Starting phenix.real_space_refine on Wed Feb 14 08:39:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcx_34667/02_2024/8hcx_34667_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcx_34667/02_2024/8hcx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcx_34667/02_2024/8hcx_34667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcx_34667/02_2024/8hcx_34667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcx_34667/02_2024/8hcx_34667_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcx_34667/02_2024/8hcx_34667_neut.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5695 2.51 5 N 1505 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 292": "OE1" <-> "OE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8933 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1780 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2190 Classifications: {'peptide': 292} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1770 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 5.41, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.63 Conformation dependent library (CDL) restraints added in 1.9 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 39.3% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.585A pdb=" N LYS A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.701A pdb=" N CYS A 212 " --> pdb=" O TRP A 209 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 214 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 215 " --> pdb=" O CYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 296 through 317 removed outlier: 4.482A pdb=" N SER A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.821A pdb=" N ARG B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 4.097A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 129 removed outlier: 3.534A pdb=" N LEU C 122 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 164 removed outlier: 3.580A pdb=" N LEU C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Proline residue: C 156 - end of helix removed outlier: 3.808A pdb=" N LEU C 162 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 4.288A pdb=" N MET C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 204 removed outlier: 3.514A pdb=" N PHE C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 238 removed outlier: 3.521A pdb=" N VAL C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.667A pdb=" N ILE C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 272 removed outlier: 3.516A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 282 Processing helix chain 'C' and resid 282 through 302 removed outlier: 3.820A pdb=" N TYR C 293 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 350 Proline residue: C 338 - end of helix removed outlier: 3.843A pdb=" N ARG C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 390 removed outlier: 3.522A pdb=" N CYS C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) Proline residue: C 383 - end of helix removed outlier: 3.539A pdb=" N TYR C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.001A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.670A pdb=" N LYS E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.988A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.574A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 189 removed outlier: 3.717A pdb=" N MET A 196 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 187 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG A 35 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 37 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 222 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU A 39 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ASP A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 219 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE A 255 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 221 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 257 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 223 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 256 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.752A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 7.119A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 77 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.101A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.577A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.833A pdb=" N SER B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.973A pdb=" N ALA B 236 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 257 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.192A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 240 through 245 removed outlier: 3.630A pdb=" N LEU C 256 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 252 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.511A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 116 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.511A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 116 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.504A pdb=" N VAL E 226 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 3.73 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: 99.10 - 106.09: 153 106.09 - 113.07: 4926 113.07 - 120.06: 3109 120.06 - 127.05: 4097 127.05 - 134.03: 96 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 2.440 nonbonded pdb=" O ASP E 89 " pdb=" OH TYR E 93 " model vdw 2.168 2.440 nonbonded pdb=" OD1 ASN B 318 " pdb=" N ARG B 319 " model vdw 2.224 2.520 nonbonded pdb=" O GLY E 7 " pdb=" OG1 THR E 114 " model vdw 2.250 2.440 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.286 2.440 ... (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 ========== 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: 1.010 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: 3.930 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.830 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- 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 9118 Z= 0.168 Angle : 0.624 11.707 12381 Z= 0.311 Chirality : 0.040 0.170 1423 Planarity : 0.005 0.106 1570 Dihedral : 16.427 78.322 3217 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.46 % Favored : 97.19 % Rotamer: Outliers : 0.31 % Allowed : 31.37 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1137 helix: 0.61 (0.27), residues: 392 sheet: 0.58 (0.34), residues: 264 loop : -0.52 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 87 HIS 0.004 0.001 HIS C 150 PHE 0.024 0.001 PHE C 280 TYR 0.014 0.001 TYR B 150 ARG 0.009 0.001 ARG A 307 *********************** 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 fitting. rotamer outliers: 3 poor density : 278 time to evaluate : 1.004 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: 0.2410 time to fit residues: 89.7902 Evaluate side-chains 285 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN C 181 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9118 Z= 0.238 Angle : 0.607 8.379 12381 Z= 0.316 Chirality : 0.042 0.152 1423 Planarity : 0.005 0.074 1570 Dihedral : 3.877 20.517 1247 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.46 % Favored : 97.27 % Rotamer: Outliers : 5.14 % Allowed : 26.76 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1137 helix: 1.21 (0.27), residues: 390 sheet: 0.45 (0.32), residues: 280 loop : -0.45 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 216 HIS 0.004 0.001 HIS B 59 PHE 0.024 0.002 PHE C 280 TYR 0.014 0.001 TYR E 101 ARG 0.007 0.001 ARG A 298 *********************** 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 362 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 313 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7257 (tpp) cc_final: 0.6946 (tpp) REVERT: A 190 ASP cc_start: 0.8012 (t0) cc_final: 0.7761 (t0) REVERT: A 195 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7024 (t-90) REVERT: A 239 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7859 (ttmm) REVERT: A 350 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7942 (tp-100) REVERT: B 318 ASN cc_start: 0.8228 (t0) cc_final: 0.7911 (t0) REVERT: C 148 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7822 (mm) REVERT: C 180 ILE cc_start: 0.8199 (mt) cc_final: 0.7779 (mt) REVERT: C 346 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8003 (ttmm) REVERT: C 369 TYR cc_start: 0.7492 (m-80) cc_final: 0.7212 (m-80) REVERT: E 10 LEU cc_start: 0.8322 (tp) cc_final: 0.8082 (tt) REVERT: E 102 TYR cc_start: 0.7818 (t80) cc_final: 0.7267 (t80) REVERT: E 226 VAL cc_start: 0.8337 (t) cc_final: 0.7873 (p) outliers start: 49 outliers final: 29 residues processed: 330 average time/residue: 0.2373 time to fit residues: 103.4711 Evaluate side-chains 346 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 314 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 239 LYS 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 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 ASP 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 184 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 296 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 73 ASP 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 57 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9118 Z= 0.204 Angle : 0.598 7.888 12381 Z= 0.304 Chirality : 0.042 0.157 1423 Planarity : 0.004 0.062 1570 Dihedral : 3.873 16.040 1245 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.46 % Favored : 97.27 % Rotamer: Outliers : 5.46 % Allowed : 28.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1137 helix: 1.34 (0.27), residues: 392 sheet: 0.39 (0.32), residues: 280 loop : -0.47 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 216 HIS 0.003 0.001 HIS C 150 PHE 0.032 0.002 PHE C 280 TYR 0.016 0.001 TYR C 281 ARG 0.007 0.001 ARG A 307 *********************** 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 365 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 313 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7411 (tt0) cc_final: 0.7177 (tt0) REVERT: A 17 LYS cc_start: 0.7650 (mttt) cc_final: 0.7413 (mttt) REVERT: A 18 MET cc_start: 0.7260 (tpp) cc_final: 0.6866 (tpp) REVERT: A 25 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6334 (tm-30) REVERT: A 190 ASP cc_start: 0.8034 (t0) cc_final: 0.7790 (t0) REVERT: A 195 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7007 (t-90) REVERT: A 210 ILE cc_start: 0.8010 (tp) cc_final: 0.7613 (tp) REVERT: A 215 ASP cc_start: 0.7057 (t0) cc_final: 0.6627 (t0) REVERT: A 260 ASP cc_start: 0.7730 (p0) cc_final: 0.7524 (p0) REVERT: A 261 LEU cc_start: 0.8171 (mp) cc_final: 0.7886 (mp) REVERT: A 350 GLN cc_start: 0.8276 (tp-100) cc_final: 0.8004 (tp-100) REVERT: B 75 LEU cc_start: 0.7472 (tt) cc_final: 0.7192 (tp) REVERT: B 202 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7237 (tpp80) REVERT: B 259 ASP cc_start: 0.7323 (t0) cc_final: 0.6991 (t0) REVERT: B 264 GLN cc_start: 0.7565 (mt0) cc_final: 0.7172 (mt0) REVERT: B 294 TYR cc_start: 0.7445 (m-80) cc_final: 0.6701 (m-80) REVERT: B 313 LEU cc_start: 0.8253 (mp) cc_final: 0.8014 (mt) REVERT: B 318 ASN cc_start: 0.8237 (t0) cc_final: 0.7957 (t0) REVERT: C 112 PHE cc_start: 0.7535 (t80) cc_final: 0.7157 (t80) REVERT: C 134 ASN cc_start: 0.7314 (t0) cc_final: 0.7087 (t0) REVERT: C 148 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7723 (mm) REVERT: C 149 LEU cc_start: 0.8445 (tt) cc_final: 0.8234 (tt) REVERT: C 180 ILE cc_start: 0.8207 (mt) cc_final: 0.7831 (mt) REVERT: C 369 TYR cc_start: 0.7465 (m-80) cc_final: 0.7213 (m-80) REVERT: E 10 LEU cc_start: 0.8335 (tp) cc_final: 0.8105 (tt) REVERT: E 102 TYR cc_start: 0.7871 (t80) cc_final: 0.7348 (t80) REVERT: E 167 HIS cc_start: 0.7681 (t-90) cc_final: 0.7366 (t-90) REVERT: E 226 VAL cc_start: 0.8398 (t) cc_final: 0.7906 (p) outliers start: 52 outliers final: 39 residues processed: 330 average time/residue: 0.2414 time to fit residues: 105.2802 Evaluate side-chains 350 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 309 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 THR 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 A residue 324 CYS 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 87 TRP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 178 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 234 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET 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 73 ASP 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 101 optimal weight: 0.6980 chunk 77 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.0170 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9118 Z= 0.171 Angle : 0.583 7.977 12381 Z= 0.296 Chirality : 0.041 0.148 1423 Planarity : 0.004 0.058 1570 Dihedral : 3.848 17.181 1245 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.10 % Rotamer: Outliers : 5.35 % Allowed : 28.02 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1137 helix: 1.42 (0.27), residues: 392 sheet: 0.35 (0.32), residues: 280 loop : -0.45 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 216 HIS 0.003 0.001 HIS A 327 PHE 0.030 0.001 PHE C 280 TYR 0.015 0.001 TYR C 281 ARG 0.007 0.000 ARG A 307 *********************** 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 370 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 319 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7437 (tt0) cc_final: 0.7192 (tt0) REVERT: A 17 LYS cc_start: 0.7671 (mttt) cc_final: 0.7462 (mttt) REVERT: A 18 MET cc_start: 0.7277 (tpp) cc_final: 0.6817 (tpp) REVERT: A 25 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6059 (tm-30) REVERT: A 29 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7473 (mtmm) REVERT: A 35 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7251 (mtm-85) REVERT: A 190 ASP cc_start: 0.8017 (t0) cc_final: 0.7792 (t0) REVERT: A 195 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7048 (t-90) REVERT: A 210 ILE cc_start: 0.8042 (tp) cc_final: 0.7638 (tp) REVERT: A 215 ASP cc_start: 0.7043 (t0) cc_final: 0.6217 (t0) REVERT: A 260 ASP cc_start: 0.7704 (p0) cc_final: 0.7493 (p0) REVERT: A 261 LEU cc_start: 0.8177 (mp) cc_final: 0.7833 (mp) REVERT: A 350 GLN cc_start: 0.8303 (tp-100) cc_final: 0.8031 (tp-100) REVERT: B 202 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7318 (tpp80) REVERT: B 219 ARG cc_start: 0.7320 (ptp90) cc_final: 0.6654 (ptp90) REVERT: B 259 ASP cc_start: 0.7270 (t0) cc_final: 0.6935 (t0) REVERT: B 294 TYR cc_start: 0.7460 (m-80) cc_final: 0.6799 (m-80) REVERT: B 313 LEU cc_start: 0.8287 (mp) cc_final: 0.8050 (mt) REVERT: C 112 PHE cc_start: 0.7542 (t80) cc_final: 0.7129 (t80) REVERT: C 149 LEU cc_start: 0.8350 (tt) cc_final: 0.8141 (tt) REVERT: C 180 ILE cc_start: 0.8194 (mt) cc_final: 0.7805 (mt) REVERT: C 181 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7720 (pp30) REVERT: C 345 LEU cc_start: 0.7314 (mt) cc_final: 0.7105 (mt) REVERT: C 369 TYR cc_start: 0.7447 (m-80) cc_final: 0.7247 (m-80) REVERT: E 10 LEU cc_start: 0.8356 (tp) cc_final: 0.8120 (tt) REVERT: E 102 TYR cc_start: 0.7883 (t80) cc_final: 0.7397 (t80) REVERT: E 167 HIS cc_start: 0.7702 (t-90) cc_final: 0.7381 (t-90) REVERT: E 226 VAL cc_start: 0.8402 (t) cc_final: 0.7903 (p) outliers start: 51 outliers final: 40 residues processed: 336 average time/residue: 0.2408 time to fit residues: 106.8760 Evaluate side-chains 355 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 312 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 216 VAL 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 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 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 234 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET 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 73 ASP 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 62 optimal weight: 0.0020 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9118 Z= 0.215 Angle : 0.602 7.945 12381 Z= 0.311 Chirality : 0.042 0.164 1423 Planarity : 0.004 0.053 1570 Dihedral : 4.026 17.371 1245 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.90 % Favored : 96.92 % Rotamer: Outliers : 5.88 % Allowed : 28.44 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1137 helix: 1.54 (0.27), residues: 383 sheet: 0.27 (0.32), residues: 274 loop : -0.51 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 216 HIS 0.004 0.001 HIS A 327 PHE 0.031 0.002 PHE C 280 TYR 0.017 0.001 TYR C 281 ARG 0.006 0.000 ARG A 307 *********************** 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 386 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 330 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7456 (tt0) cc_final: 0.7219 (tt0) REVERT: A 17 LYS cc_start: 0.7564 (mttt) cc_final: 0.7226 (mttt) REVERT: A 18 MET cc_start: 0.7293 (tpp) cc_final: 0.6825 (tpp) REVERT: A 25 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6069 (tm-30) REVERT: A 29 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7530 (mtmm) REVERT: A 35 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7346 (mtm-85) REVERT: A 184 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6872 (mt-10) REVERT: A 210 ILE cc_start: 0.8074 (tp) cc_final: 0.7682 (tp) REVERT: A 215 ASP cc_start: 0.7143 (t0) cc_final: 0.6442 (t0) REVERT: A 257 ASN cc_start: 0.8105 (m-40) cc_final: 0.7777 (m-40) REVERT: A 261 LEU cc_start: 0.8215 (mp) cc_final: 0.7878 (mp) REVERT: A 346 ASP cc_start: 0.7993 (t0) cc_final: 0.7611 (t0) REVERT: A 350 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8083 (tp-100) REVERT: A 354 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7355 (ttm-80) REVERT: B 60 LEU cc_start: 0.8721 (mm) cc_final: 0.8463 (mt) REVERT: B 75 LEU cc_start: 0.7538 (tt) cc_final: 0.7215 (tp) REVERT: B 202 ARG cc_start: 0.7701 (tpp80) cc_final: 0.7383 (tpp80) REVERT: B 219 ARG cc_start: 0.7468 (ptp90) cc_final: 0.6743 (ptp90) REVERT: B 259 ASP cc_start: 0.7345 (t0) cc_final: 0.6961 (t0) REVERT: B 294 TYR cc_start: 0.7548 (m-80) cc_final: 0.6823 (m-80) REVERT: B 313 LEU cc_start: 0.8316 (mp) cc_final: 0.8089 (mt) REVERT: B 318 ASN cc_start: 0.8274 (t0) cc_final: 0.8036 (t0) REVERT: C 112 PHE cc_start: 0.7615 (t80) cc_final: 0.7126 (t80) REVERT: C 148 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8060 (tp) REVERT: C 180 ILE cc_start: 0.8194 (mt) cc_final: 0.7816 (mt) REVERT: C 242 ILE cc_start: 0.8305 (mp) cc_final: 0.7890 (tt) REVERT: C 345 LEU cc_start: 0.7501 (mt) cc_final: 0.7292 (mt) REVERT: C 346 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7943 (ttmm) REVERT: E 10 LEU cc_start: 0.8402 (tp) cc_final: 0.8169 (tt) REVERT: E 102 TYR cc_start: 0.7933 (t80) cc_final: 0.7441 (t80) REVERT: E 219 LEU cc_start: 0.8449 (tt) cc_final: 0.8216 (tt) REVERT: E 226 VAL cc_start: 0.8412 (t) cc_final: 0.7934 (p) REVERT: G 17 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7416 (mm-30) outliers start: 56 outliers final: 46 residues processed: 346 average time/residue: 0.2375 time to fit residues: 107.9429 Evaluate side-chains 373 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 325 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 GLU 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 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 234 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 207 SER 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 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 73 ASP 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 E residue 215 THR 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 98 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9118 Z= 0.280 Angle : 0.645 7.910 12381 Z= 0.333 Chirality : 0.044 0.176 1423 Planarity : 0.004 0.051 1570 Dihedral : 4.215 17.075 1245 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Rotamer: Outliers : 5.67 % Allowed : 29.91 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1137 helix: 1.40 (0.27), residues: 380 sheet: 0.17 (0.32), residues: 273 loop : -0.53 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 216 HIS 0.005 0.001 HIS A 327 PHE 0.031 0.002 PHE C 280 TYR 0.020 0.001 TYR C 281 ARG 0.007 0.001 ARG A 307 *********************** 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 388 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 334 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7506 (tt0) cc_final: 0.7293 (tt0) REVERT: A 17 LYS cc_start: 0.7587 (mttt) cc_final: 0.7258 (mttt) REVERT: A 18 MET cc_start: 0.7367 (tpp) cc_final: 0.6900 (tpp) REVERT: A 25 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6101 (tm-30) REVERT: A 29 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7630 (mtmm) REVERT: A 35 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7451 (mtm-85) REVERT: A 184 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 210 ILE cc_start: 0.8148 (tp) cc_final: 0.7776 (tp) REVERT: A 215 ASP cc_start: 0.7236 (t0) cc_final: 0.6619 (t0) REVERT: A 257 ASN cc_start: 0.8147 (m-40) cc_final: 0.7838 (m-40) REVERT: A 261 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8006 (mp) REVERT: A 346 ASP cc_start: 0.8047 (t0) cc_final: 0.7620 (t0) REVERT: A 350 GLN cc_start: 0.8376 (tp-100) cc_final: 0.8147 (tp-100) REVERT: A 354 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.7311 (ttm-80) REVERT: B 60 LEU cc_start: 0.8745 (mm) cc_final: 0.8452 (mt) REVERT: B 75 LEU cc_start: 0.7599 (tt) cc_final: 0.7239 (tp) REVERT: B 87 TRP cc_start: 0.8248 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: B 128 ILE cc_start: 0.7547 (tt) cc_final: 0.7215 (pt) REVERT: B 138 VAL cc_start: 0.8377 (t) cc_final: 0.8155 (m) REVERT: B 202 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7360 (tpp80) REVERT: B 259 ASP cc_start: 0.7338 (t0) cc_final: 0.6952 (t0) REVERT: B 264 GLN cc_start: 0.7591 (mt0) cc_final: 0.7320 (mt0) REVERT: B 294 TYR cc_start: 0.7557 (m-80) cc_final: 0.6879 (m-80) REVERT: B 313 LEU cc_start: 0.8335 (mp) cc_final: 0.8121 (mt) REVERT: C 112 PHE cc_start: 0.7659 (t80) cc_final: 0.7165 (t80) REVERT: C 158 ASN cc_start: 0.8055 (m110) cc_final: 0.7732 (m-40) REVERT: C 180 ILE cc_start: 0.8182 (mt) cc_final: 0.7820 (mt) REVERT: C 242 ILE cc_start: 0.8302 (mp) cc_final: 0.7880 (tt) REVERT: C 269 TYR cc_start: 0.7867 (t80) cc_final: 0.7500 (t80) REVERT: C 345 LEU cc_start: 0.7680 (mt) cc_final: 0.7449 (mt) REVERT: C 346 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8004 (ttmm) REVERT: E 102 TYR cc_start: 0.8011 (t80) cc_final: 0.7451 (t80) REVERT: E 167 HIS cc_start: 0.7801 (t-90) cc_final: 0.7527 (t-90) REVERT: G 17 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7432 (mm-30) outliers start: 54 outliers final: 41 residues processed: 349 average time/residue: 0.2486 time to fit residues: 113.0324 Evaluate side-chains 374 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 330 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 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 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 234 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 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 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 73 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9118 Z= 0.240 Angle : 0.651 9.473 12381 Z= 0.331 Chirality : 0.043 0.172 1423 Planarity : 0.004 0.050 1570 Dihedral : 4.285 18.892 1245 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.99 % Favored : 96.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1137 helix: 1.36 (0.27), residues: 380 sheet: 0.04 (0.31), residues: 280 loop : -0.51 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 216 HIS 0.005 0.001 HIS A 327 PHE 0.028 0.002 PHE C 280 TYR 0.022 0.001 TYR C 281 ARG 0.008 0.001 ARG B 224 *********************** 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 393 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 333 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7521 (tt0) cc_final: 0.7312 (tt0) REVERT: A 17 LYS cc_start: 0.7609 (mttt) cc_final: 0.7254 (mttt) REVERT: A 18 MET cc_start: 0.7368 (tpp) cc_final: 0.6881 (tpp) REVERT: A 25 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6071 (tm-30) REVERT: A 29 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7610 (mtmm) REVERT: A 35 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7479 (mtm-85) REVERT: A 184 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 210 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7768 (tp) REVERT: A 215 ASP cc_start: 0.7235 (t0) cc_final: 0.6716 (t0) REVERT: A 248 ARG cc_start: 0.7051 (ptp-170) cc_final: 0.6710 (ptp-170) REVERT: A 257 ASN cc_start: 0.8171 (m-40) cc_final: 0.7860 (m-40) REVERT: A 261 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 346 ASP cc_start: 0.8080 (t0) cc_final: 0.7622 (t0) REVERT: A 350 GLN cc_start: 0.8360 (tp-100) cc_final: 0.8144 (tp-100) REVERT: A 354 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.7313 (ttm-80) REVERT: B 60 LEU cc_start: 0.8724 (mm) cc_final: 0.8436 (mt) REVERT: B 75 LEU cc_start: 0.7560 (tt) cc_final: 0.7222 (tp) REVERT: B 128 ILE cc_start: 0.7532 (tt) cc_final: 0.7231 (pt) REVERT: B 138 VAL cc_start: 0.8379 (t) cc_final: 0.8157 (m) REVERT: B 202 ARG cc_start: 0.7735 (tpp80) cc_final: 0.7517 (tpp80) REVERT: B 259 ASP cc_start: 0.7321 (t0) cc_final: 0.6940 (t0) REVERT: B 294 TYR cc_start: 0.7537 (m-80) cc_final: 0.6858 (m-80) REVERT: C 112 PHE cc_start: 0.7704 (t80) cc_final: 0.7198 (t80) REVERT: C 158 ASN cc_start: 0.8055 (m110) cc_final: 0.7716 (m-40) REVERT: C 180 ILE cc_start: 0.8162 (mt) cc_final: 0.7802 (mt) REVERT: C 198 ASP cc_start: 0.7312 (m-30) cc_final: 0.7089 (m-30) REVERT: C 242 ILE cc_start: 0.8308 (mp) cc_final: 0.7868 (tt) REVERT: C 281 TYR cc_start: 0.5548 (m-80) cc_final: 0.5087 (m-80) REVERT: C 345 LEU cc_start: 0.7660 (mt) cc_final: 0.7413 (mt) REVERT: C 346 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8021 (ttmm) REVERT: E 102 TYR cc_start: 0.8011 (t80) cc_final: 0.7448 (t80) REVERT: E 167 HIS cc_start: 0.7849 (t-90) cc_final: 0.7579 (t-90) REVERT: E 186 GLN cc_start: 0.7318 (pt0) cc_final: 0.7007 (pt0) REVERT: E 226 VAL cc_start: 0.8425 (t) cc_final: 0.7923 (p) REVERT: G 17 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7393 (mm-30) outliers start: 60 outliers final: 47 residues processed: 354 average time/residue: 0.2526 time to fit residues: 116.3639 Evaluate side-chains 382 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 332 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 199 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 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 87 TRP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 117 VAL 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 234 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 369 TYR 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 73 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN C 181 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9118 Z= 0.229 Angle : 0.662 10.001 12381 Z= 0.333 Chirality : 0.043 0.174 1423 Planarity : 0.004 0.050 1570 Dihedral : 4.324 19.916 1245 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.75 % Rotamer: Outliers : 6.61 % Allowed : 30.43 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1137 helix: 1.39 (0.27), residues: 379 sheet: -0.01 (0.32), residues: 281 loop : -0.49 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 216 HIS 0.004 0.001 HIS A 327 PHE 0.026 0.001 PHE C 280 TYR 0.016 0.001 TYR C 281 ARG 0.007 0.001 ARG B 224 *********************** 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 396 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 333 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7509 (tt0) cc_final: 0.7301 (tt0) REVERT: A 17 LYS cc_start: 0.7623 (mttt) cc_final: 0.7260 (mttt) REVERT: A 18 MET cc_start: 0.7376 (tpp) cc_final: 0.6862 (tpp) REVERT: A 25 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6077 (tm-30) REVERT: A 29 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7600 (mtmm) REVERT: A 35 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7602 (mtm-85) REVERT: A 184 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7070 (mt-10) REVERT: A 206 ARG cc_start: 0.5947 (ttm-80) cc_final: 0.5698 (ttm-80) REVERT: A 210 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7772 (tp) REVERT: A 257 ASN cc_start: 0.8126 (m-40) cc_final: 0.7818 (m-40) REVERT: A 261 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7956 (mp) REVERT: A 312 ASP cc_start: 0.7131 (t0) cc_final: 0.6858 (t0) REVERT: A 346 ASP cc_start: 0.8055 (t0) cc_final: 0.7564 (t0) REVERT: A 350 GLN cc_start: 0.8352 (tp-100) cc_final: 0.8135 (tp-100) REVERT: B 60 LEU cc_start: 0.8713 (mm) cc_final: 0.8424 (mt) REVERT: B 75 LEU cc_start: 0.7592 (tt) cc_final: 0.7245 (tp) REVERT: B 128 ILE cc_start: 0.7536 (tt) cc_final: 0.7252 (pt) REVERT: B 138 VAL cc_start: 0.8377 (t) cc_final: 0.8152 (m) REVERT: B 181 GLN cc_start: 0.8052 (mt0) cc_final: 0.7701 (mt0) REVERT: B 191 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7612 (p0) REVERT: B 294 TYR cc_start: 0.7543 (m-80) cc_final: 0.6833 (m-80) REVERT: C 112 PHE cc_start: 0.7718 (t80) cc_final: 0.7199 (t80) REVERT: C 158 ASN cc_start: 0.8079 (m110) cc_final: 0.7792 (m-40) REVERT: C 180 ILE cc_start: 0.8160 (mt) cc_final: 0.7822 (mt) REVERT: C 198 ASP cc_start: 0.7300 (m-30) cc_final: 0.7054 (m-30) REVERT: C 242 ILE cc_start: 0.8343 (mp) cc_final: 0.7887 (tt) REVERT: C 281 TYR cc_start: 0.5577 (m-80) cc_final: 0.4728 (m-80) REVERT: C 345 LEU cc_start: 0.7767 (mt) cc_final: 0.7467 (mt) REVERT: C 346 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8012 (ttmm) REVERT: E 102 TYR cc_start: 0.8019 (t80) cc_final: 0.7492 (t80) REVERT: E 157 ILE cc_start: 0.7837 (pt) cc_final: 0.7599 (mp) REVERT: E 167 HIS cc_start: 0.7869 (t-90) cc_final: 0.7611 (t-90) REVERT: E 186 GLN cc_start: 0.7325 (pt0) cc_final: 0.7021 (pt0) REVERT: E 226 VAL cc_start: 0.8437 (t) cc_final: 0.7945 (p) REVERT: G 17 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7389 (mm-30) outliers start: 63 outliers final: 51 residues processed: 356 average time/residue: 0.2578 time to fit residues: 119.7484 Evaluate side-chains 389 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 334 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 42 ASP Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 VAL 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 87 TRP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 191 ASP 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 234 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 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 73 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 91 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 107 optimal weight: 0.0970 chunk 65 optimal weight: 0.7980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9118 Z= 0.186 Angle : 0.683 11.368 12381 Z= 0.337 Chirality : 0.042 0.163 1423 Planarity : 0.004 0.050 1570 Dihedral : 4.231 19.227 1245 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.81 % Favored : 97.01 % Rotamer: Outliers : 5.35 % Allowed : 32.84 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1137 helix: 1.44 (0.27), residues: 381 sheet: 0.03 (0.32), residues: 281 loop : -0.44 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 216 HIS 0.003 0.001 HIS A 322 PHE 0.027 0.001 PHE C 280 TYR 0.015 0.001 TYR C 281 ARG 0.007 0.001 ARG B 224 *********************** 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 384 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 333 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7645 (mttt) cc_final: 0.7287 (mttt) REVERT: A 18 MET cc_start: 0.7380 (tpp) cc_final: 0.6832 (tpp) REVERT: A 25 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6051 (tm-30) REVERT: A 29 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7551 (mtmm) REVERT: A 35 ARG cc_start: 0.7970 (ptp-110) cc_final: 0.7582 (mtm-85) REVERT: A 184 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6712 (mt-10) REVERT: A 195 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.6869 (t-90) REVERT: A 206 ARG cc_start: 0.5882 (ttm-80) cc_final: 0.5660 (ttm-80) REVERT: A 210 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7713 (tp) REVERT: A 257 ASN cc_start: 0.8096 (m-40) cc_final: 0.7791 (m-40) REVERT: A 261 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 346 ASP cc_start: 0.8035 (t0) cc_final: 0.7541 (t0) REVERT: A 350 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8117 (tp-100) REVERT: B 60 LEU cc_start: 0.8673 (mm) cc_final: 0.8401 (mt) REVERT: B 75 LEU cc_start: 0.7494 (tt) cc_final: 0.7160 (tp) REVERT: B 128 ILE cc_start: 0.7479 (tt) cc_final: 0.7215 (pt) REVERT: B 138 VAL cc_start: 0.8347 (t) cc_final: 0.8083 (m) REVERT: B 181 GLN cc_start: 0.8031 (mt0) cc_final: 0.7665 (mt0) REVERT: B 191 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7657 (p0) REVERT: B 294 TYR cc_start: 0.7523 (m-80) cc_final: 0.6786 (m-80) REVERT: B 313 LEU cc_start: 0.8181 (mp) cc_final: 0.7943 (mt) REVERT: C 112 PHE cc_start: 0.7711 (t80) cc_final: 0.7142 (t80) REVERT: C 151 ILE cc_start: 0.8178 (pt) cc_final: 0.7728 (mp) REVERT: C 158 ASN cc_start: 0.8043 (m110) cc_final: 0.7744 (m-40) REVERT: C 180 ILE cc_start: 0.8089 (mt) cc_final: 0.7741 (mt) REVERT: C 198 ASP cc_start: 0.7233 (m-30) cc_final: 0.7009 (m-30) REVERT: C 242 ILE cc_start: 0.8306 (mp) cc_final: 0.7891 (tt) REVERT: C 281 TYR cc_start: 0.5476 (m-10) cc_final: 0.4575 (m-80) REVERT: C 345 LEU cc_start: 0.7643 (mt) cc_final: 0.7387 (mt) REVERT: C 346 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8021 (ttmm) REVERT: E 102 TYR cc_start: 0.7997 (t80) cc_final: 0.7527 (t80) REVERT: E 157 ILE cc_start: 0.7826 (pt) cc_final: 0.7572 (mp) REVERT: E 167 HIS cc_start: 0.7975 (t-90) cc_final: 0.7719 (t-90) REVERT: E 186 GLN cc_start: 0.7303 (pt0) cc_final: 0.7002 (pt0) REVERT: E 219 LEU cc_start: 0.8412 (tt) cc_final: 0.8157 (tt) REVERT: E 226 VAL cc_start: 0.8385 (t) cc_final: 0.7901 (p) REVERT: G 17 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7366 (mm-30) outliers start: 51 outliers final: 41 residues processed: 350 average time/residue: 0.2484 time to fit residues: 113.4450 Evaluate side-chains 376 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 331 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 VAL 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 87 TRP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 191 ASP 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 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 CYS 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 177 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 246 ASP 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 377 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 73 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.0060 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 95 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9118 Z= 0.202 Angle : 0.701 11.189 12381 Z= 0.343 Chirality : 0.042 0.140 1423 Planarity : 0.004 0.050 1570 Dihedral : 4.219 19.465 1245 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.34 % Favored : 96.48 % Rotamer: Outliers : 4.51 % Allowed : 33.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1137 helix: 1.44 (0.27), residues: 381 sheet: 0.06 (0.32), residues: 281 loop : -0.40 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 216 HIS 0.009 0.001 HIS A 327 PHE 0.025 0.001 PHE C 280 TYR 0.014 0.001 TYR E 235 ARG 0.009 0.001 ARG A 307 ********************** 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 377 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 334 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7622 (mttt) cc_final: 0.7276 (mttt) REVERT: A 18 MET cc_start: 0.7366 (tpp) cc_final: 0.6832 (tpp) REVERT: A 25 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6091 (tm-30) REVERT: A 29 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7584 (mtmm) REVERT: A 35 ARG cc_start: 0.7951 (ptp-110) cc_final: 0.7583 (mtm-85) REVERT: A 184 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6733 (mt-10) REVERT: A 195 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.6892 (t-90) REVERT: A 206 ARG cc_start: 0.5959 (ttm-80) cc_final: 0.5735 (ttm-80) REVERT: A 210 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7714 (tp) REVERT: A 257 ASN cc_start: 0.8095 (m-40) cc_final: 0.7794 (m-40) REVERT: A 261 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 346 ASP cc_start: 0.8050 (t0) cc_final: 0.7559 (t0) REVERT: B 60 LEU cc_start: 0.8680 (mm) cc_final: 0.8405 (mt) REVERT: B 75 LEU cc_start: 0.7530 (tt) cc_final: 0.7198 (tp) REVERT: B 128 ILE cc_start: 0.7484 (tt) cc_final: 0.7213 (pt) REVERT: B 138 VAL cc_start: 0.8341 (t) cc_final: 0.8080 (m) REVERT: B 181 GLN cc_start: 0.8031 (mt0) cc_final: 0.7664 (mt0) REVERT: B 294 TYR cc_start: 0.7545 (m-80) cc_final: 0.6904 (m-80) REVERT: B 313 LEU cc_start: 0.8230 (mp) cc_final: 0.7986 (mt) REVERT: C 112 PHE cc_start: 0.7714 (t80) cc_final: 0.7149 (t80) REVERT: C 151 ILE cc_start: 0.8200 (pt) cc_final: 0.7744 (mp) REVERT: C 158 ASN cc_start: 0.8043 (m110) cc_final: 0.7817 (m110) REVERT: C 180 ILE cc_start: 0.8132 (mt) cc_final: 0.7788 (mt) REVERT: C 242 ILE cc_start: 0.8312 (mp) cc_final: 0.7908 (tt) REVERT: C 281 TYR cc_start: 0.5527 (m-10) cc_final: 0.4586 (m-80) REVERT: C 345 LEU cc_start: 0.7660 (mt) cc_final: 0.7417 (mt) REVERT: C 346 LYS cc_start: 0.8455 (ttmm) cc_final: 0.7995 (ttmm) REVERT: E 102 TYR cc_start: 0.8001 (t80) cc_final: 0.7493 (t80) REVERT: E 157 ILE cc_start: 0.7798 (pt) cc_final: 0.7574 (mp) REVERT: E 167 HIS cc_start: 0.7982 (t-90) cc_final: 0.7729 (t-90) REVERT: E 186 GLN cc_start: 0.7331 (pt0) cc_final: 0.7023 (pt0) REVERT: E 219 LEU cc_start: 0.8414 (tt) cc_final: 0.8167 (tt) REVERT: E 226 VAL cc_start: 0.8416 (t) cc_final: 0.7921 (p) REVERT: G 17 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7368 (mm-30) outliers start: 43 outliers final: 38 residues processed: 346 average time/residue: 0.2516 time to fit residues: 113.6427 Evaluate side-chains 373 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 332 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 VAL 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 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 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 CYS 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 207 SER Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 373 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 73 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 181 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.129914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116622 restraints weight = 15091.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120461 restraints weight = 6474.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122754 restraints weight = 3398.103| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9118 Z= 0.200 Angle : 0.701 11.341 12381 Z= 0.341 Chirality : 0.042 0.144 1423 Planarity : 0.004 0.050 1570 Dihedral : 4.194 19.349 1245 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 4.72 % Allowed : 34.10 % Favored : 61.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1137 helix: 1.47 (0.27), residues: 378 sheet: 0.11 (0.32), residues: 279 loop : -0.44 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 216 HIS 0.005 0.001 HIS A 327 PHE 0.026 0.001 PHE C 280 TYR 0.014 0.001 TYR C 281 ARG 0.009 0.001 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.89 seconds wall clock time: 49 minutes 32.26 seconds (2972.26 seconds total)