_start: 0.7850 (t80) cc_final: 0.7443 (t80) REVERT: E 167 HIS cc_start: 0.7700 (t-90) cc_final: 0.7402 (t-90) outliers start: 41 outliers final: 29 residues processed: 332 average time/residue: 0.2344 time to fit residues: 103.3120 Evaluate side-chains 342 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 311 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119286 restraints weight = 15383.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123153 restraints weight = 6668.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125532 restraints weight = 3527.716| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9120 Z= 0.141 Angle : 0.605 8.254 12385 Z= 0.314 Chirality : 0.043 0.157 1423 Planarity : 0.004 0.056 1570 Dihedral : 3.968 16.921 1245 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.99 % Favored : 96.83 % Rotamer: Outliers : 5.35 % Allowed : 28.12 % Favored : 66.53 % 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: 0.51 (0.26), residues: 1137 helix: 1.36 (0.27), residues: 391 sheet: 0.32 (0.32), residues: 280 loop : -0.45 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 216 HIS 0.005 0.001 HIS C 150 PHE 0.033 0.001 PHE C 280 TYR 0.015 0.001 TYR C 281 ARG 0.006 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 436) hydrogen bonds : angle 4.81951 ( 1227) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.49281 ( 4) covalent geometry : bond 0.00305 ( 9118) covalent geometry : angle 0.60459 (12381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 324 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7406 (tt0) cc_final: 0.7188 (tt0) REVERT: A 17 LYS cc_start: 0.7687 (mttt) cc_final: 0.7463 (mttt) REVERT: A 18 MET cc_start: 0.7246 (tpp) cc_final: 0.6839 (tpp) REVERT: A 25 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6362 (tm-30) REVERT: A 195 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7076 (t-90) REVERT: A 210 ILE cc_start: 0.8079 (tp) cc_final: 0.7693 (tp) REVERT: A 215 ASP cc_start: 0.7070 (t0) cc_final: 0.6661 (t0) REVERT: A 257 ASN cc_start: 0.8002 (m-40) cc_final: 0.7714 (m-40) REVERT: A 261 LEU cc_start: 0.8122 (mp) cc_final: 0.7855 (mp) REVERT: A 309 GLU cc_start: 0.6375 (tp30) cc_final: 0.6168 (tp30) REVERT: A 346 ASP cc_start: 0.7946 (t0) cc_final: 0.7552 (t0) REVERT: A 350 GLN cc_start: 0.8300 (tp-100) cc_final: 0.8029 (tp-100) REVERT: B 115 ASN cc_start: 0.7591 (m110) cc_final: 0.7209 (m-40) REVERT: B 202 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7180 (tpp80) REVERT: B 259 ASP cc_start: 0.7320 (t0) cc_final: 0.7051 (t0) REVERT: B 264 GLN cc_start: 0.7673 (mt0) cc_final: 0.7307 (mt0) REVERT: B 294 TYR cc_start: 0.7393 (m-80) cc_final: 0.6715 (m-80) REVERT: B 313 LEU cc_start: 0.8325 (mp) cc_final: 0.8061 (mt) REVERT: C 112 PHE cc_start: 0.7507 (t80) cc_final: 0.7109 (t80) REVERT: C 129 ASN cc_start: 0.7895 (t0) cc_final: 0.7635 (t0) REVERT: C 149 LEU cc_start: 0.8344 (tt) cc_final: 0.8116 (tt) REVERT: C 346 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7915 (ttmm) REVERT: C 369 TYR cc_start: 0.7434 (m-80) cc_final: 0.7188 (m-80) REVERT: E 10 LEU cc_start: 0.8318 (tp) cc_final: 0.8030 (tt) REVERT: E 102 TYR cc_start: 0.7876 (t80) cc_final: 0.7487 (t80) REVERT: E 226 VAL cc_start: 0.8409 (t) cc_final: 0.7914 (p) outliers start: 51 outliers final: 36 residues processed: 342 average time/residue: 0.2289 time to fit residues: 104.6350 Evaluate side-chains 360 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 323 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115795 restraints weight = 15302.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119592 restraints weight = 6626.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121952 restraints weight = 3500.751| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9120 Z= 0.191 Angle : 0.638 7.970 12385 Z= 0.337 Chirality : 0.044 0.169 1423 Planarity : 0.005 0.066 1570 Dihedral : 4.209 18.136 1245 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.90 % Favored : 96.92 % Rotamer: Outliers : 5.14 % Allowed : 27.60 % Favored : 67.26 % 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: 0.43 (0.25), residues: 1137 helix: 1.37 (0.27), residues: 380 sheet: 0.17 (0.32), residues: 280 loop : -0.45 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 216 HIS 0.008 0.001 HIS A 327 PHE 0.033 0.002 PHE C 280 TYR 0.022 0.002 TYR C 281 ARG 0.008 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 436) hydrogen bonds : angle 4.85066 ( 1227) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.43508 ( 4) covalent geometry : bond 0.00407 ( 9118) covalent geometry : angle 0.63802 (12381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 336 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7460 (tt0) cc_final: 0.7223 (tt0) REVERT: A 18 MET cc_start: 0.7258 (tpp) cc_final: 0.6891 (tpp) REVERT: A 25 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6055 (tm-30) REVERT: A 29 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7597 (mtmm) REVERT: A 35 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7362 (mtm-85) REVERT: A 210 ILE cc_start: 0.8242 (tp) cc_final: 0.7850 (tp) REVERT: A 215 ASP cc_start: 0.7197 (t0) cc_final: 0.6483 (t0) REVERT: A 257 ASN cc_start: 0.8043 (m-40) cc_final: 0.7768 (m-40) REVERT: A 261 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8005 (mp) REVERT: A 262 LEU cc_start: 0.8407 (tp) cc_final: 0.7902 (tp) REVERT: A 309 GLU cc_start: 0.6416 (tp30) cc_final: 0.6096 (tp30) REVERT: A 335 GLU cc_start: 0.7448 (mp0) cc_final: 0.7189 (mp0) REVERT: A 346 ASP cc_start: 0.8051 (t0) cc_final: 0.7635 (t0) REVERT: A 350 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8125 (tp-100) REVERT: B 60 LEU cc_start: 0.8706 (mm) cc_final: 0.8435 (mt) REVERT: B 87 TRP cc_start: 0.8342 (OUTLIER) cc_final: 0.8116 (m-10) REVERT: B 115 ASN cc_start: 0.7648 (m110) cc_final: 0.7175 (m-40) REVERT: B 169 THR cc_start: 0.7436 (p) cc_final: 0.7092 (p) REVERT: B 202 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7375 (tpp80) REVERT: B 259 ASP cc_start: 0.7418 (t0) cc_final: 0.7123 (t0) REVERT: B 283 PHE cc_start: 0.8158 (m-80) cc_final: 0.7950 (m-80) REVERT: B 294 TYR cc_start: 0.7517 (m-80) cc_final: 0.6863 (m-80) REVERT: B 318 ASN cc_start: 0.8316 (t0) cc_final: 0.7954 (t0) REVERT: B 323 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7478 (tp) REVERT: C 112 PHE cc_start: 0.7572 (t80) cc_final: 0.7123 (t80) REVERT: C 129 ASN cc_start: 0.7998 (t0) cc_final: 0.7671 (t0) REVERT: C 180 ILE cc_start: 0.8173 (mt) cc_final: 0.7819 (mt) REVERT: C 200 TYR cc_start: 0.7569 (t80) cc_final: 0.7344 (t80) REVERT: C 281 TYR cc_start: 0.5793 (m-10) cc_final: 0.5575 (m-80) REVERT: C 346 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7981 (ttmm) REVERT: C 369 TYR cc_start: 0.7420 (m-80) cc_final: 0.7125 (m-80) REVERT: E 10 LEU cc_start: 0.8402 (tp) cc_final: 0.8167 (tt) REVERT: E 102 TYR cc_start: 0.7942 (t80) cc_final: 0.7485 (t80) REVERT: E 167 HIS cc_start: 0.7782 (t-90) cc_final: 0.7535 (t-90) REVERT: E 186 GLN cc_start: 0.7331 (pt0) cc_final: 0.7040 (pt0) REVERT: G 17 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7410 (mm-30) outliers start: 49 outliers final: 36 residues processed: 352 average time/residue: 0.2434 time to fit residues: 113.4078 Evaluate side-chains 364 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 324 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 0.1980 chunk 92 optimal weight: 0.0050 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** 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 = 0.3766 r_free = 0.3766 target = 0.131741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118259 restraints weight = 15264.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.122105 restraints weight = 6624.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124459 restraints weight = 3493.358| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9120 Z= 0.126 Angle : 0.622 9.881 12385 Z= 0.319 Chirality : 0.042 0.156 1423 Planarity : 0.004 0.058 1570 Dihedral : 4.074 16.541 1245 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.10 % Rotamer: Outliers : 5.88 % Allowed : 28.75 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1137 helix: 1.41 (0.27), residues: 382 sheet: 0.08 (0.32), residues: 285 loop : -0.36 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 216 HIS 0.008 0.001 HIS A 327 PHE 0.031 0.001 PHE C 280 TYR 0.021 0.001 TYR C 281 ARG 0.006 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 436) hydrogen bonds : angle 4.76002 ( 1227) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.50707 ( 4) covalent geometry : bond 0.00280 ( 9118) covalent geometry : angle 0.62164 (12381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 327 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7514 (tt0) cc_final: 0.7272 (tt0) REVERT: A 18 MET cc_start: 0.7284 (tpp) cc_final: 0.6851 (tpp) REVERT: A 25 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6016 (tm-30) REVERT: A 29 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7530 (mtmm) REVERT: A 35 ARG cc_start: 0.7950 (ptp-110) cc_final: 0.7412 (mtm-85) REVERT: A 195 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.6953 (t-90) REVERT: A 210 ILE cc_start: 0.8146 (tp) cc_final: 0.7763 (tp) REVERT: A 215 ASP cc_start: 0.7115 (t0) cc_final: 0.6494 (t0) REVERT: A 221 PHE cc_start: 0.7970 (t80) cc_final: 0.7673 (t80) REVERT: A 257 ASN cc_start: 0.7987 (m-40) cc_final: 0.7710 (m-40) REVERT: A 261 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 346 ASP cc_start: 0.7992 (t0) cc_final: 0.7565 (t0) REVERT: A 350 GLN cc_start: 0.8348 (tp-100) cc_final: 0.8106 (tp-100) REVERT: B 60 LEU cc_start: 0.8676 (mm) cc_final: 0.8409 (mt) REVERT: B 115 ASN cc_start: 0.7589 (m110) cc_final: 0.7141 (m110) REVERT: B 259 ASP cc_start: 0.7405 (t0) cc_final: 0.7117 (t0) REVERT: B 264 GLN cc_start: 0.7692 (mt0) cc_final: 0.7391 (mt0) REVERT: B 294 TYR cc_start: 0.7492 (m-80) cc_final: 0.6913 (m-80) REVERT: C 112 PHE cc_start: 0.7590 (t80) cc_final: 0.7130 (t80) REVERT: C 129 ASN cc_start: 0.7951 (t0) cc_final: 0.7646 (t0) REVERT: C 180 ILE cc_start: 0.8182 (mt) cc_final: 0.7811 (mt) REVERT: C 200 TYR cc_start: 0.7526 (t80) cc_final: 0.7282 (t80) REVERT: C 242 ILE cc_start: 0.8318 (mp) cc_final: 0.7799 (tt) REVERT: C 281 TYR cc_start: 0.5645 (m-10) cc_final: 0.5278 (m-80) REVERT: C 346 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7924 (ttmm) REVERT: C 369 TYR cc_start: 0.7379 (m-80) cc_final: 0.7065 (m-80) REVERT: E 10 LEU cc_start: 0.8383 (tp) cc_final: 0.8146 (tt) REVERT: E 102 TYR cc_start: 0.7937 (t80) cc_final: 0.7562 (t80) REVERT: E 167 HIS cc_start: 0.7763 (t-90) cc_final: 0.7526 (t-90) REVERT: E 186 GLN cc_start: 0.7315 (pt0) cc_final: 0.6992 (pt0) REVERT: E 226 VAL cc_start: 0.8375 (t) cc_final: 0.7874 (p) REVERT: G 17 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7365 (mm-30) outliers start: 56 outliers final: 44 residues processed: 349 average time/residue: 0.2387 time to fit residues: 110.7296 Evaluate side-chains 368 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 373 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 18 optimal weight: 0.0470 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** 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 = 0.3764 r_free = 0.3764 target = 0.131626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118181 restraints weight = 15370.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122006 restraints weight = 6643.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124359 restraints weight = 3505.512| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9120 Z= 0.129 Angle : 0.635 8.905 12385 Z= 0.325 Chirality : 0.042 0.159 1423 Planarity : 0.004 0.052 1570 Dihedral : 4.091 20.443 1245 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.10 % Rotamer: Outliers : 5.77 % Allowed : 29.17 % Favored : 65.06 % 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: 0.45 (0.26), residues: 1137 helix: 1.40 (0.27), residues: 382 sheet: 0.04 (0.31), residues: 285 loop : -0.35 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 216 HIS 0.004 0.001 HIS A 322 PHE 0.030 0.001 PHE C 280 TYR 0.020 0.001 TYR C 281 ARG 0.007 0.001 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 436) hydrogen bonds : angle 4.74403 ( 1227) SS BOND : bond 0.00514 ( 2) SS BOND : angle 0.65405 ( 4) covalent geometry : bond 0.00286 ( 9118) covalent geometry : angle 0.63544 (12381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7525 (tt0) cc_final: 0.7271 (tt0) REVERT: A 15 ARG cc_start: 0.8551 (ttt90) cc_final: 0.8321 (ttt-90) REVERT: A 18 MET cc_start: 0.7301 (tpp) cc_final: 0.6835 (tpp) REVERT: A 25 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6007 (tm-30) REVERT: A 29 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7518 (mtmm) REVERT: A 35 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7398 (mtm-85) REVERT: A 195 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.6970 (t-90) REVERT: A 210 ILE cc_start: 0.8144 (tp) cc_final: 0.7760 (tp) REVERT: A 215 ASP cc_start: 0.7096 (t0) cc_final: 0.6473 (t0) REVERT: A 257 ASN cc_start: 0.7993 (m-40) cc_final: 0.7728 (m-40) REVERT: A 261 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7960 (mp) REVERT: A 346 ASP cc_start: 0.8003 (t0) cc_final: 0.7583 (t0) REVERT: A 350 GLN cc_start: 0.8325 (tp-100) cc_final: 0.8092 (tp-100) REVERT: B 60 LEU cc_start: 0.8654 (mm) cc_final: 0.8359 (mm) REVERT: B 115 ASN cc_start: 0.7599 (m110) cc_final: 0.7160 (m-40) REVERT: B 259 ASP cc_start: 0.7390 (t0) cc_final: 0.7110 (t0) REVERT: B 264 GLN cc_start: 0.7665 (mt0) cc_final: 0.7386 (mt0) REVERT: B 288 ARG cc_start: 0.7615 (tpt170) cc_final: 0.7248 (tpt170) REVERT: B 294 TYR cc_start: 0.7498 (m-80) cc_final: 0.6898 (m-80) REVERT: B 313 LEU cc_start: 0.8284 (mp) cc_final: 0.8054 (mt) REVERT: C 112 PHE cc_start: 0.7585 (t80) cc_final: 0.7105 (t80) REVERT: C 129 ASN cc_start: 0.7925 (t0) cc_final: 0.7619 (t0) REVERT: C 134 ASN cc_start: 0.7375 (t0) cc_final: 0.7167 (t0) REVERT: C 160 TYR cc_start: 0.6811 (t80) cc_final: 0.6574 (t80) REVERT: C 180 ILE cc_start: 0.8178 (mt) cc_final: 0.7816 (mt) REVERT: C 200 TYR cc_start: 0.7536 (t80) cc_final: 0.7321 (t80) REVERT: C 242 ILE cc_start: 0.8322 (mp) cc_final: 0.7806 (tt) REVERT: C 281 TYR cc_start: 0.5754 (m-10) cc_final: 0.5292 (m-80) REVERT: C 346 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7935 (ttmm) REVERT: C 369 TYR cc_start: 0.7366 (m-80) cc_final: 0.7069 (m-80) REVERT: E 10 LEU cc_start: 0.8463 (tp) cc_final: 0.8249 (tt) REVERT: E 102 TYR cc_start: 0.7922 (t80) cc_final: 0.7554 (t80) REVERT: E 167 HIS cc_start: 0.7774 (t-90) cc_final: 0.7536 (t-90) REVERT: E 186 GLN cc_start: 0.7286 (pt0) cc_final: 0.6972 (pt0) REVERT: E 226 VAL cc_start: 0.8380 (t) cc_final: 0.7888 (p) REVERT: G 17 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7368 (mm-30) outliers start: 55 outliers final: 43 residues processed: 355 average time/residue: 0.2342 time to fit residues: 110.4672 Evaluate side-chains 381 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 335 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 373 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114647 restraints weight = 15564.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118476 restraints weight = 6669.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120797 restraints weight = 3498.446| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9120 Z= 0.194 Angle : 0.670 8.948 12385 Z= 0.344 Chirality : 0.044 0.178 1423 Planarity : 0.005 0.055 1570 Dihedral : 4.258 20.627 1245 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 5.98 % Allowed : 29.49 % Favored : 64.53 % 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: 0.34 (0.26), residues: 1137 helix: 1.34 (0.27), residues: 382 sheet: -0.11 (0.31), residues: 286 loop : -0.37 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.015 0.002 HIS A 327 PHE 0.030 0.002 PHE C 280 TYR 0.021 0.002 TYR C 281 ARG 0.007 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 436) hydrogen bonds : angle 4.77044 ( 1227) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.59281 ( 4) covalent geometry : bond 0.00419 ( 9118) covalent geometry : angle 0.67052 (12381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7504 (tt0) cc_final: 0.7264 (tt0) REVERT: A 18 MET cc_start: 0.7282 (tpp) cc_final: 0.6823 (tpp) REVERT: A 25 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6074 (tm-30) REVERT: A 29 LYS cc_start: 0.8306 (mtmm) cc_final: 0.7623 (mtmm) REVERT: A 35 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7477 (mtm-85) REVERT: A 184 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6341 (mt-10) REVERT: A 195 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6772 (t-90) REVERT: A 210 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7841 (tp) REVERT: A 215 ASP cc_start: 0.7180 (t0) cc_final: 0.6609 (t0) REVERT: A 221 PHE cc_start: 0.7994 (t80) cc_final: 0.7634 (t80) REVERT: A 257 ASN cc_start: 0.8064 (m-40) cc_final: 0.7783 (m-40) REVERT: A 261 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8043 (mp) REVERT: A 346 ASP cc_start: 0.8119 (t0) cc_final: 0.7666 (t0) REVERT: A 350 GLN cc_start: 0.8364 (tp-100) cc_final: 0.8113 (tp-100) REVERT: A 354 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7379 (ttm-80) REVERT: B 60 LEU cc_start: 0.8661 (mm) cc_final: 0.8360 (mt) REVERT: B 87 TRP cc_start: 0.8359 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: B 128 ILE cc_start: 0.7499 (tt) cc_final: 0.7262 (pt) REVERT: B 169 THR cc_start: 0.7402 (p) cc_final: 0.7084 (p) REVERT: B 219 ARG cc_start: 0.7621 (ptp90) cc_final: 0.6706 (ptp90) REVERT: B 259 ASP cc_start: 0.7386 (t0) cc_final: 0.7111 (t0) REVERT: B 264 GLN cc_start: 0.7695 (mt0) cc_final: 0.7429 (mt0) REVERT: B 294 TYR cc_start: 0.7523 (m-80) cc_final: 0.6877 (m-80) REVERT: C 104 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7279 (m110) REVERT: C 112 PHE cc_start: 0.7608 (t80) cc_final: 0.7098 (t80) REVERT: C 129 ASN cc_start: 0.7970 (t0) cc_final: 0.7628 (t0) REVERT: C 158 ASN cc_start: 0.8331 (m110) cc_final: 0.7513 (m110) REVERT: C 162 LEU cc_start: 0.8289 (mt) cc_final: 0.7981 (mp) REVERT: C 180 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7852 (mt) REVERT: C 198 ASP cc_start: 0.7381 (m-30) cc_final: 0.7112 (m-30) REVERT: C 242 ILE cc_start: 0.8360 (mp) cc_final: 0.7847 (tt) REVERT: C 281 TYR cc_start: 0.5814 (m-10) cc_final: 0.5072 (m-80) REVERT: C 346 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8040 (ttmm) REVERT: C 369 TYR cc_start: 0.7366 (m-80) cc_final: 0.6970 (m-80) REVERT: E 102 TYR cc_start: 0.7982 (t80) cc_final: 0.7513 (t80) REVERT: E 186 GLN cc_start: 0.7294 (pt0) cc_final: 0.6984 (pt0) REVERT: G 17 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7376 (mm-30) outliers start: 57 outliers final: 42 residues processed: 363 average time/residue: 0.2915 time to fit residues: 143.9501 Evaluate side-chains 386 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 337 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 373 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115278 restraints weight = 15316.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119090 restraints weight = 6590.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121442 restraints weight = 3472.360| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9120 Z= 0.167 Angle : 0.697 9.758 12385 Z= 0.349 Chirality : 0.044 0.174 1423 Planarity : 0.005 0.061 1570 Dihedral : 4.315 21.246 1245 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.34 % Favored : 96.48 % Rotamer: Outliers : 5.35 % Allowed : 30.75 % Favored : 63.90 % 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 (0.25), residues: 1137 helix: 1.36 (0.27), residues: 380 sheet: -0.16 (0.31), residues: 286 loop : -0.40 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.003 0.001 HIS A 322 PHE 0.031 0.001 PHE C 280 TYR 0.018 0.001 TYR C 281 ARG 0.007 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 436) hydrogen bonds : angle 4.79068 ( 1227) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.52096 ( 4) covalent geometry : bond 0.00372 ( 9118) covalent geometry : angle 0.69660 (12381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 352 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7552 (tt0) cc_final: 0.7301 (tt0) REVERT: A 18 MET cc_start: 0.7259 (tpp) cc_final: 0.6800 (tpp) REVERT: A 25 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6088 (tm-30) REVERT: A 29 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7625 (mtmm) REVERT: A 35 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7630 (mtm-85) REVERT: A 184 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6390 (mt-10) REVERT: A 195 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.6776 (t-90) REVERT: A 206 ARG cc_start: 0.5695 (ttm-80) cc_final: 0.5468 (ttm-80) REVERT: A 210 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7822 (tp) REVERT: A 221 PHE cc_start: 0.7977 (t80) cc_final: 0.7588 (t80) REVERT: A 257 ASN cc_start: 0.8104 (m-40) cc_final: 0.7824 (m-40) REVERT: A 261 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8041 (mp) REVERT: A 312 ASP cc_start: 0.7056 (t0) cc_final: 0.6841 (t0) REVERT: A 346 ASP cc_start: 0.8129 (t0) cc_final: 0.7684 (t0) REVERT: A 350 GLN cc_start: 0.8348 (tp-100) cc_final: 0.8107 (tp-100) REVERT: B 60 LEU cc_start: 0.8626 (mm) cc_final: 0.8347 (mm) REVERT: B 128 ILE cc_start: 0.7526 (tt) cc_final: 0.7288 (pt) REVERT: B 219 ARG cc_start: 0.7575 (ptp90) cc_final: 0.6796 (ptp90) REVERT: B 258 PHE cc_start: 0.8433 (m-80) cc_final: 0.7955 (m-80) REVERT: B 264 GLN cc_start: 0.7658 (mt0) cc_final: 0.7441 (mt0) REVERT: B 283 PHE cc_start: 0.8226 (m-80) cc_final: 0.7714 (m-80) REVERT: B 294 TYR cc_start: 0.7521 (m-80) cc_final: 0.6946 (m-80) REVERT: B 318 ASN cc_start: 0.8325 (t0) cc_final: 0.8093 (t0) REVERT: C 104 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7290 (m110) REVERT: C 112 PHE cc_start: 0.7594 (t80) cc_final: 0.7084 (t80) REVERT: C 129 ASN cc_start: 0.7953 (t0) cc_final: 0.7583 (t0) REVERT: C 148 LEU cc_start: 0.8398 (tp) cc_final: 0.8041 (tp) REVERT: C 158 ASN cc_start: 0.8347 (m110) cc_final: 0.7543 (m-40) REVERT: C 162 LEU cc_start: 0.8289 (mt) cc_final: 0.7989 (mp) REVERT: C 198 ASP cc_start: 0.7365 (m-30) cc_final: 0.7096 (m-30) REVERT: C 242 ILE cc_start: 0.8364 (mp) cc_final: 0.7869 (tt) REVERT: C 281 TYR cc_start: 0.5952 (m-10) cc_final: 0.5268 (m-80) REVERT: C 346 LYS cc_start: 0.8443 (ttmm) cc_final: 0.7993 (ttmm) REVERT: C 369 TYR cc_start: 0.7341 (m-80) cc_final: 0.6935 (m-80) REVERT: E 102 TYR cc_start: 0.7986 (t80) cc_final: 0.7498 (t80) REVERT: E 167 HIS cc_start: 0.7870 (t-90) cc_final: 0.7644 (t-90) REVERT: E 186 GLN cc_start: 0.7293 (pt0) cc_final: 0.6989 (pt0) REVERT: G 17 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7343 (mm-30) outliers start: 51 outliers final: 41 residues processed: 371 average time/residue: 0.2391 time to fit residues: 117.1636 Evaluate side-chains 396 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 350 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 373 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 81 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115346 restraints weight = 15215.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119150 restraints weight = 6521.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.121504 restraints weight = 3423.872| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9120 Z= 0.159 Angle : 0.716 10.871 12385 Z= 0.355 Chirality : 0.044 0.176 1423 Planarity : 0.005 0.064 1570 Dihedral : 4.333 21.352 1245 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Rotamer: Outliers : 5.67 % Allowed : 31.90 % Favored : 62.43 % 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: 0.33 (0.26), residues: 1137 helix: 1.33 (0.27), residues: 380 sheet: -0.13 (0.31), residues: 284 loop : -0.36 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.004 0.001 HIS A 327 PHE 0.030 0.002 PHE C 280 TYR 0.014 0.001 TYR C 281 ARG 0.009 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 436) hydrogen bonds : angle 4.78173 ( 1227) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.54148 ( 4) covalent geometry : bond 0.00353 ( 9118) covalent geometry : angle 0.71612 (12381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 355 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7495 (tt0) cc_final: 0.7242 (tt0) REVERT: A 18 MET cc_start: 0.7271 (tpp) cc_final: 0.6781 (tpp) REVERT: A 23 LEU cc_start: 0.8104 (mp) cc_final: 0.7903 (mp) REVERT: A 25 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6138 (tm-30) REVERT: A 29 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7655 (mtmm) REVERT: A 35 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7654 (mtm-85) REVERT: A 184 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6419 (mt-10) REVERT: A 195 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.6842 (t-90) REVERT: A 206 ARG cc_start: 0.5841 (ttm-80) cc_final: 0.5591 (ttm-80) REVERT: A 210 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7787 (tp) REVERT: A 221 PHE cc_start: 0.7944 (t80) cc_final: 0.7569 (t80) REVERT: A 257 ASN cc_start: 0.8200 (m-40) cc_final: 0.7919 (m-40) REVERT: A 261 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8031 (mp) REVERT: A 265 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7676 (ptmt) REVERT: A 312 ASP cc_start: 0.7048 (t0) cc_final: 0.6804 (t0) REVERT: A 335 GLU cc_start: 0.7454 (mp0) cc_final: 0.7178 (mp0) REVERT: A 346 ASP cc_start: 0.8165 (t0) cc_final: 0.7724 (t0) REVERT: B 22 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7999 (tm-30) REVERT: B 60 LEU cc_start: 0.8591 (mm) cc_final: 0.8352 (mm) REVERT: B 128 ILE cc_start: 0.7504 (tt) cc_final: 0.7287 (pt) REVERT: B 219 ARG cc_start: 0.7588 (ptp90) cc_final: 0.6784 (ptp90) REVERT: B 258 PHE cc_start: 0.8383 (m-80) cc_final: 0.7937 (m-80) REVERT: B 283 PHE cc_start: 0.8127 (m-80) cc_final: 0.7614 (m-80) REVERT: B 294 TYR cc_start: 0.7540 (m-80) cc_final: 0.6931 (m-80) REVERT: C 104 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7227 (m110) REVERT: C 112 PHE cc_start: 0.7584 (t80) cc_final: 0.7062 (t80) REVERT: C 129 ASN cc_start: 0.7941 (t0) cc_final: 0.7583 (t0) REVERT: C 148 LEU cc_start: 0.8383 (tp) cc_final: 0.8114 (tp) REVERT: C 158 ASN cc_start: 0.8344 (m110) cc_final: 0.7523 (m-40) REVERT: C 160 TYR cc_start: 0.6866 (t80) cc_final: 0.6583 (t80) REVERT: C 162 LEU cc_start: 0.8290 (mt) cc_final: 0.7978 (mp) REVERT: C 198 ASP cc_start: 0.7367 (m-30) cc_final: 0.7094 (m-30) REVERT: C 242 ILE cc_start: 0.8360 (mp) cc_final: 0.7914 (tt) REVERT: C 281 TYR cc_start: 0.5905 (m-10) cc_final: 0.5221 (m-80) REVERT: C 346 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7944 (ttmm) REVERT: C 369 TYR cc_start: 0.7336 (m-80) cc_final: 0.6889 (m-80) REVERT: E 102 TYR cc_start: 0.7988 (t80) cc_final: 0.7500 (t80) REVERT: E 167 HIS cc_start: 0.7885 (t-90) cc_final: 0.7666 (t-90) REVERT: E 186 GLN cc_start: 0.7310 (pt0) cc_final: 0.7012 (pt0) REVERT: E 226 VAL cc_start: 0.8445 (t) cc_final: 0.7949 (p) REVERT: G 17 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7330 (mm-30) outliers start: 54 outliers final: 44 residues processed: 376 average time/residue: 0.2316 time to fit residues: 115.1616 Evaluate side-chains 402 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 373 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 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 = 0.3720 r_free = 0.3720 target = 0.128344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115086 restraints weight = 15314.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118863 restraints weight = 6549.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.121195 restraints weight = 3441.472| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9120 Z= 0.167 Angle : 0.737 12.079 12385 Z= 0.364 Chirality : 0.044 0.153 1423 Planarity : 0.005 0.060 1570 Dihedral : 4.389 22.431 1245 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.52 % Favored : 96.31 % Rotamer: Outliers : 5.25 % Allowed : 32.53 % Favored : 62.22 % 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 (0.26), residues: 1137 helix: 1.32 (0.27), residues: 379 sheet: -0.16 (0.31), residues: 284 loop : -0.35 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.009 0.001 HIS A 327 PHE 0.029 0.002 PHE C 280 TYR 0.017 0.001 TYR E 235 ARG 0.010 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 436) hydrogen bonds : angle 4.79300 ( 1227) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.53886 ( 4) covalent geometry : bond 0.00371 ( 9118) covalent geometry : angle 0.73733 (12381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.16 seconds wall clock time: 66 minutes 25.01 seconds (3985.01 seconds total)