Starting phenix.real_space_refine on Tue Nov 14 16:32:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/11_2023/8iul_35725_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/11_2023/8iul_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_35725/11_2023/8iul_35725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/11_2023/8iul_35725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/11_2023/8iul_35725_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iul_35725/11_2023/8iul_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-1.21rc1-5144/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: 5.20, per 1000 atoms: 0.58 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: 3.62 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: 1.78 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: 2.52 Time building geometry restraints manager: 3.90 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 - 21.62: 5337 21.62 - 43.25: 102 43.25 - 64.87: 19 64.87 - 86.50: 5 86.50 - 108.12: 2 Dihedral angle restraints: 5465 sinusoidal: 2146 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 5462 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.110 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.930 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.930 ------------------------------------------------------------------------------- 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 : 9.077 108.122 3318 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 *********************** 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 : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 321 average time/residue: 1.0638 time to fit residues: 365.7376 Evaluate side-chains 170 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.3865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 29 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7335 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 0.027 9195 Z= 0.172 Angle : 0.533 7.244 12435 Z= 0.276 Chirality : 0.041 0.142 1411 Planarity : 0.005 0.072 1572 Dihedral : 5.052 83.569 1250 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.36 % Allowed : 15.26 % Favored : 81.38 % 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: 0.15 (0.25), residues: 1129 helix: 1.15 (0.26), residues: 413 sheet: 0.13 (0.31), residues: 262 loop : -0.83 (0.28), residues: 454 *********************** 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 228 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 209 average time/residue: 1.1124 time to fit residues: 249.4115 Evaluate side-chains 168 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.1643 time to fit residues: 3.1428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 111 optimal weight: 0.0670 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 93 ASN B 235 ASN B 273 ASN E 142 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN R 314 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9195 Z= 0.259 Angle : 0.578 6.785 12435 Z= 0.303 Chirality : 0.044 0.201 1411 Planarity : 0.005 0.075 1572 Dihedral : 5.331 79.153 1250 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.07 % Allowed : 16.79 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1129 helix: 1.32 (0.26), residues: 410 sheet: 0.28 (0.31), residues: 263 loop : -0.49 (0.29), residues: 456 *********************** 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 205 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 187 average time/residue: 1.2177 time to fit residues: 242.7764 Evaluate side-chains 156 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.3428 time to fit residues: 3.3982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 0.0970 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 80 GLN B 93 ASN B 181 GLN B 225 GLN B 273 ASN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9195 Z= 0.162 Angle : 0.502 7.628 12435 Z= 0.264 Chirality : 0.040 0.137 1411 Planarity : 0.004 0.064 1572 Dihedral : 4.859 68.051 1250 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.26 % Allowed : 18.82 % Favored : 77.92 % 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: 0.78 (0.25), residues: 1129 helix: 1.56 (0.26), residues: 412 sheet: 0.50 (0.32), residues: 259 loop : -0.37 (0.28), residues: 458 *********************** 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 185 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 175 average time/residue: 1.1604 time to fit residues: 217.3910 Evaluate side-chains 164 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.1217 time to fit residues: 2.0991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN B 93 ASN B 225 GLN B 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9195 Z= 0.279 Angle : 0.566 8.036 12435 Z= 0.299 Chirality : 0.043 0.167 1411 Planarity : 0.004 0.060 1572 Dihedral : 5.042 61.123 1250 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.37 % Allowed : 17.60 % 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: 0.72 (0.25), residues: 1129 helix: 1.48 (0.26), residues: 410 sheet: 0.46 (0.32), residues: 252 loop : -0.34 (0.28), residues: 467 *********************** 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 186 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 0.979 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 27 residues processed: 173 average time/residue: 1.2344 time to fit residues: 228.2509 Evaluate side-chains 156 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.2132 time to fit residues: 2.6154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 329 HIS B 273 ASN R 151 HIS R 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4946 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 8.565 12435 Z= 0.266 Chirality : 0.040 0.137 1411 Planarity : 0.004 0.054 1572 Dihedral : 4.665 55.540 1250 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.17 % Allowed : 19.43 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1129 helix: 1.61 (0.26), residues: 419 sheet: 0.48 (0.32), residues: 260 loop : -0.23 (0.29), residues: 450 *********************** 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 188 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 175 average time/residue: 1.2358 time to fit residues: 231.7771 Evaluate side-chains 157 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.1309 time to fit residues: 2.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN R 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9195 Z= 0.148 Angle : 0.502 8.962 12435 Z= 0.263 Chirality : 0.040 0.135 1411 Planarity : 0.004 0.053 1572 Dihedral : 4.310 48.489 1250 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.36 % Allowed : 20.14 % Favored : 76.50 % 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: 1.08 (0.25), residues: 1129 helix: 1.75 (0.26), residues: 419 sheet: 0.64 (0.32), residues: 258 loop : -0.13 (0.29), residues: 452 *********************** 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 175 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.035 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 168 average time/residue: 1.2708 time to fit residues: 227.8318 Evaluate side-chains 153 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 0.4903 time to fit residues: 3.7266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9195 Z= 0.158 Angle : 0.514 9.212 12435 Z= 0.266 Chirality : 0.040 0.136 1411 Planarity : 0.004 0.048 1572 Dihedral : 4.103 34.239 1250 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.36 % Allowed : 20.96 % 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: 1.12 (0.25), residues: 1129 helix: 1.75 (0.26), residues: 420 sheet: 0.66 (0.33), residues: 260 loop : -0.09 (0.29), residues: 449 *********************** 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 170 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.101 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 160 average time/residue: 1.2590 time to fit residues: 215.4663 Evaluate side-chains 154 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.1007 time to fit residues: 2.3516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9195 Z= 0.147 Angle : 0.511 9.442 12435 Z= 0.264 Chirality : 0.040 0.140 1411 Planarity : 0.004 0.053 1572 Dihedral : 3.959 28.454 1250 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.85 % Allowed : 21.26 % Favored : 75.89 % 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: 1.18 (0.25), residues: 1129 helix: 1.77 (0.26), residues: 421 sheet: 0.79 (0.33), residues: 257 loop : -0.10 (0.29), residues: 451 *********************** 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 171 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.061 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 164 average time/residue: 1.1697 time to fit residues: 205.6100 Evaluate side-chains 154 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.4886 time to fit residues: 3.7259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9195 Z= 0.180 Angle : 0.528 9.411 12435 Z= 0.275 Chirality : 0.041 0.137 1411 Planarity : 0.004 0.046 1572 Dihedral : 4.039 28.100 1250 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.44 % Allowed : 22.58 % Favored : 74.97 % 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: 1.17 (0.25), residues: 1129 helix: 1.80 (0.26), residues: 421 sheet: 0.74 (0.32), residues: 258 loop : -0.10 (0.29), residues: 450 ********************** 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 156 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.961 Fit side-chains outliers start: 24 outliers final: 21 residues processed: 152 average time/residue: 1.2467 time to fit residues: 202.3254 Evaluate side-chains 147 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.1317 time to fit residues: 1.8683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 273 ASN ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.158141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120883 restraints weight = 10327.379| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.17 r_work: 0.3368 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9195 Z= 0.186 Angle : 0.530 8.950 12435 Z= 0.276 Chirality : 0.042 0.206 1411 Planarity : 0.004 0.046 1572 Dihedral : 4.120 29.693 1250 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.75 % Allowed : 22.08 % 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: 1.15 (0.25), residues: 1129 helix: 1.78 (0.26), residues: 421 sheet: 0.69 (0.32), residues: 260 loop : -0.08 (0.29), residues: 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4145.28 seconds wall clock time: 74 minutes 10.09 seconds (4450.09 seconds total)