Starting phenix.real_space_refine on Wed Feb 14 10:03:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/02_2024/8iul_35725_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/02_2024/8iul_35725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/02_2024/8iul_35725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/02_2024/8iul_35725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/02_2024/8iul_35725_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/02_2024/8iul_35725_neut_updated.pdb" } resolution = 2.78 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= 0.000 sd= 0.004 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 64 5.16 5 C 5725 2.51 5 N 1551 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "R ARG 308": "NH1" <-> "NH2" 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: 9016 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2342 Unusual residues: {'7WT': 1} Classifications: {'peptide': 293, 'undetermined': 1} Link IDs: {'PTRANS': 5, 'TRANS': 287, None: 1} Not linked: pdbres="CYS R 323 " pdbres="7WT R 401 " Chain breaks: 1 Time building chain proxies: 5.04, per 1000 atoms: 0.56 Number of scatterers: 9016 At special positions: 0 Unit cell: (122.776, 92.288, 128.544, 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 64 16.00 O 1676 8.00 N 1551 7.00 C 5725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 12 sheets defined 36.0% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.625A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.770A pdb=" N GLN A 234 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 299 through 317 Processing helix chain 'A' and resid 336 through 359 removed outlier: 4.175A pdb=" N ALA A 339 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 350 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 356 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 359 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.564A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 29 through 46 removed outlier: 5.261A pdb=" N LYS G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'R' and resid 30 through 60 removed outlier: 3.585A pdb=" N VAL R 39 " --> pdb=" O ILE R 35 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY R 40 " --> pdb=" O PHE R 36 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLN R 60 " --> pdb=" O GLN R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 92 removed outlier: 3.578A pdb=" N GLY R 85 " --> pdb=" O HIS R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 101 No H-bonds generated for 'chain 'R' and resid 98 through 101' Processing helix chain 'R' and resid 107 through 138 removed outlier: 4.470A pdb=" N MET R 115 " --> pdb=" O PHE R 111 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER R 118 " --> pdb=" O CYS R 114 " (cutoff:3.500A) Proline residue: R 122 - end of helix removed outlier: 4.028A pdb=" N GLY R 126 " --> pdb=" O PRO R 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA R 130 " --> pdb=" O GLY R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 149 through 169 Processing helix chain 'R' and resid 171 through 173 No H-bonds generated for 'chain 'R' and resid 171 through 173' Processing helix chain 'R' and resid 196 through 232 Processing helix chain 'R' and resid 244 through 278 removed outlier: 3.587A pdb=" N CYS R 259 " --> pdb=" O MET R 255 " (cutoff:3.500A) Proline residue: R 264 - end of helix removed outlier: 7.220A pdb=" N ASN R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS R 278 " --> pdb=" O ILE R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 295 Processing helix chain 'R' and resid 299 through 303 Processing helix chain 'R' and resid 309 through 322 Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.778A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 34 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.829A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.665A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.810A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.841A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.380A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER B 250 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.497A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.330A 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: 6.312A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 52 through 56 removed outlier: 6.807A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.688A pdb=" N ARG E 17 " --> pdb=" O MET E 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.613A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA E 39 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU E 44 " --> pdb=" O ALA E 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.958A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.566A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1095 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: 2.68 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1481 1.31 - 1.44: 2528 1.44 - 1.56: 5090 1.56 - 1.69: 4 1.69 - 1.81: 92 Bond restraints: 9195 Sorted by residual: bond pdb=" C02 7WT R 401 " pdb=" C06 7WT R 401 " ideal model delta sigma weight residual 1.525 1.339 0.186 2.00e-02 2.50e+03 8.66e+01 bond pdb=" C03 7WT R 401 " pdb=" C04 7WT R 401 " ideal model delta sigma weight residual 1.538 1.372 0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C02 7WT R 401 " pdb=" C03 7WT R 401 " ideal model delta sigma weight residual 1.527 1.662 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" CA VAL R 30 " pdb=" C VAL R 30 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.27e-02 6.20e+03 4.20e+01 bond pdb=" N PHE R 31 " pdb=" CA PHE R 31 " ideal model delta sigma weight residual 1.459 1.399 0.060 1.23e-02 6.61e+03 2.41e+01 ... (remaining 9190 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.24: 128 105.24 - 112.43: 4665 112.43 - 119.62: 3007 119.62 - 126.81: 4517 126.81 - 134.00: 118 Bond angle restraints: 12435 Sorted by residual: angle pdb=" N ILE R 298 " pdb=" CA ILE R 298 " pdb=" C ILE R 298 " ideal model delta sigma weight residual 111.67 98.24 13.43 9.50e-01 1.11e+00 2.00e+02 angle pdb=" N ASN R 296 " pdb=" CA ASN R 296 " pdb=" C ASN R 296 " ideal model delta sigma weight residual 113.97 98.25 15.72 1.28e+00 6.10e-01 1.51e+02 angle pdb=" N PHE R 111 " pdb=" CA PHE R 111 " pdb=" C PHE R 111 " ideal model delta sigma weight residual 112.97 102.86 10.11 1.06e+00 8.90e-01 9.09e+01 angle pdb=" N TYR R 92 " pdb=" CA TYR R 92 " pdb=" C TYR R 92 " ideal model delta sigma weight residual 113.50 103.29 10.21 1.23e+00 6.61e-01 6.89e+01 angle pdb=" N LEU R 290 " pdb=" CA LEU R 290 " pdb=" C LEU R 290 " ideal model delta sigma weight residual 111.36 103.15 8.21 1.09e+00 8.42e-01 5.68e+01 ... (remaining 12430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.41: 5392 25.41 - 50.81: 77 50.81 - 76.22: 14 76.22 - 101.63: 2 101.63 - 127.03: 4 Dihedral angle restraints: 5489 sinusoidal: 2170 harmonic: 3319 Sorted by residual: dihedral pdb=" CD ARG A 209 " pdb=" NE ARG A 209 " pdb=" CZ ARG A 209 " pdb=" NH1 ARG A 209 " ideal model delta sinusoidal sigma weight residual 0.00 86.80 -86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" C LEU R 120 " pdb=" N LEU R 120 " pdb=" CA LEU R 120 " pdb=" CB LEU R 120 " ideal model delta harmonic sigma weight residual -122.60 -133.86 11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CA LEU R 120 " pdb=" CB LEU R 120 " ideal model delta harmonic sigma weight residual 122.80 133.92 -11.12 0 2.50e+00 1.60e-01 1.98e+01 ... (remaining 5486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1335 0.108 - 0.216: 56 0.216 - 0.324: 11 0.324 - 0.432: 6 0.432 - 0.540: 3 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA PRO R 122 " pdb=" N PRO R 122 " pdb=" C PRO R 122 " pdb=" CB PRO R 122 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA CYS R 114 " pdb=" N CYS R 114 " pdb=" C CYS R 114 " pdb=" CB CYS R 114 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 1408 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 209 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 209 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 209 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 209 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 121 " 0.104 5.00e-02 4.00e+02 1.51e-01 3.67e+01 pdb=" N PRO R 122 " -0.261 5.00e-02 4.00e+02 pdb=" CA PRO R 122 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO R 122 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 300 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO R 301 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " 0.059 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 191 2.67 - 3.23: 8901 3.23 - 3.79: 13658 3.79 - 4.34: 19025 4.34 - 4.90: 31683 Nonbonded interactions: 73458 Sorted by model distance: nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.116 2.440 nonbonded pdb=" OD1 ASP A 226 " pdb=" OG SER A 228 " model vdw 2.143 2.440 nonbonded pdb=" OD1 ASN A 216 " pdb=" NZ LYS B 62 " model vdw 2.146 2.520 nonbonded pdb=" ND2 ASN E 169 " pdb=" OD1 ASN E 171 " model vdw 2.190 2.520 nonbonded pdb=" O ALA A 318 " pdb=" OG SER A 319 " model vdw 2.238 2.440 ... (remaining 73453 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 4.180 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.580 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.006 0.186 9195 Z= 0.381 Angle : 0.659 15.725 12435 Z= 0.433 Chirality : 0.058 0.540 1411 Planarity : 0.014 0.492 1572 Dihedral : 9.740 127.032 3342 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.61 % Allowed : 4.48 % Favored : 94.91 % Cbeta Deviations : 0.09 % 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: -1.10 (0.24), residues: 1129 helix: 0.07 (0.25), residues: 418 sheet: -0.53 (0.30), residues: 257 loop : -1.51 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 302 HIS 0.004 0.000 HIS R 81 PHE 0.011 0.001 PHE R 117 TYR 0.005 0.000 TYR R 92 ARG 0.002 0.000 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 317 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7006 (m-40) cc_final: 0.6643 (m-40) REVERT: A 227 SER cc_start: 0.7758 (p) cc_final: 0.7519 (p) REVERT: A 298 ASP cc_start: 0.7698 (t0) cc_final: 0.7469 (t0) REVERT: A 310 LYS cc_start: 0.7746 (tptt) cc_final: 0.7331 (tptt) REVERT: A 314 ASP cc_start: 0.6837 (m-30) cc_final: 0.6590 (m-30) REVERT: B 42 ILE cc_start: 0.7703 (tt) cc_final: 0.7459 (pt) REVERT: B 252 ASP cc_start: 0.6133 (t0) cc_final: 0.4766 (t0) REVERT: B 306 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6773 (mmmm) REVERT: E 230 MET cc_start: 0.8471 (ttp) cc_final: 0.8259 (ttt) outliers start: 6 outliers final: 2 residues processed: 321 average time/residue: 1.1041 time to fit residues: 378.8771 Evaluate side-chains 173 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN B 225 GLN B 273 ASN B 298 ASN E 12 GLN E 34 HIS E 142 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 58 ASN R 277 ASN R 297 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9195 Z= 0.175 Angle : 0.524 7.267 12435 Z= 0.273 Chirality : 0.041 0.136 1411 Planarity : 0.005 0.073 1572 Dihedral : 6.317 97.808 1277 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.05 % Allowed : 15.06 % Favored : 81.89 % 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: 0.11 (0.25), residues: 1129 helix: 1.15 (0.26), residues: 413 sheet: 0.07 (0.31), residues: 264 loop : -0.87 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.005 0.001 HIS A 324 PHE 0.021 0.002 PHE R 207 TYR 0.012 0.001 TYR R 92 ARG 0.008 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7127 (mtpt) cc_final: 0.6479 (mmpt) REVERT: A 34 LEU cc_start: 0.7289 (mt) cc_final: 0.7063 (mp) REVERT: A 182 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7682 (p) REVERT: A 276 GLU cc_start: 0.6730 (tp30) cc_final: 0.6377 (tp30) REVERT: A 314 ASP cc_start: 0.7043 (m-30) cc_final: 0.6758 (m-30) REVERT: B 64 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: E 37 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7700 (ptp90) REVERT: E 45 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: E 245 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7202 (mp) outliers start: 30 outliers final: 14 residues processed: 206 average time/residue: 1.0694 time to fit residues: 236.2524 Evaluate side-chains 177 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.1980 chunk 31 optimal weight: 0.0170 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 235 ASN E 142 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN R 151 HIS R 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9195 Z= 0.137 Angle : 0.478 6.822 12435 Z= 0.250 Chirality : 0.040 0.132 1411 Planarity : 0.004 0.073 1572 Dihedral : 6.087 91.748 1274 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.15 % Allowed : 17.50 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.25), residues: 1129 helix: 1.52 (0.26), residues: 413 sheet: 0.42 (0.32), residues: 254 loop : -0.60 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.004 0.001 HIS A 324 PHE 0.024 0.001 PHE R 200 TYR 0.009 0.001 TYR E 58 ARG 0.007 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7138 (mtpt) cc_final: 0.6471 (mmpt) REVERT: A 34 LEU cc_start: 0.7732 (mt) cc_final: 0.7501 (mp) REVERT: A 198 MET cc_start: 0.8395 (ttp) cc_final: 0.8176 (ttt) REVERT: A 276 GLU cc_start: 0.6650 (tp30) cc_final: 0.6391 (tp30) REVERT: A 310 LYS cc_start: 0.7997 (tppt) cc_final: 0.7696 (tppt) REVERT: B 27 ARG cc_start: 0.6230 (ttm170) cc_final: 0.5995 (mtt180) REVERT: B 218 VAL cc_start: 0.8582 (t) cc_final: 0.8375 (t) REVERT: E 37 ARG cc_start: 0.8166 (ptp90) cc_final: 0.7645 (ptp90) REVERT: E 45 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6786 (tt0) outliers start: 31 outliers final: 14 residues processed: 185 average time/residue: 1.2954 time to fit residues: 256.2836 Evaluate side-chains 164 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.0470 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 overall best weight: 2.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN B 225 GLN B 235 ASN B 273 ASN B 298 ASN E 12 GLN E 171 ASN G 58 ASN R 56 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9195 Z= 0.295 Angle : 0.596 7.895 12435 Z= 0.311 Chirality : 0.044 0.185 1411 Planarity : 0.004 0.068 1572 Dihedral : 6.388 104.906 1274 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.07 % Allowed : 17.90 % Favored : 78.03 % 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: 0.69 (0.25), residues: 1129 helix: 1.41 (0.26), residues: 411 sheet: 0.49 (0.32), residues: 253 loop : -0.34 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 35 HIS 0.008 0.002 HIS B 188 PHE 0.024 0.002 PHE R 207 TYR 0.017 0.002 TYR E 190 ARG 0.009 0.001 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 1.086 Fit side-chains REVERT: A 182 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7615 (p) REVERT: A 247 ARG cc_start: 0.7731 (ptm160) cc_final: 0.7314 (ttt180) REVERT: A 250 ARG cc_start: 0.7771 (ptp-110) cc_final: 0.7453 (ptp-170) REVERT: A 256 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7895 (tt) REVERT: B 27 ARG cc_start: 0.6328 (ttm170) cc_final: 0.6057 (mtt180) REVERT: B 143 GLU cc_start: 0.7982 (tt0) cc_final: 0.7765 (tt0) REVERT: E 45 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6978 (tt0) REVERT: E 77 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8096 (m) outliers start: 40 outliers final: 17 residues processed: 174 average time/residue: 1.3132 time to fit residues: 242.5642 Evaluate side-chains 154 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.0270 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 93 ASN B 235 ASN B 273 ASN G 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9195 Z= 0.156 Angle : 0.504 7.996 12435 Z= 0.265 Chirality : 0.040 0.166 1411 Planarity : 0.004 0.061 1572 Dihedral : 5.980 97.784 1274 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.54 % Allowed : 20.35 % Favored : 77.11 % 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: 0.93 (0.25), residues: 1129 helix: 1.66 (0.26), residues: 413 sheet: 0.56 (0.32), residues: 260 loop : -0.24 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.005 0.001 HIS B 188 PHE 0.023 0.001 PHE R 207 TYR 0.009 0.001 TYR E 190 ARG 0.011 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.023 Fit side-chains REVERT: A 247 ARG cc_start: 0.7698 (ptm160) cc_final: 0.7234 (ttt180) REVERT: A 250 ARG cc_start: 0.7684 (ptp-110) cc_final: 0.7468 (ptp-170) REVERT: A 256 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7941 (tt) REVERT: A 310 LYS cc_start: 0.8078 (tppt) cc_final: 0.7852 (tppt) REVERT: B 27 ARG cc_start: 0.6306 (ttm170) cc_final: 0.6068 (mtt180) REVERT: B 280 SER cc_start: 0.8663 (m) cc_final: 0.8352 (m) outliers start: 25 outliers final: 14 residues processed: 161 average time/residue: 1.2473 time to fit residues: 213.7946 Evaluate side-chains 143 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 105 optimal weight: 0.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS B 93 ASN B 264 GLN B 273 ASN R 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9195 Z= 0.154 Angle : 0.507 8.882 12435 Z= 0.263 Chirality : 0.040 0.165 1411 Planarity : 0.004 0.057 1572 Dihedral : 5.768 97.172 1274 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.85 % Allowed : 20.24 % Favored : 76.91 % 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: 1.05 (0.25), residues: 1129 helix: 1.77 (0.26), residues: 414 sheet: 0.59 (0.32), residues: 262 loop : -0.16 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 PHE 0.023 0.001 PHE R 207 TYR 0.010 0.001 TYR E 190 ARG 0.011 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8276 (mmmt) REVERT: A 247 ARG cc_start: 0.7700 (ptm160) cc_final: 0.7235 (ttt180) REVERT: A 250 ARG cc_start: 0.7661 (ptp-110) cc_final: 0.7456 (ptp-170) REVERT: A 256 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7944 (tt) REVERT: B 49 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7615 (mm-40) REVERT: B 280 SER cc_start: 0.8667 (m) cc_final: 0.8357 (m) REVERT: G 45 LYS cc_start: 0.8440 (mppt) cc_final: 0.8170 (pttt) outliers start: 28 outliers final: 15 residues processed: 153 average time/residue: 1.3388 time to fit residues: 217.5793 Evaluate side-chains 145 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 0.0010 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 181 GLN B 264 GLN R 271 ASN R 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9195 Z= 0.188 Angle : 0.523 8.696 12435 Z= 0.271 Chirality : 0.041 0.175 1411 Planarity : 0.004 0.054 1572 Dihedral : 5.769 97.512 1274 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.15 % Allowed : 21.16 % Favored : 75.69 % 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: 1.04 (0.25), residues: 1129 helix: 1.76 (0.26), residues: 416 sheet: 0.61 (0.32), residues: 260 loop : -0.18 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 PHE 0.025 0.001 PHE R 207 TYR 0.012 0.001 TYR E 190 ARG 0.010 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.043 Fit side-chains REVERT: A 247 ARG cc_start: 0.7718 (ptm160) cc_final: 0.7330 (ttt180) REVERT: A 256 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7966 (tt) REVERT: B 139 ARG cc_start: 0.7698 (ptm160) cc_final: 0.7374 (ptm160) REVERT: B 280 SER cc_start: 0.8639 (m) cc_final: 0.8334 (m) REVERT: E 45 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: E 75 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7565 (mtmm) REVERT: E 234 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6397 (mt-10) REVERT: G 45 LYS cc_start: 0.8500 (mppt) cc_final: 0.8229 (pttt) outliers start: 31 outliers final: 22 residues processed: 154 average time/residue: 1.3075 time to fit residues: 214.5963 Evaluate side-chains 151 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN R 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9195 Z= 0.231 Angle : 0.547 9.144 12435 Z= 0.284 Chirality : 0.042 0.179 1411 Planarity : 0.004 0.052 1572 Dihedral : 5.851 95.227 1274 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.46 % Allowed : 21.36 % Favored : 75.18 % 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: 0.98 (0.25), residues: 1129 helix: 1.71 (0.26), residues: 416 sheet: 0.49 (0.32), residues: 262 loop : -0.15 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.007 0.001 HIS B 188 PHE 0.030 0.002 PHE E 67 TYR 0.014 0.001 TYR E 190 ARG 0.010 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.739 Fit side-chains REVERT: A 247 ARG cc_start: 0.7741 (ptm160) cc_final: 0.7302 (ttt180) REVERT: A 256 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7975 (tt) REVERT: B 139 ARG cc_start: 0.7655 (ptm160) cc_final: 0.7390 (ptm160) REVERT: B 280 SER cc_start: 0.8624 (m) cc_final: 0.8309 (m) REVERT: E 45 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: E 183 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7351 (mm-40) REVERT: E 234 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: G 45 LYS cc_start: 0.8550 (mppt) cc_final: 0.8272 (pttt) outliers start: 34 outliers final: 24 residues processed: 157 average time/residue: 1.4235 time to fit residues: 239.2297 Evaluate side-chains 156 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER 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: 0.0000 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 273 ASN ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9195 Z= 0.153 Angle : 0.512 9.398 12435 Z= 0.265 Chirality : 0.040 0.172 1411 Planarity : 0.004 0.051 1572 Dihedral : 5.682 90.406 1274 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.75 % Allowed : 22.18 % Favored : 75.08 % 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: 1.12 (0.25), residues: 1129 helix: 1.84 (0.26), residues: 417 sheet: 0.63 (0.32), residues: 256 loop : -0.16 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.005 0.001 HIS B 188 PHE 0.024 0.001 PHE R 207 TYR 0.009 0.001 TYR E 190 ARG 0.009 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.087 Fit side-chains REVERT: A 182 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7548 (p) REVERT: A 247 ARG cc_start: 0.7706 (ptm160) cc_final: 0.7302 (ttt180) REVERT: A 256 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7899 (tt) REVERT: A 314 ASP cc_start: 0.7334 (m-30) cc_final: 0.7086 (m-30) REVERT: B 280 SER cc_start: 0.8591 (m) cc_final: 0.8284 (m) REVERT: E 45 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: E 183 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7239 (mm-40) REVERT: E 234 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6398 (mt-10) REVERT: G 45 LYS cc_start: 0.8545 (mppt) cc_final: 0.8276 (pttt) outliers start: 27 outliers final: 16 residues processed: 155 average time/residue: 1.2141 time to fit residues: 201.0817 Evaluate side-chains 148 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.0470 chunk 74 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN R 105 ASN ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9195 Z= 0.158 Angle : 0.523 9.673 12435 Z= 0.272 Chirality : 0.041 0.172 1411 Planarity : 0.004 0.051 1572 Dihedral : 5.349 74.990 1274 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.44 % Allowed : 22.99 % Favored : 74.57 % 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: 1.16 (0.25), residues: 1129 helix: 1.81 (0.26), residues: 422 sheet: 0.67 (0.32), residues: 256 loop : -0.08 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 176 HIS 0.005 0.001 HIS B 188 PHE 0.026 0.001 PHE R 207 TYR 0.009 0.001 TYR E 190 ARG 0.005 0.000 ARG A 323 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.970 Fit side-chains REVERT: A 182 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 247 ARG cc_start: 0.7700 (ptm160) cc_final: 0.7299 (ttt180) REVERT: A 256 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7905 (tt) REVERT: B 139 ARG cc_start: 0.7575 (ptm160) cc_final: 0.7305 (mtm110) REVERT: B 280 SER cc_start: 0.8560 (m) cc_final: 0.8244 (m) REVERT: E 183 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7133 (mm-40) REVERT: E 234 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6352 (mt-10) REVERT: G 45 LYS cc_start: 0.8539 (mppt) cc_final: 0.8272 (pttt) outliers start: 24 outliers final: 15 residues processed: 149 average time/residue: 1.2336 time to fit residues: 196.1563 Evaluate side-chains 144 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 264 GLN B 273 ASN ** R 271 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 = 0.3966 r_free = 0.3966 target = 0.160708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123860 restraints weight = 10280.104| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.16 r_work: 0.3398 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9195 Z= 0.186 Angle : 0.541 10.150 12435 Z= 0.278 Chirality : 0.041 0.177 1411 Planarity : 0.004 0.050 1572 Dihedral : 5.161 47.680 1274 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.34 % Allowed : 23.09 % Favored : 74.57 % 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: 1.12 (0.25), residues: 1129 helix: 1.80 (0.26), residues: 419 sheet: 0.62 (0.32), residues: 256 loop : -0.11 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 PHE 0.026 0.001 PHE R 207 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG E 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4272.91 seconds wall clock time: 76 minutes 41.05 seconds (4601.05 seconds total)