Starting phenix.real_space_refine on Sat Aug 23 01:22:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hcx_34667/08_2025/8hcx_34667_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hcx_34667/08_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_34667/08_2025/8hcx_34667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hcx_34667/08_2025/8hcx_34667.map" model { file = "/net/cci-nas-00/data/ceres_data/8hcx_34667/08_2025/8hcx_34667_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hcx_34667/08_2025/8hcx_34667_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'GLU:plan': 6, 'ARG:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} 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: {'ARG:plan': 1, 'GLU:plan': 2} 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: 1.41, per 1000 atoms: 0.16 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: 0.63 Conformation dependent library (CDL) restraints added in 239.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.21 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: 1.14 Time building geometry restraints manager: 0.84 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.140 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (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 ARG 0.009 0.001 ARG A 307 TYR 0.014 0.001 TYR B 150 PHE 0.024 0.001 PHE C 280 TRP 0.022 0.001 TRP B 87 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9118) covalent geometry : angle 0.62434 (12381) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.35229 ( 4) hydrogen bonds : bond 0.24598 ( 436) hydrogen bonds : angle 8.25104 ( 1227) *********************** 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 : 0.185 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: 0.0792 time to fit residues: 30.0414 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 : 0.230 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0010 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.140379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126519 restraints weight = 14971.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130607 restraints weight = 6374.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133156 restraints weight = 3319.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134740 restraints weight = 1974.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135766 restraints weight = 1304.949| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9120 Z= 0.144 Angle : 0.614 8.795 12385 Z= 0.320 Chirality : 0.042 0.144 1423 Planarity : 0.005 0.074 1570 Dihedral : 3.840 23.607 1247 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.29 % Favored : 97.45 % Rotamer: Outliers : 4.51 % Allowed : 26.97 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.26), residues: 1137 helix: 1.15 (0.27), residues: 389 sheet: 0.41 (0.32), residues: 285 loop : -0.36 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 298 TYR 0.012 0.001 TYR C 160 PHE 0.023 0.001 PHE C 280 TRP 0.018 0.001 TRP B 216 HIS 0.003 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9118) covalent geometry : angle 0.61413 (12381) SS BOND : bond 0.00308 ( 2) SS BOND : angle 1.14482 ( 4) hydrogen bonds : bond 0.04381 ( 436) hydrogen bonds : angle 5.34646 ( 1227) *********************** 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 354 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 190 ASP cc_start: 0.7900 (t0) cc_final: 0.7687 (t0) REVERT: A 195 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.6987 (t-90) REVERT: A 298 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: A 350 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7944 (tp-100) REVERT: B 115 ASN cc_start: 0.7506 (m-40) cc_final: 0.7253 (m-40) REVERT: B 217 ASP cc_start: 0.6917 (t70) cc_final: 0.6413 (p0) REVERT: B 256 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7275 (mtt180) REVERT: B 294 TYR cc_start: 0.7275 (m-80) cc_final: 0.6805 (m-80) REVERT: C 148 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7923 (mm) REVERT: C 180 ILE cc_start: 0.8189 (mt) cc_final: 0.7792 (mt) REVERT: C 181 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7773 (pp30) REVERT: C 292 PHE cc_start: 0.6309 (m-80) cc_final: 0.6104 (m-10) REVERT: C 346 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7982 (ttmm) REVERT: C 369 TYR cc_start: 0.7442 (m-80) cc_final: 0.7123 (m-80) REVERT: E 10 LEU cc_start: 0.8280 (tp) cc_final: 0.7984 (tt) outliers start: 43 outliers final: 25 residues processed: 324 average time/residue: 0.0811 time to fit residues: 35.6321 Evaluate side-chains 329 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 301 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 195 HIS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 98 ILE 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 222 MET 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 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 99 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 0.0070 chunk 109 optimal weight: 4.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 ** 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 = 0.3826 r_free = 0.3826 target = 0.136595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123081 restraints weight = 15059.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127142 restraints weight = 6284.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129602 restraints weight = 3233.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131106 restraints weight = 1913.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132056 restraints weight = 1265.879| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1767 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= 0.156 Angle : 0.614 8.540 12385 Z= 0.316 Chirality : 0.042 0.157 1423 Planarity : 0.004 0.062 1570 Dihedral : 3.891 16.849 1245 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.46 % Favored : 97.27 % Rotamer: Outliers : 4.83 % Allowed : 28.12 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.26), residues: 1137 helix: 1.30 (0.26), residues: 391 sheet: 0.38 (0.32), residues: 280 loop : -0.48 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 307 TYR 0.010 0.001 TYR C 281 PHE 0.026 0.002 PHE C 280 TRP 0.017 0.001 TRP B 216 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9118) covalent geometry : angle 0.61371 (12381) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.55283 ( 4) hydrogen bonds : bond 0.04013 ( 436) hydrogen bonds : angle 5.02340 ( 1227) *********************** 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 356 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7719 (mttt) cc_final: 0.7458 (mttt) REVERT: A 18 MET cc_start: 0.7251 (tpp) cc_final: 0.6900 (tpp) REVERT: A 190 ASP cc_start: 0.7932 (t0) cc_final: 0.7714 (t0) REVERT: A 195 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7019 (t-90) REVERT: A 215 ASP cc_start: 0.7078 (t0) cc_final: 0.6645 (t0) REVERT: A 346 ASP cc_start: 0.7947 (t0) cc_final: 0.7572 (t0) REVERT: A 350 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7988 (tp-100) REVERT: B 115 ASN cc_start: 0.7520 (m-40) cc_final: 0.7193 (m-40) REVERT: B 259 ASP cc_start: 0.7343 (t0) cc_final: 0.7077 (t0) REVERT: B 264 GLN cc_start: 0.7650 (mt0) cc_final: 0.7400 (mt0) REVERT: B 282 SER cc_start: 0.7473 (m) cc_final: 0.7268 (p) REVERT: B 288 ARG cc_start: 0.7427 (tpt170) cc_final: 0.7153 (tpt170) REVERT: B 294 TYR cc_start: 0.7336 (m-80) cc_final: 0.6798 (m-80) REVERT: B 313 LEU cc_start: 0.8229 (mp) cc_final: 0.7989 (mt) REVERT: B 318 ASN cc_start: 0.8131 (t0) cc_final: 0.7853 (t0) REVERT: C 112 PHE cc_start: 0.7444 (t80) cc_final: 0.7061 (t80) REVERT: C 129 ASN cc_start: 0.7954 (t0) cc_final: 0.7684 (t0) REVERT: C 148 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7753 (mm) REVERT: C 180 ILE cc_start: 0.8223 (mt) cc_final: 0.7840 (mt) REVERT: C 369 TYR cc_start: 0.7462 (m-80) cc_final: 0.7186 (m-80) REVERT: E 10 LEU cc_start: 0.8246 (tp) cc_final: 0.7996 (tt) REVERT: E 102 TYR cc_start: 0.7853 (t80) cc_final: 0.7365 (t80) REVERT: E 167 HIS cc_start: 0.7724 (t-90) cc_final: 0.7438 (t-90) REVERT: E 226 VAL cc_start: 0.8369 (t) cc_final: 0.7892 (p) outliers start: 46 outliers final: 30 residues processed: 322 average time/residue: 0.0865 time to fit residues: 37.1678 Evaluate side-chains 336 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 304 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 218 VAL 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 280 SER 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 181 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 242 ILE 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 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 91 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** 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 = 0.3740 r_free = 0.3740 target = 0.130217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116565 restraints weight = 15607.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120532 restraints weight = 6598.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122975 restraints weight = 3439.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124511 restraints weight = 2054.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125433 restraints weight = 1368.317| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9120 Z= 0.191 Angle : 0.638 8.339 12385 Z= 0.329 Chirality : 0.044 0.180 1423 Planarity : 0.004 0.056 1570 Dihedral : 4.137 17.231 1245 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.81 % Favored : 97.01 % Rotamer: Outliers : 6.30 % Allowed : 26.76 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.26), residues: 1137 helix: 1.30 (0.27), residues: 391 sheet: 0.21 (0.32), residues: 280 loop : -0.52 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.029 0.001 TYR C 281 PHE 0.037 0.002 PHE C 280 TRP 0.016 0.002 TRP B 216 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9118) covalent geometry : angle 0.63835 (12381) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.45743 ( 4) hydrogen bonds : bond 0.03862 ( 436) hydrogen bonds : angle 4.90243 ( 1227) *********************** 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 395 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7453 (tt0) cc_final: 0.7247 (tt0) REVERT: A 18 MET cc_start: 0.7272 (tpp) cc_final: 0.6905 (tpp) REVERT: A 25 GLU cc_start: 0.6660 (tm-30) cc_final: 0.5914 (tm-30) REVERT: A 29 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7547 (mtmm) REVERT: A 35 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7371 (mtm-85) REVERT: A 190 ASP cc_start: 0.7967 (t0) cc_final: 0.7762 (t0) REVERT: A 195 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7001 (t-90) REVERT: A 210 ILE cc_start: 0.8103 (tp) cc_final: 0.7694 (tp) REVERT: A 215 ASP cc_start: 0.7180 (t0) cc_final: 0.6465 (t0) REVERT: A 257 ASN cc_start: 0.8072 (m-40) cc_final: 0.7756 (m-40) REVERT: A 346 ASP cc_start: 0.8001 (t0) cc_final: 0.7572 (t0) REVERT: A 350 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8068 (tp-100) REVERT: B 87 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: B 115 ASN cc_start: 0.7612 (m110) cc_final: 0.7216 (m-40) REVERT: B 169 THR cc_start: 0.7368 (p) cc_final: 0.7048 (p) REVERT: B 202 ARG cc_start: 0.7619 (tpp80) cc_final: 0.6914 (tpp80) REVERT: B 219 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6647 (ptp-170) REVERT: B 259 ASP cc_start: 0.7365 (t0) cc_final: 0.7071 (t0) REVERT: B 264 GLN cc_start: 0.7687 (mt0) cc_final: 0.7303 (mt0) REVERT: B 313 LEU cc_start: 0.8363 (mp) cc_final: 0.8121 (mt) REVERT: C 112 PHE cc_start: 0.7506 (t80) cc_final: 0.7100 (t80) REVERT: C 129 ASN cc_start: 0.7933 (t0) cc_final: 0.7619 (t0) REVERT: C 134 ASN cc_start: 0.7372 (t0) cc_final: 0.7162 (t0) REVERT: C 180 ILE cc_start: 0.8210 (mt) cc_final: 0.7849 (mt) REVERT: C 281 TYR cc_start: 0.5836 (m-10) cc_final: 0.5429 (m-80) REVERT: C 345 LEU cc_start: 0.7469 (mt) cc_final: 0.7238 (mt) REVERT: C 369 TYR cc_start: 0.7480 (m-80) cc_final: 0.7223 (m-80) REVERT: C 378 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7526 (t0) REVERT: E 10 LEU cc_start: 0.8362 (tp) cc_final: 0.8146 (tt) REVERT: E 102 TYR cc_start: 0.7927 (t80) cc_final: 0.7418 (t80) outliers start: 60 outliers final: 37 residues processed: 355 average time/residue: 0.0804 time to fit residues: 38.4472 Evaluate side-chains 365 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 323 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 223 VAL 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 42 ILE 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 98 ILE 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 218 VAL Chi-restraints excluded: chain B residue 219 ARG 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 181 GLN Chi-restraints excluded: chain C residue 224 LEU 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 378 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 93 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 211 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.127753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114421 restraints weight = 15385.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118205 restraints weight = 6640.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120430 restraints weight = 3503.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121965 restraints weight = 2155.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122809 restraints weight = 1446.338| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9120 Z= 0.216 Angle : 0.664 8.477 12385 Z= 0.346 Chirality : 0.045 0.175 1423 Planarity : 0.004 0.054 1570 Dihedral : 4.315 16.898 1245 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.75 % Rotamer: Outliers : 5.77 % Allowed : 28.02 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.25), residues: 1137 helix: 1.26 (0.27), residues: 384 sheet: 0.07 (0.32), residues: 280 loop : -0.53 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 307 TYR 0.025 0.002 TYR C 281 PHE 0.033 0.002 PHE C 280 TRP 0.016 0.002 TRP B 87 HIS 0.005 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9118) covalent geometry : angle 0.66370 (12381) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.42887 ( 4) hydrogen bonds : bond 0.03932 ( 436) hydrogen bonds : angle 4.93843 ( 1227) *********************** 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 398 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 343 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7503 (tt0) cc_final: 0.7286 (tt0) REVERT: A 15 ARG cc_start: 0.8407 (ttt90) cc_final: 0.8191 (ttt-90) REVERT: A 18 MET cc_start: 0.7272 (tpp) cc_final: 0.6891 (tpp) REVERT: A 25 GLU cc_start: 0.6709 (tm-30) cc_final: 0.5959 (tm-30) REVERT: A 29 LYS cc_start: 0.8291 (mtmm) cc_final: 0.7652 (mtmm) REVERT: A 35 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7422 (mtm-85) REVERT: A 210 ILE cc_start: 0.8260 (tp) cc_final: 0.7877 (tp) REVERT: A 215 ASP cc_start: 0.7194 (t0) cc_final: 0.6560 (t0) REVERT: A 221 PHE cc_start: 0.8005 (t80) cc_final: 0.7779 (t80) REVERT: A 257 ASN cc_start: 0.8059 (m-40) cc_final: 0.7753 (m-40) REVERT: A 262 LEU cc_start: 0.8483 (tp) cc_final: 0.8071 (tp) REVERT: A 335 GLU cc_start: 0.7368 (mp0) cc_final: 0.7132 (mp0) REVERT: A 346 ASP cc_start: 0.8045 (t0) cc_final: 0.7674 (t0) REVERT: A 350 GLN cc_start: 0.8380 (tp-100) cc_final: 0.8144 (tp-100) REVERT: B 87 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: B 115 ASN cc_start: 0.7643 (m110) cc_final: 0.7152 (m-40) REVERT: B 128 ILE cc_start: 0.7570 (tt) cc_final: 0.7285 (pt) REVERT: B 138 VAL cc_start: 0.8384 (t) cc_final: 0.8148 (m) REVERT: B 169 THR cc_start: 0.7532 (p) cc_final: 0.7242 (p) REVERT: B 202 ARG cc_start: 0.7700 (tpp80) cc_final: 0.7113 (tpp80) REVERT: B 233 ASP cc_start: 0.7794 (t0) cc_final: 0.7556 (t0) REVERT: B 258 PHE cc_start: 0.8465 (m-80) cc_final: 0.7976 (m-80) REVERT: B 259 ASP cc_start: 0.7467 (t0) cc_final: 0.7183 (t0) REVERT: B 294 TYR cc_start: 0.7475 (m-80) cc_final: 0.6796 (m-80) REVERT: B 318 ASN cc_start: 0.8417 (t0) cc_final: 0.8143 (t0) REVERT: C 112 PHE cc_start: 0.7566 (t80) cc_final: 0.7112 (t80) REVERT: C 129 ASN cc_start: 0.8003 (t0) cc_final: 0.7639 (t0) REVERT: C 158 ASN cc_start: 0.8265 (m110) cc_final: 0.7672 (m-40) REVERT: C 198 ASP cc_start: 0.7387 (m-30) cc_final: 0.7182 (m-30) REVERT: C 242 ILE cc_start: 0.8329 (mp) cc_final: 0.7901 (tt) REVERT: C 281 TYR cc_start: 0.5976 (m-10) cc_final: 0.5473 (m-80) REVERT: C 346 LYS cc_start: 0.8415 (ttmm) cc_final: 0.7994 (ttmm) REVERT: C 369 TYR cc_start: 0.7463 (m-80) cc_final: 0.7206 (m-80) REVERT: E 10 LEU cc_start: 0.8391 (tp) cc_final: 0.8168 (tt) REVERT: E 42 LYS cc_start: 0.8678 (mttt) cc_final: 0.8469 (mttt) REVERT: E 102 TYR cc_start: 0.7987 (t80) cc_final: 0.7431 (t80) REVERT: E 167 HIS cc_start: 0.7848 (t-90) cc_final: 0.7607 (t-90) REVERT: E 186 GLN cc_start: 0.7330 (pt0) cc_final: 0.7033 (pt0) REVERT: G 17 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7361 (mm-30) outliers start: 55 outliers final: 42 residues processed: 365 average time/residue: 0.0767 time to fit residues: 37.1529 Evaluate side-chains 380 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 336 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 264 GLU 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 42 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 133 THR 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 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 152 VAL Chi-restraints excluded: chain C residue 177 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 321 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 373 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 340 HIS ** 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 = 0.3736 r_free = 0.3736 target = 0.129579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116147 restraints weight = 15299.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119986 restraints weight = 6602.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122335 restraints weight = 3475.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123842 restraints weight = 2098.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124773 restraints weight = 1405.387| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9120 Z= 0.151 Angle : 0.659 9.990 12385 Z= 0.336 Chirality : 0.044 0.166 1423 Planarity : 0.004 0.056 1570 Dihedral : 4.283 17.281 1245 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.90 % Favored : 96.92 % Rotamer: Outliers : 5.67 % Allowed : 29.49 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1137 helix: 1.26 (0.27), residues: 382 sheet: 0.05 (0.32), residues: 280 loop : -0.54 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.019 0.001 TYR C 281 PHE 0.029 0.002 PHE C 280 TRP 0.015 0.001 TRP B 216 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9118) covalent geometry : angle 0.65943 (12381) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.67935 ( 4) hydrogen bonds : bond 0.03708 ( 436) hydrogen bonds : angle 4.86396 ( 1227) *********************** 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 392 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 338 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7497 (tt0) cc_final: 0.7279 (tt0) REVERT: A 18 MET cc_start: 0.7269 (tpp) cc_final: 0.6844 (tpp) REVERT: A 25 GLU cc_start: 0.6711 (tm-30) cc_final: 0.5922 (tm-30) REVERT: A 29 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7612 (mtmm) REVERT: A 35 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7448 (mtm-85) REVERT: A 184 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6606 (mt-10) REVERT: A 210 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7834 (tp) REVERT: A 215 ASP cc_start: 0.7122 (t0) cc_final: 0.6536 (t0) REVERT: A 221 PHE cc_start: 0.7941 (t80) cc_final: 0.7689 (t80) REVERT: A 257 ASN cc_start: 0.8016 (m-40) cc_final: 0.7711 (m-40) REVERT: A 262 LEU cc_start: 0.8556 (tp) cc_final: 0.8162 (tp) REVERT: A 335 GLU cc_start: 0.7386 (mp0) cc_final: 0.7163 (mp0) REVERT: A 346 ASP cc_start: 0.8027 (t0) cc_final: 0.7611 (t0) REVERT: A 350 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8137 (tp-100) REVERT: B 115 ASN cc_start: 0.7606 (m110) cc_final: 0.7107 (m-40) REVERT: B 128 ILE cc_start: 0.7525 (tt) cc_final: 0.7270 (pt) REVERT: B 138 VAL cc_start: 0.8364 (t) cc_final: 0.8110 (m) REVERT: B 202 ARG cc_start: 0.7510 (tpp80) cc_final: 0.7181 (tpp80) REVERT: B 219 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6591 (ptp-170) REVERT: B 233 ASP cc_start: 0.7806 (t0) cc_final: 0.7541 (t0) REVERT: B 259 ASP cc_start: 0.7467 (t0) cc_final: 0.7170 (t0) REVERT: B 294 TYR cc_start: 0.7453 (m-80) cc_final: 0.6805 (m-80) REVERT: B 323 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7529 (tp) REVERT: C 112 PHE cc_start: 0.7544 (t80) cc_final: 0.7080 (t80) REVERT: C 129 ASN cc_start: 0.8018 (t0) cc_final: 0.7670 (t0) REVERT: C 158 ASN cc_start: 0.8263 (m110) cc_final: 0.7648 (m-40) REVERT: C 198 ASP cc_start: 0.7349 (m-30) cc_final: 0.7114 (m-30) REVERT: C 242 ILE cc_start: 0.8324 (mp) cc_final: 0.7883 (tt) REVERT: C 281 TYR cc_start: 0.6026 (m-10) cc_final: 0.5354 (m-10) REVERT: C 346 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8027 (ttmm) REVERT: C 369 TYR cc_start: 0.7418 (m-80) cc_final: 0.7111 (m-80) REVERT: E 10 LEU cc_start: 0.8347 (tp) cc_final: 0.8105 (tt) REVERT: E 42 LYS cc_start: 0.8683 (mttt) cc_final: 0.8382 (mttt) REVERT: E 102 TYR cc_start: 0.7972 (t80) cc_final: 0.7490 (t80) REVERT: E 167 HIS cc_start: 0.7833 (t-90) cc_final: 0.7607 (t-90) REVERT: E 186 GLN cc_start: 0.7275 (pt0) cc_final: 0.6956 (pt0) REVERT: E 226 VAL cc_start: 0.8416 (t) cc_final: 0.7933 (p) REVERT: G 17 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7338 (mm-30) outliers start: 54 outliers final: 45 residues processed: 358 average time/residue: 0.0918 time to fit residues: 43.4319 Evaluate side-chains 382 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 333 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 98 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 323 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 152 VAL Chi-restraints excluded: chain C residue 181 GLN 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 327 CYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 373 ASN 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 160 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.128627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115201 restraints weight = 15516.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119034 restraints weight = 6678.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.121411 restraints weight = 3515.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122898 restraints weight = 2112.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123857 restraints weight = 1418.000| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2942 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= 0.171 Angle : 0.677 9.343 12385 Z= 0.344 Chirality : 0.044 0.174 1423 Planarity : 0.004 0.057 1570 Dihedral : 4.322 17.646 1245 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Rotamer: Outliers : 5.77 % Allowed : 29.91 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.25), residues: 1137 helix: 1.23 (0.27), residues: 383 sheet: -0.00 (0.32), residues: 281 loop : -0.52 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 307 TYR 0.017 0.001 TYR C 281 PHE 0.031 0.002 PHE C 280 TRP 0.013 0.002 TRP B 87 HIS 0.005 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9118) covalent geometry : angle 0.67670 (12381) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.52744 ( 4) hydrogen bonds : bond 0.03689 ( 436) hydrogen bonds : angle 4.87447 ( 1227) *********************** 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 397 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7477 (tt0) cc_final: 0.7255 (tt0) REVERT: A 18 MET cc_start: 0.7249 (tpp) cc_final: 0.6830 (tpp) REVERT: A 25 GLU cc_start: 0.6757 (tm-30) cc_final: 0.5949 (tm-30) REVERT: A 29 LYS cc_start: 0.8377 (mtmm) cc_final: 0.7695 (mtmm) REVERT: A 35 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7488 (mtm-85) REVERT: A 184 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6667 (mt-10) REVERT: A 210 ILE cc_start: 0.8211 (tp) cc_final: 0.7837 (tp) REVERT: A 215 ASP cc_start: 0.7134 (t0) cc_final: 0.6577 (t0) REVERT: A 221 PHE cc_start: 0.8006 (t80) cc_final: 0.7768 (t80) REVERT: A 257 ASN cc_start: 0.8120 (m-40) cc_final: 0.7836 (m-40) REVERT: A 262 LEU cc_start: 0.8580 (tp) cc_final: 0.8180 (tp) REVERT: A 335 GLU cc_start: 0.7413 (mp0) cc_final: 0.7177 (mp0) REVERT: A 346 ASP cc_start: 0.8078 (t0) cc_final: 0.7618 (t0) REVERT: A 350 GLN cc_start: 0.8369 (tp-100) cc_final: 0.8142 (tp-100) REVERT: B 128 ILE cc_start: 0.7540 (tt) cc_final: 0.7282 (pt) REVERT: B 138 VAL cc_start: 0.8378 (t) cc_final: 0.8131 (m) REVERT: B 202 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7227 (tpp80) REVERT: B 233 ASP cc_start: 0.7752 (t0) cc_final: 0.7482 (t0) REVERT: B 259 ASP cc_start: 0.7462 (t0) cc_final: 0.7168 (t0) REVERT: B 294 TYR cc_start: 0.7464 (m-80) cc_final: 0.6784 (m-80) REVERT: B 313 LEU cc_start: 0.8278 (mp) cc_final: 0.8052 (mt) REVERT: C 112 PHE cc_start: 0.7545 (t80) cc_final: 0.7066 (t80) REVERT: C 129 ASN cc_start: 0.7998 (t0) cc_final: 0.7656 (t0) REVERT: C 158 ASN cc_start: 0.8258 (m110) cc_final: 0.7540 (m-40) REVERT: C 162 LEU cc_start: 0.8279 (mt) cc_final: 0.7848 (mp) REVERT: C 198 ASP cc_start: 0.7378 (m-30) cc_final: 0.7109 (m-30) REVERT: C 242 ILE cc_start: 0.8335 (mp) cc_final: 0.7870 (tt) REVERT: C 281 TYR cc_start: 0.6042 (m-10) cc_final: 0.5329 (m-10) REVERT: C 346 LYS cc_start: 0.8420 (ttmm) cc_final: 0.7977 (ttmm) REVERT: C 369 TYR cc_start: 0.7381 (m-80) cc_final: 0.6968 (m-80) REVERT: E 10 LEU cc_start: 0.8355 (tp) cc_final: 0.8115 (tt) REVERT: E 42 LYS cc_start: 0.8709 (mttt) cc_final: 0.8479 (mttt) REVERT: E 102 TYR cc_start: 0.7986 (t80) cc_final: 0.7499 (t80) REVERT: E 167 HIS cc_start: 0.7869 (t-90) cc_final: 0.7647 (t-90) REVERT: E 186 GLN cc_start: 0.7292 (pt0) cc_final: 0.6986 (pt0) REVERT: E 226 VAL cc_start: 0.8427 (t) cc_final: 0.7951 (p) REVERT: G 17 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7331 (mm-30) outliers start: 55 outliers final: 46 residues processed: 363 average time/residue: 0.0898 time to fit residues: 43.3545 Evaluate side-chains 383 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 336 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 223 VAL 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 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 98 ILE 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 282 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 152 VAL Chi-restraints excluded: chain C residue 181 GLN 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 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 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 90 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 211 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111928 restraints weight = 15335.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115685 restraints weight = 6611.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118008 restraints weight = 3490.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119467 restraints weight = 2112.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120309 restraints weight = 1427.967| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9120 Z= 0.252 Angle : 0.739 9.625 12385 Z= 0.381 Chirality : 0.047 0.197 1423 Planarity : 0.005 0.056 1570 Dihedral : 4.660 20.294 1245 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.43 % Favored : 96.39 % Rotamer: Outliers : 6.30 % Allowed : 30.22 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.25), residues: 1137 helix: 1.08 (0.26), residues: 379 sheet: -0.12 (0.32), residues: 279 loop : -0.55 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 343 TYR 0.018 0.002 TYR C 281 PHE 0.032 0.002 PHE C 280 TRP 0.018 0.002 TRP B 87 HIS 0.013 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 9118) covalent geometry : angle 0.73910 (12381) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.60962 ( 4) hydrogen bonds : bond 0.03969 ( 436) hydrogen bonds : angle 5.03168 ( 1227) *********************** 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 426 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 366 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7485 (tt0) cc_final: 0.7252 (tt0) REVERT: A 18 MET cc_start: 0.7280 (tpp) cc_final: 0.6845 (tpp) REVERT: A 25 GLU cc_start: 0.6780 (tm-30) cc_final: 0.5986 (tm-30) REVERT: A 29 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7777 (mtmm) REVERT: A 35 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7673 (mtm-85) REVERT: A 184 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6848 (mt-10) REVERT: A 206 ARG cc_start: 0.5854 (ttm-80) cc_final: 0.5597 (ttm-80) REVERT: A 210 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7849 (tp) REVERT: A 221 PHE cc_start: 0.8080 (t80) cc_final: 0.7685 (t80) REVERT: A 248 ARG cc_start: 0.7237 (ptp-170) cc_final: 0.6929 (ptp-170) REVERT: A 257 ASN cc_start: 0.8344 (m-40) cc_final: 0.8033 (m-40) REVERT: A 262 LEU cc_start: 0.8614 (tp) cc_final: 0.8189 (tp) REVERT: A 312 ASP cc_start: 0.7090 (t0) cc_final: 0.6856 (t0) REVERT: A 321 ARG cc_start: 0.7637 (mmp-170) cc_final: 0.7397 (mmp-170) REVERT: A 335 GLU cc_start: 0.7454 (mp0) cc_final: 0.7220 (mp0) REVERT: A 346 ASP cc_start: 0.8100 (t0) cc_final: 0.7800 (t0) REVERT: A 354 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7491 (ttm-80) REVERT: B 22 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 87 TRP cc_start: 0.8326 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: B 128 ILE cc_start: 0.7734 (tt) cc_final: 0.7401 (pt) REVERT: B 138 VAL cc_start: 0.8420 (t) cc_final: 0.8217 (m) REVERT: B 202 ARG cc_start: 0.7586 (tpp80) cc_final: 0.7232 (tpp80) REVERT: B 233 ASP cc_start: 0.7708 (t0) cc_final: 0.7357 (t0) REVERT: B 258 PHE cc_start: 0.8505 (m-80) cc_final: 0.8025 (m-80) REVERT: B 283 PHE cc_start: 0.8343 (m-80) cc_final: 0.8038 (m-80) REVERT: B 294 TYR cc_start: 0.7559 (m-80) cc_final: 0.6933 (m-80) REVERT: B 323 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7527 (tp) REVERT: C 112 PHE cc_start: 0.7525 (t80) cc_final: 0.7058 (t80) REVERT: C 129 ASN cc_start: 0.8083 (t0) cc_final: 0.7677 (t0) REVERT: C 158 ASN cc_start: 0.8308 (m110) cc_final: 0.7850 (m-40) REVERT: C 198 ASP cc_start: 0.7472 (m-30) cc_final: 0.7225 (m-30) REVERT: C 242 ILE cc_start: 0.8398 (mp) cc_final: 0.7888 (tt) REVERT: C 281 TYR cc_start: 0.6157 (m-10) cc_final: 0.5257 (m-10) REVERT: C 346 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8012 (ttmm) REVERT: E 102 TYR cc_start: 0.8038 (t80) cc_final: 0.7484 (t80) REVERT: E 167 HIS cc_start: 0.7939 (t-90) cc_final: 0.7442 (t-90) REVERT: E 176 TRP cc_start: 0.8111 (m100) cc_final: 0.7765 (m100) REVERT: E 186 GLN cc_start: 0.7283 (pt0) cc_final: 0.6982 (pt0) REVERT: G 17 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7351 (mm-30) outliers start: 60 outliers final: 45 residues processed: 390 average time/residue: 0.0910 time to fit residues: 46.9835 Evaluate side-chains 416 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 367 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 195 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 VAL 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 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 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 323 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 152 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 238 ILE 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 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 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 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 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 244 ASN ** C 181 GLN ** 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 = 0.3695 r_free = 0.3695 target = 0.126585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113182 restraints weight = 15389.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116998 restraints weight = 6603.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119333 restraints weight = 3477.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120705 restraints weight = 2102.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.121693 restraints weight = 1445.087| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9120 Z= 0.199 Angle : 0.742 9.962 12385 Z= 0.378 Chirality : 0.045 0.151 1423 Planarity : 0.005 0.055 1570 Dihedral : 4.648 21.783 1245 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.34 % Favored : 96.48 % Rotamer: Outliers : 5.67 % Allowed : 31.48 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.25), residues: 1137 helix: 1.11 (0.26), residues: 379 sheet: -0.15 (0.32), residues: 277 loop : -0.52 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 224 TYR 0.017 0.002 TYR C 281 PHE 0.028 0.002 PHE C 280 TRP 0.014 0.002 TRP B 87 HIS 0.021 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9118) covalent geometry : angle 0.74226 (12381) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.55830 ( 4) hydrogen bonds : bond 0.03818 ( 436) hydrogen bonds : angle 4.96229 ( 1227) *********************** 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 425 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 371 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7470 (tt0) cc_final: 0.7241 (tt0) REVERT: A 18 MET cc_start: 0.7271 (tpp) cc_final: 0.6826 (tpp) REVERT: A 25 GLU cc_start: 0.6771 (tm-30) cc_final: 0.5968 (tm-30) REVERT: A 29 LYS cc_start: 0.8394 (mtmm) cc_final: 0.7734 (mtmm) REVERT: A 35 ARG cc_start: 0.7962 (ptp-110) cc_final: 0.7645 (mtm-85) REVERT: A 184 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 210 ILE cc_start: 0.8221 (tp) cc_final: 0.7817 (tp) REVERT: A 221 PHE cc_start: 0.8041 (t80) cc_final: 0.7621 (t80) REVERT: A 244 ASN cc_start: 0.7830 (m-40) cc_final: 0.7614 (m110) REVERT: A 248 ARG cc_start: 0.7149 (ptp-170) cc_final: 0.6826 (ptp-170) REVERT: A 257 ASN cc_start: 0.8374 (m-40) cc_final: 0.8052 (m-40) REVERT: A 262 LEU cc_start: 0.8633 (tp) cc_final: 0.8231 (tp) REVERT: A 312 ASP cc_start: 0.7087 (t0) cc_final: 0.6830 (t0) REVERT: A 321 ARG cc_start: 0.7644 (mmp-170) cc_final: 0.7422 (mmp-170) REVERT: A 335 GLU cc_start: 0.7473 (mp0) cc_final: 0.7232 (mp0) REVERT: A 346 ASP cc_start: 0.8109 (t0) cc_final: 0.7773 (t0) REVERT: B 22 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 87 TRP cc_start: 0.8305 (OUTLIER) cc_final: 0.7915 (m-10) REVERT: B 128 ILE cc_start: 0.7687 (tt) cc_final: 0.7377 (pt) REVERT: B 138 VAL cc_start: 0.8410 (t) cc_final: 0.8196 (m) REVERT: B 202 ARG cc_start: 0.7535 (tpp80) cc_final: 0.7275 (tpp80) REVERT: B 258 PHE cc_start: 0.8489 (m-80) cc_final: 0.7995 (m-80) REVERT: B 283 PHE cc_start: 0.8352 (m-80) cc_final: 0.7986 (m-80) REVERT: B 294 TYR cc_start: 0.7535 (m-80) cc_final: 0.6995 (m-80) REVERT: B 323 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7537 (tp) REVERT: C 112 PHE cc_start: 0.7529 (t80) cc_final: 0.7057 (t80) REVERT: C 129 ASN cc_start: 0.8051 (t0) cc_final: 0.7636 (t0) REVERT: C 155 ILE cc_start: 0.8287 (mm) cc_final: 0.8036 (mm) REVERT: C 158 ASN cc_start: 0.8138 (m110) cc_final: 0.7895 (m-40) REVERT: C 180 ILE cc_start: 0.8188 (mt) cc_final: 0.7842 (tp) REVERT: C 198 ASP cc_start: 0.7441 (m-30) cc_final: 0.7198 (m-30) REVERT: C 242 ILE cc_start: 0.8388 (mp) cc_final: 0.7914 (tt) REVERT: C 281 TYR cc_start: 0.6048 (m-10) cc_final: 0.5177 (m-10) REVERT: C 346 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8001 (ttmm) REVERT: E 102 TYR cc_start: 0.8045 (t80) cc_final: 0.7485 (t80) REVERT: E 167 HIS cc_start: 0.8018 (t-90) cc_final: 0.7777 (t-90) REVERT: E 186 GLN cc_start: 0.7316 (pt0) cc_final: 0.7010 (pt0) REVERT: E 226 VAL cc_start: 0.8466 (t) cc_final: 0.7986 (p) REVERT: G 17 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7320 (mm-30) outliers start: 54 outliers final: 47 residues processed: 393 average time/residue: 0.0890 time to fit residues: 46.3971 Evaluate side-chains 415 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 366 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 223 VAL 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 299 VAL 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 219 ARG Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 323 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 152 VAL 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 300 MET Chi-restraints excluded: chain C residue 321 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 99 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 211 GLN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115701 restraints weight = 15206.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119527 restraints weight = 6549.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121888 restraints weight = 3457.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123397 restraints weight = 2098.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124248 restraints weight = 1411.676| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3414 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= 0.147 Angle : 0.739 10.242 12385 Z= 0.372 Chirality : 0.044 0.169 1423 Planarity : 0.005 0.056 1570 Dihedral : 4.529 20.649 1245 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.22 % Rotamer: Outliers : 5.04 % Allowed : 32.95 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.26), residues: 1137 helix: 1.18 (0.27), residues: 380 sheet: -0.21 (0.30), residues: 303 loop : -0.49 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 354 TYR 0.024 0.002 TYR C 369 PHE 0.035 0.002 PHE A 187 TRP 0.014 0.001 TRP B 216 HIS 0.021 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9118) covalent geometry : angle 0.73859 (12381) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.53184 ( 4) hydrogen bonds : bond 0.03687 ( 436) hydrogen bonds : angle 4.89074 ( 1227) ********************** 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 407 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 359 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7436 (tt0) cc_final: 0.7201 (tt0) REVERT: A 18 MET cc_start: 0.7261 (tpp) cc_final: 0.6805 (tpp) REVERT: A 25 GLU cc_start: 0.6765 (tm-30) cc_final: 0.5963 (tm-30) REVERT: A 29 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7691 (mtmm) REVERT: A 35 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7625 (mtm-85) REVERT: A 184 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6774 (mt-10) REVERT: A 206 ARG cc_start: 0.5688 (ttm-80) cc_final: 0.5350 (ttm-80) REVERT: A 210 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 221 PHE cc_start: 0.7990 (t80) cc_final: 0.7570 (t80) REVERT: A 257 ASN cc_start: 0.8290 (m-40) cc_final: 0.8010 (m-40) REVERT: A 262 LEU cc_start: 0.8561 (tp) cc_final: 0.8210 (tp) REVERT: A 312 ASP cc_start: 0.7047 (t0) cc_final: 0.6790 (t0) REVERT: A 335 GLU cc_start: 0.7418 (mp0) cc_final: 0.7208 (mp0) REVERT: A 346 ASP cc_start: 0.8078 (t0) cc_final: 0.7577 (t0) REVERT: B 22 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 128 ILE cc_start: 0.7601 (tt) cc_final: 0.7350 (pt) REVERT: B 138 VAL cc_start: 0.8368 (t) cc_final: 0.8108 (m) REVERT: B 202 ARG cc_start: 0.7476 (tpp80) cc_final: 0.7023 (tpp80) REVERT: B 294 TYR cc_start: 0.7517 (m-80) cc_final: 0.6978 (m-80) REVERT: B 323 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7520 (tp) REVERT: C 112 PHE cc_start: 0.7571 (t80) cc_final: 0.7094 (t80) REVERT: C 129 ASN cc_start: 0.7936 (t0) cc_final: 0.7580 (t0) REVERT: C 155 ILE cc_start: 0.8287 (mm) cc_final: 0.8041 (mm) REVERT: C 158 ASN cc_start: 0.8106 (m110) cc_final: 0.7853 (m-40) REVERT: C 198 ASP cc_start: 0.7353 (m-30) cc_final: 0.7075 (m-30) REVERT: C 281 TYR cc_start: 0.5964 (m-10) cc_final: 0.5165 (m-10) REVERT: C 346 LYS cc_start: 0.8446 (ttmm) cc_final: 0.7950 (ttmm) REVERT: E 102 TYR cc_start: 0.8001 (t80) cc_final: 0.7489 (t80) REVERT: E 167 HIS cc_start: 0.8001 (t-90) cc_final: 0.7783 (t-90) REVERT: E 226 VAL cc_start: 0.8391 (t) cc_final: 0.7875 (p) REVERT: G 17 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7325 (mm-30) outliers start: 48 outliers final: 39 residues processed: 375 average time/residue: 0.0890 time to fit residues: 44.7317 Evaluate side-chains 398 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 356 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain A residue 223 VAL 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 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 98 ILE 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 282 SER Chi-restraints excluded: chain B residue 323 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 152 VAL 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 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 206 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 78 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 211 GLN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.127660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114295 restraints weight = 15159.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118052 restraints weight = 6545.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120428 restraints weight = 3476.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121911 restraints weight = 2103.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122807 restraints weight = 1412.911| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9120 Z= 0.178 Angle : 0.751 10.387 12385 Z= 0.377 Chirality : 0.045 0.162 1423 Planarity : 0.005 0.058 1570 Dihedral : 4.539 20.699 1245 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Rotamer: Outliers : 4.83 % Allowed : 33.47 % Favored : 61.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.26), residues: 1137 helix: 1.06 (0.26), residues: 388 sheet: -0.18 (0.30), residues: 298 loop : -0.62 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 307 TYR 0.025 0.002 TYR C 369 PHE 0.028 0.002 PHE C 280 TRP 0.014 0.002 TRP B 216 HIS 0.004 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9118) covalent geometry : angle 0.75119 (12381) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.57348 ( 4) hydrogen bonds : bond 0.03671 ( 436) hydrogen bonds : angle 4.89644 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1518.12 seconds wall clock time: 26 minutes 51.58 seconds (1611.58 seconds total)