Starting phenix.real_space_refine on Wed Jul 30 19:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnc_27563/07_2025/8dnc_27563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnc_27563/07_2025/8dnc_27563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnc_27563/07_2025/8dnc_27563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnc_27563/07_2025/8dnc_27563.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnc_27563/07_2025/8dnc_27563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnc_27563/07_2025/8dnc_27563.cif" } resolution = 3.3 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= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2340 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 7099 2.51 5 N 1671 2.21 5 O 1867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'UBH': 1, 'UBO': 1, 'XXR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.27, per 1000 atoms: 0.68 Number of scatterers: 10672 At special positions: 0 Unit cell: (91.8, 100.44, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 2 15.00 Mg 1 11.99 O 1867 8.00 N 1671 7.00 C 7099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ?1-2 " XXR E 1 " - " UBO E 2 " ?1-3 " UBO E 2 " - " UBH E 3 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 13 sheets defined 51.8% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 removed outlier: 4.186A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.888A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.561A pdb=" N ASN A 136 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.558A pdb=" N THR A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.892A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.878A pdb=" N VAL A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 190 removed outlier: 3.746A pdb=" N GLN A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.683A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 20 through 26 Processing helix chain 'B' and resid 30 through 48 removed outlier: 3.853A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 80 removed outlier: 3.672A pdb=" N TYR B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.779A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.690A pdb=" N ILE B 134 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.612A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.560A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.654A pdb=" N THR B 183 " --> pdb=" O PHE B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.730A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 192 " --> pdb=" O LEU B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 192' Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 223 through 254 Proline residue: B 235 - end of helix removed outlier: 4.665A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 114 through 130 removed outlier: 5.056A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.577A pdb=" N THR C 141 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 167 through 171 removed outlier: 4.202A pdb=" N ALA C 170 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 173 through 191 removed outlier: 3.573A pdb=" N GLN C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 4.242A pdb=" N LYS C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 207' Processing helix chain 'C' and resid 224 through 240 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 22 through 43 removed outlier: 3.729A pdb=" N TRP D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.722A pdb=" N LEU D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.741A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 80 through 88 removed outlier: 4.455A pdb=" N PHE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N THR D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.075A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 101 through 129 removed outlier: 4.362A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 139 through 165 removed outlier: 4.184A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 removed outlier: 3.969A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.760A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 226 through 254 Proline residue: D 235 - end of helix removed outlier: 4.806A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 4.316A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.771A pdb=" N GLU A 32 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.340A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLU A 48 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE A 196 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A 221 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS A 215 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 265 removed outlier: 5.516A pdb=" N ILE A 259 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU A 287 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU A 261 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 390 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 333 " --> pdb=" O GLU C 388 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 276 removed outlier: 6.149A pdb=" N PHE A 274 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY A 373 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 345 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS A 367 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR A 343 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE A 369 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 341 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA A 297 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A 313 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 299 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 311 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 301 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA7, first strand: chain 'A' and resid 380 through 381 removed outlier: 6.777A pdb=" N ILE C 301 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY C 311 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 299 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN C 313 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 297 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 392 removed outlier: 3.804A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 392 removed outlier: 3.804A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'C' and resid 84 through 86 removed outlier: 3.687A pdb=" N VAL C 85 " --> pdb=" O CYS C 162 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 195 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 341 through 342 499 hydrogen bonds defined for protein. 1419 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: 3.08 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3196 1.34 - 1.46: 2700 1.46 - 1.58: 5000 1.58 - 1.70: 3 1.70 - 1.82: 52 Bond restraints: 10951 Sorted by residual: bond pdb=" N PRO D 103 " pdb=" CD PRO D 103 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" N GLY C 326 " pdb=" CA GLY C 326 " ideal model delta sigma weight residual 1.447 1.475 -0.028 9.20e-03 1.18e+04 9.24e+00 bond pdb=" N LYS C 325 " pdb=" CA LYS C 325 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.28e-02 6.10e+03 7.37e+00 bond pdb=" N LYS C 327 " pdb=" CA LYS C 327 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.22e-02 6.72e+03 6.17e+00 bond pdb=" C5 UBH E 3 " pdb=" O5 UBH E 3 " ideal model delta sigma weight residual 1.438 1.396 0.042 2.00e-02 2.50e+03 4.34e+00 ... (remaining 10946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14563 2.09 - 4.18: 211 4.18 - 6.27: 33 6.27 - 8.36: 10 8.36 - 10.46: 1 Bond angle restraints: 14818 Sorted by residual: angle pdb=" C LEU B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta sigma weight residual 122.38 115.50 6.88 1.81e+00 3.05e-01 1.44e+01 angle pdb=" CA GLY C 326 " pdb=" C GLY C 326 " pdb=" O GLY C 326 " ideal model delta sigma weight residual 121.48 118.50 2.98 9.90e-01 1.02e+00 9.07e+00 angle pdb=" CB ARG B 11 " pdb=" CG ARG B 11 " pdb=" CD ARG B 11 " ideal model delta sigma weight residual 111.30 118.18 -6.88 2.30e+00 1.89e-01 8.95e+00 angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 126.76 -10.46 3.50e+00 8.16e-02 8.92e+00 angle pdb=" CG ARG B 11 " pdb=" CD ARG B 11 " pdb=" NE ARG B 11 " ideal model delta sigma weight residual 112.00 118.54 -6.54 2.20e+00 2.07e-01 8.83e+00 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.91: 5856 19.91 - 39.81: 506 39.81 - 59.72: 62 59.72 - 79.62: 10 79.62 - 99.53: 7 Dihedral angle restraints: 6441 sinusoidal: 2661 harmonic: 3780 Sorted by residual: dihedral pdb=" O1B ADP A 502 " pdb=" O3A ADP A 502 " pdb=" PB ADP A 502 " pdb=" PA ADP A 502 " ideal model delta sinusoidal sigma weight residual -60.00 -159.53 99.53 1 2.00e+01 2.50e-03 2.80e+01 dihedral pdb=" CA TRP B 26 " pdb=" C TRP B 26 " pdb=" N TRP B 27 " pdb=" CA TRP B 27 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LEU C 87 " pdb=" C LEU C 87 " pdb=" N LEU C 88 " pdb=" CA LEU C 88 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 6438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 966 0.031 - 0.061: 461 0.061 - 0.092: 147 0.092 - 0.122: 74 0.122 - 0.153: 15 Chirality restraints: 1663 Sorted by residual: chirality pdb=" CG LEU A 64 " pdb=" CB LEU A 64 " pdb=" CD1 LEU A 64 " pdb=" CD2 LEU A 64 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ASP C 354 " pdb=" N ASP C 354 " pdb=" C ASP C 354 " pdb=" CB ASP C 354 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA PHE A 134 " pdb=" N PHE A 134 " pdb=" C PHE A 134 " pdb=" CB PHE A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1660 not shown) Planarity restraints: 1815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 362 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C TRP C 362 " 0.033 2.00e-02 2.50e+03 pdb=" O TRP C 362 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE C 363 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 102 " 0.032 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO D 103 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 324 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C LYS C 324 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS C 324 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS C 325 " 0.010 2.00e-02 2.50e+03 ... (remaining 1812 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 70 2.57 - 3.15: 8647 3.15 - 3.74: 15996 3.74 - 4.32: 21911 4.32 - 4.90: 37776 Nonbonded interactions: 84400 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O2B ADP A 502 " model vdw 1.989 2.170 nonbonded pdb=" O LYS B 89 " pdb=" OG1 THR B 93 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR B 60 " pdb=" O VAL B 186 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 331 " pdb=" OD1 ASN C 390 " model vdw 2.244 3.040 nonbonded pdb=" O SER A 99 " pdb=" ND2 ASN A 103 " model vdw 2.247 3.120 ... (remaining 84395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 395) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 27.730 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.004 0.057 10953 Z= 0.174 Angle : 0.655 10.455 14824 Z= 0.347 Chirality : 0.043 0.153 1663 Planarity : 0.004 0.047 1815 Dihedral : 14.468 99.531 4025 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.24), residues: 1292 helix: 0.46 (0.22), residues: 616 sheet: -0.93 (0.40), residues: 186 loop : -1.96 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 26 HIS 0.006 0.001 HIS C 361 PHE 0.023 0.002 PHE D 126 TYR 0.019 0.001 TYR A 315 ARG 0.018 0.001 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.15673 ( 490) hydrogen bonds : angle 6.07800 ( 1419) glycosidic custom : bond 0.04038 ( 2) glycosidic custom : angle 1.82970 ( 6) covalent geometry : bond 0.00366 (10951) covalent geometry : angle 0.65392 (14818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.380 Fit side-chains REVERT: C 23 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6773 (tt0) REVERT: C 146 MET cc_start: 0.5387 (mtp) cc_final: 0.4041 (tpt) REVERT: C 261 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6339 (mm-30) REVERT: D 110 GLU cc_start: 0.6758 (tp30) cc_final: 0.6463 (tp30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2247 time to fit residues: 67.6531 Evaluate side-chains 158 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 0.0670 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.185065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140404 restraints weight = 14329.488| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.42 r_work: 0.3491 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10953 Z= 0.116 Angle : 0.591 10.567 14824 Z= 0.298 Chirality : 0.043 0.163 1663 Planarity : 0.004 0.035 1815 Dihedral : 5.347 93.502 1467 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.21 % Allowed : 8.45 % Favored : 90.34 % 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: -0.71 (0.24), residues: 1292 helix: 0.70 (0.22), residues: 617 sheet: -0.96 (0.39), residues: 197 loop : -1.77 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 26 HIS 0.005 0.001 HIS C 355 PHE 0.031 0.001 PHE B 92 TYR 0.020 0.001 TYR C 252 ARG 0.004 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 490) hydrogen bonds : angle 4.79080 ( 1419) glycosidic custom : bond 0.00151 ( 2) glycosidic custom : angle 1.32127 ( 6) covalent geometry : bond 0.00256 (10951) covalent geometry : angle 0.59101 (14818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.283 Fit side-chains REVERT: A 19 ASP cc_start: 0.8190 (t0) cc_final: 0.7325 (m-30) REVERT: A 118 ILE cc_start: 0.8139 (mm) cc_final: 0.7781 (mt) REVERT: A 119 ASP cc_start: 0.7764 (m-30) cc_final: 0.7537 (m-30) REVERT: A 129 SER cc_start: 0.8313 (t) cc_final: 0.8034 (p) REVERT: A 285 ASP cc_start: 0.7045 (m-30) cc_final: 0.6796 (t0) REVERT: C 23 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6661 (tt0) REVERT: C 146 MET cc_start: 0.5319 (mtp) cc_final: 0.3890 (tpt) REVERT: C 205 LYS cc_start: 0.8734 (ptpp) cc_final: 0.7895 (mmmm) REVERT: C 330 PHE cc_start: 0.7637 (m-10) cc_final: 0.7339 (m-80) REVERT: C 353 MET cc_start: 0.5769 (ptp) cc_final: 0.5277 (ptm) REVERT: D 12 GLN cc_start: 0.7641 (mp10) cc_final: 0.7243 (mp10) outliers start: 14 outliers final: 8 residues processed: 186 average time/residue: 0.2594 time to fit residues: 69.1825 Evaluate side-chains 166 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 378 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 0.0270 chunk 108 optimal weight: 0.1980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN C 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.187104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149753 restraints weight = 14658.590| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.75 r_work: 0.3449 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10953 Z= 0.112 Angle : 0.572 9.256 14824 Z= 0.284 Chirality : 0.042 0.246 1663 Planarity : 0.003 0.030 1815 Dihedral : 5.123 86.575 1467 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.98 % Allowed : 11.29 % Favored : 86.72 % 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: -0.60 (0.24), residues: 1292 helix: 0.79 (0.22), residues: 619 sheet: -0.82 (0.38), residues: 205 loop : -1.79 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 26 HIS 0.004 0.001 HIS C 355 PHE 0.028 0.001 PHE B 92 TYR 0.020 0.001 TYR C 252 ARG 0.005 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 490) hydrogen bonds : angle 4.54162 ( 1419) glycosidic custom : bond 0.00163 ( 2) glycosidic custom : angle 1.16017 ( 6) covalent geometry : bond 0.00255 (10951) covalent geometry : angle 0.57171 (14818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8224 (t0) cc_final: 0.7297 (m-30) REVERT: A 118 ILE cc_start: 0.8163 (mm) cc_final: 0.7840 (mt) REVERT: A 119 ASP cc_start: 0.7902 (m-30) cc_final: 0.7690 (m-30) REVERT: A 129 SER cc_start: 0.8285 (t) cc_final: 0.8042 (p) REVERT: A 285 ASP cc_start: 0.7086 (m-30) cc_final: 0.6709 (t0) REVERT: B 23 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7389 (tt) REVERT: B 26 TRP cc_start: 0.8385 (t60) cc_final: 0.8010 (t-100) REVERT: B 221 ASP cc_start: 0.8101 (p0) cc_final: 0.7827 (p0) REVERT: C 23 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6574 (tt0) REVERT: C 205 LYS cc_start: 0.8749 (ptpp) cc_final: 0.7972 (mmmm) REVERT: C 353 MET cc_start: 0.5624 (ptp) cc_final: 0.5224 (ptm) REVERT: D 17 ARG cc_start: 0.7111 (mtm110) cc_final: 0.6903 (mtm110) outliers start: 23 outliers final: 11 residues processed: 184 average time/residue: 0.2147 time to fit residues: 57.2726 Evaluate side-chains 167 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 GLN C 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.186477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.149289 restraints weight = 14471.592| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.65 r_work: 0.3422 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10953 Z= 0.116 Angle : 0.558 9.273 14824 Z= 0.277 Chirality : 0.042 0.158 1663 Planarity : 0.003 0.031 1815 Dihedral : 4.961 79.071 1467 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.64 % Allowed : 13.28 % Favored : 85.09 % 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 (0.24), residues: 1292 helix: 0.90 (0.22), residues: 619 sheet: -0.67 (0.39), residues: 208 loop : -1.78 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 26 HIS 0.004 0.001 HIS C 355 PHE 0.025 0.001 PHE B 92 TYR 0.017 0.001 TYR C 252 ARG 0.005 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 490) hydrogen bonds : angle 4.38643 ( 1419) glycosidic custom : bond 0.00179 ( 2) glycosidic custom : angle 1.11142 ( 6) covalent geometry : bond 0.00273 (10951) covalent geometry : angle 0.55752 (14818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.382 Fit side-chains REVERT: A 19 ASP cc_start: 0.8238 (t0) cc_final: 0.7353 (m-30) REVERT: A 30 PHE cc_start: 0.7450 (m-10) cc_final: 0.7106 (m-10) REVERT: A 118 ILE cc_start: 0.8202 (mm) cc_final: 0.7882 (mt) REVERT: A 119 ASP cc_start: 0.7869 (m-30) cc_final: 0.7668 (m-30) REVERT: A 129 SER cc_start: 0.8274 (t) cc_final: 0.8037 (p) REVERT: A 285 ASP cc_start: 0.7200 (m-30) cc_final: 0.6850 (t0) REVERT: B 26 TRP cc_start: 0.8389 (t60) cc_final: 0.8169 (t-100) REVERT: B 118 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7577 (tp) REVERT: B 205 MET cc_start: 0.8127 (mmm) cc_final: 0.7837 (mmm) REVERT: B 221 ASP cc_start: 0.7976 (p0) cc_final: 0.7675 (p0) REVERT: C 23 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6586 (tt0) REVERT: C 205 LYS cc_start: 0.8723 (ptpp) cc_final: 0.8138 (mmmm) REVERT: C 250 ASN cc_start: 0.7240 (m-40) cc_final: 0.6831 (m110) REVERT: C 260 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7503 (mmtt) REVERT: D 17 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6946 (mtm110) outliers start: 19 outliers final: 12 residues processed: 178 average time/residue: 0.2682 time to fit residues: 71.8805 Evaluate side-chains 164 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 0.0470 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 5 optimal weight: 0.0020 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 overall best weight: 0.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.194113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156013 restraints weight = 14422.932| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.25 r_work: 0.3552 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10953 Z= 0.100 Angle : 0.542 9.782 14824 Z= 0.270 Chirality : 0.041 0.159 1663 Planarity : 0.003 0.030 1815 Dihedral : 4.634 62.507 1467 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.98 % Allowed : 14.22 % Favored : 83.79 % 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: -0.31 (0.24), residues: 1292 helix: 1.07 (0.22), residues: 618 sheet: -0.53 (0.39), residues: 199 loop : -1.77 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 181 HIS 0.003 0.001 HIS C 355 PHE 0.025 0.001 PHE B 92 TYR 0.022 0.001 TYR C 252 ARG 0.006 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 490) hydrogen bonds : angle 4.28931 ( 1419) glycosidic custom : bond 0.00082 ( 2) glycosidic custom : angle 0.89341 ( 6) covalent geometry : bond 0.00218 (10951) covalent geometry : angle 0.54147 (14818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.306 Fit side-chains REVERT: A 19 ASP cc_start: 0.8160 (t0) cc_final: 0.7397 (m-30) REVERT: A 30 PHE cc_start: 0.7232 (m-10) cc_final: 0.6949 (m-10) REVERT: A 104 ILE cc_start: 0.8896 (mt) cc_final: 0.8547 (mt) REVERT: A 118 ILE cc_start: 0.8255 (mm) cc_final: 0.7968 (mt) REVERT: A 285 ASP cc_start: 0.7023 (m-30) cc_final: 0.6770 (t0) REVERT: B 171 ILE cc_start: 0.8852 (mt) cc_final: 0.8616 (mm) REVERT: B 205 MET cc_start: 0.8010 (mmm) cc_final: 0.7718 (mmm) REVERT: B 221 ASP cc_start: 0.7827 (p0) cc_final: 0.7571 (p0) REVERT: C 23 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6643 (tt0) REVERT: C 87 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.4970 (tt) REVERT: C 90 LEU cc_start: 0.4897 (mt) cc_final: 0.4155 (pp) REVERT: C 139 LEU cc_start: 0.6869 (tt) cc_final: 0.6602 (tt) REVERT: C 205 LYS cc_start: 0.8738 (ptpp) cc_final: 0.8215 (mttt) REVERT: D 17 ARG cc_start: 0.7271 (mtm110) cc_final: 0.6967 (mtm110) REVERT: D 224 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8119 (tt) outliers start: 23 outliers final: 15 residues processed: 182 average time/residue: 0.2373 time to fit residues: 62.2091 Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 0.0980 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 GLN C 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144889 restraints weight = 14573.176| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.64 r_work: 0.3369 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10953 Z= 0.173 Angle : 0.607 10.605 14824 Z= 0.302 Chirality : 0.044 0.285 1663 Planarity : 0.003 0.032 1815 Dihedral : 4.797 57.104 1467 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.33 % Allowed : 14.83 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1292 helix: 0.89 (0.22), residues: 619 sheet: -0.56 (0.40), residues: 203 loop : -1.80 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 26 HIS 0.004 0.001 HIS A 355 PHE 0.024 0.002 PHE B 92 TYR 0.025 0.001 TYR D 63 ARG 0.006 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 490) hydrogen bonds : angle 4.37614 ( 1419) glycosidic custom : bond 0.00307 ( 2) glycosidic custom : angle 1.28646 ( 6) covalent geometry : bond 0.00422 (10951) covalent geometry : angle 0.60636 (14818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8306 (t0) cc_final: 0.7404 (m-30) REVERT: A 30 PHE cc_start: 0.7574 (m-10) cc_final: 0.7134 (m-10) REVERT: A 285 ASP cc_start: 0.7084 (m-30) cc_final: 0.6845 (t0) REVERT: B 118 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7607 (tp) REVERT: B 205 MET cc_start: 0.8167 (mmm) cc_final: 0.7834 (mmm) REVERT: B 221 ASP cc_start: 0.7988 (p0) cc_final: 0.7682 (p0) REVERT: C 23 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6537 (tt0) REVERT: C 90 LEU cc_start: 0.5013 (mt) cc_final: 0.4140 (pp) REVERT: C 139 LEU cc_start: 0.6915 (tt) cc_final: 0.6684 (tt) REVERT: C 201 MET cc_start: 0.5246 (ptp) cc_final: 0.4231 (ptp) REVERT: C 205 LYS cc_start: 0.8721 (ptpp) cc_final: 0.8275 (mttt) REVERT: C 250 ASN cc_start: 0.7206 (m-40) cc_final: 0.6760 (m110) REVERT: C 260 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7663 (mmmt) REVERT: D 3 LEU cc_start: 0.7727 (tt) cc_final: 0.7520 (tt) REVERT: D 17 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7246 (mtm110) REVERT: D 224 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8374 (tt) outliers start: 27 outliers final: 19 residues processed: 174 average time/residue: 0.2503 time to fit residues: 63.0133 Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 79 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.190664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152930 restraints weight = 14743.266| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.65 r_work: 0.3501 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10953 Z= 0.127 Angle : 0.576 10.425 14824 Z= 0.287 Chirality : 0.043 0.263 1663 Planarity : 0.003 0.032 1815 Dihedral : 4.638 46.622 1467 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.98 % Allowed : 15.95 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1292 helix: 0.98 (0.22), residues: 619 sheet: -0.64 (0.39), residues: 208 loop : -1.77 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.023 0.001 PHE B 92 TYR 0.018 0.001 TYR C 252 ARG 0.007 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 490) hydrogen bonds : angle 4.33211 ( 1419) glycosidic custom : bond 0.00185 ( 2) glycosidic custom : angle 1.01727 ( 6) covalent geometry : bond 0.00302 (10951) covalent geometry : angle 0.57625 (14818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.306 Fit side-chains REVERT: A 19 ASP cc_start: 0.8176 (t0) cc_final: 0.7438 (m-30) REVERT: A 30 PHE cc_start: 0.7429 (m-10) cc_final: 0.7099 (m-10) REVERT: A 104 ILE cc_start: 0.8931 (mt) cc_final: 0.8608 (mt) REVERT: A 146 MET cc_start: 0.5830 (ptt) cc_final: 0.5563 (ptt) REVERT: A 285 ASP cc_start: 0.7007 (m-30) cc_final: 0.6729 (t0) REVERT: B 118 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7646 (tp) REVERT: B 205 MET cc_start: 0.8113 (mmm) cc_final: 0.7775 (mmm) REVERT: B 221 ASP cc_start: 0.7856 (p0) cc_final: 0.7562 (p0) REVERT: C 23 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6554 (tt0) REVERT: C 90 LEU cc_start: 0.4819 (mt) cc_final: 0.4022 (pp) REVERT: C 139 LEU cc_start: 0.6893 (tt) cc_final: 0.6666 (tt) REVERT: C 201 MET cc_start: 0.5196 (ptp) cc_final: 0.4239 (ptp) REVERT: C 205 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8311 (mttt) REVERT: C 249 GLN cc_start: 0.7274 (mp10) cc_final: 0.7018 (mp10) REVERT: C 260 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7635 (mmmt) REVERT: C 330 PHE cc_start: 0.7643 (m-10) cc_final: 0.7433 (m-80) REVERT: D 3 LEU cc_start: 0.7712 (tt) cc_final: 0.7488 (tt) REVERT: D 12 GLN cc_start: 0.7628 (mp10) cc_final: 0.7391 (mp10) REVERT: D 17 ARG cc_start: 0.7580 (mtm110) cc_final: 0.7275 (mtm110) REVERT: D 224 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8247 (tt) outliers start: 23 outliers final: 19 residues processed: 169 average time/residue: 0.2156 time to fit residues: 52.6657 Evaluate side-chains 172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN B 12 GLN C 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.185174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147725 restraints weight = 14543.685| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.72 r_work: 0.3417 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10953 Z= 0.127 Angle : 0.572 10.559 14824 Z= 0.286 Chirality : 0.042 0.171 1663 Planarity : 0.003 0.032 1815 Dihedral : 4.534 35.203 1467 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.07 % Allowed : 16.21 % Favored : 81.72 % 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: -0.36 (0.24), residues: 1292 helix: 1.01 (0.22), residues: 619 sheet: -0.61 (0.39), residues: 208 loop : -1.74 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.022 0.001 PHE B 92 TYR 0.026 0.001 TYR C 252 ARG 0.008 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 490) hydrogen bonds : angle 4.29523 ( 1419) glycosidic custom : bond 0.00177 ( 2) glycosidic custom : angle 1.03590 ( 6) covalent geometry : bond 0.00301 (10951) covalent geometry : angle 0.57124 (14818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.155 Fit side-chains REVERT: A 19 ASP cc_start: 0.8235 (t0) cc_final: 0.7369 (m-30) REVERT: A 30 PHE cc_start: 0.7477 (m-10) cc_final: 0.7050 (m-10) REVERT: A 104 ILE cc_start: 0.8837 (mt) cc_final: 0.8528 (mt) REVERT: B 68 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8705 (tt) REVERT: B 118 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7619 (tp) REVERT: B 205 MET cc_start: 0.8173 (mmm) cc_final: 0.7816 (mmm) REVERT: B 221 ASP cc_start: 0.7998 (p0) cc_final: 0.7644 (p0) REVERT: C 23 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6544 (tt0) REVERT: C 90 LEU cc_start: 0.4961 (mt) cc_final: 0.4156 (pp) REVERT: C 139 LEU cc_start: 0.6929 (tt) cc_final: 0.6707 (tt) REVERT: C 201 MET cc_start: 0.5255 (ptp) cc_final: 0.4274 (ptp) REVERT: C 205 LYS cc_start: 0.8748 (ptpp) cc_final: 0.8357 (mttt) REVERT: C 249 GLN cc_start: 0.7294 (mp10) cc_final: 0.6963 (mp10) REVERT: C 260 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7590 (mmmt) REVERT: C 330 PHE cc_start: 0.7621 (m-10) cc_final: 0.7419 (m-80) REVERT: D 3 LEU cc_start: 0.7683 (tt) cc_final: 0.7455 (tt) REVERT: D 12 GLN cc_start: 0.7592 (mp10) cc_final: 0.7310 (mp10) REVERT: D 17 ARG cc_start: 0.7587 (mtm110) cc_final: 0.7270 (mtm110) REVERT: D 224 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8307 (tt) outliers start: 24 outliers final: 18 residues processed: 176 average time/residue: 0.2159 time to fit residues: 55.2799 Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN B 12 GLN C 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.190866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152350 restraints weight = 14622.982| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.38 r_work: 0.3510 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10953 Z= 0.127 Angle : 0.586 10.768 14824 Z= 0.292 Chirality : 0.042 0.149 1663 Planarity : 0.003 0.032 1815 Dihedral : 4.451 33.725 1467 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.98 % Allowed : 16.81 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1292 helix: 1.05 (0.22), residues: 619 sheet: -0.60 (0.39), residues: 208 loop : -1.73 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.030 0.001 PHE D 92 TYR 0.025 0.001 TYR C 252 ARG 0.009 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 490) hydrogen bonds : angle 4.26590 ( 1419) glycosidic custom : bond 0.00166 ( 2) glycosidic custom : angle 0.99549 ( 6) covalent geometry : bond 0.00304 (10951) covalent geometry : angle 0.58535 (14818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8243 (t0) cc_final: 0.7528 (m-30) REVERT: A 30 PHE cc_start: 0.7406 (m-10) cc_final: 0.7134 (m-10) REVERT: A 104 ILE cc_start: 0.8889 (mt) cc_final: 0.8558 (mt) REVERT: A 146 MET cc_start: 0.5736 (ptt) cc_final: 0.5491 (ptt) REVERT: B 11 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7406 (mtm110) REVERT: B 68 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8664 (tt) REVERT: B 118 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7604 (tp) REVERT: B 177 GLN cc_start: 0.8865 (mp10) cc_final: 0.8609 (mt0) REVERT: B 205 MET cc_start: 0.8090 (mmm) cc_final: 0.7759 (mmm) REVERT: C 23 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6621 (tt0) REVERT: C 90 LEU cc_start: 0.4914 (mt) cc_final: 0.4160 (pp) REVERT: C 201 MET cc_start: 0.5215 (ptp) cc_final: 0.4357 (ptp) REVERT: C 205 LYS cc_start: 0.8741 (ptpp) cc_final: 0.8290 (mmmm) REVERT: C 260 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7625 (mmmt) REVERT: C 330 PHE cc_start: 0.7664 (m-10) cc_final: 0.7433 (m-80) REVERT: D 3 LEU cc_start: 0.7704 (tt) cc_final: 0.7478 (tt) REVERT: D 12 GLN cc_start: 0.7730 (mp10) cc_final: 0.7444 (mp10) REVERT: D 17 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7321 (mtm110) REVERT: D 224 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8265 (tt) outliers start: 23 outliers final: 19 residues processed: 171 average time/residue: 0.2074 time to fit residues: 51.7844 Evaluate side-chains 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 82 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN B 12 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.180895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142590 restraints weight = 14552.571| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.66 r_work: 0.3338 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 10953 Z= 0.212 Angle : 0.642 10.414 14824 Z= 0.324 Chirality : 0.045 0.148 1663 Planarity : 0.004 0.033 1815 Dihedral : 4.802 38.893 1467 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.16 % Allowed : 16.81 % Favored : 81.03 % 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: -0.56 (0.24), residues: 1292 helix: 0.76 (0.22), residues: 619 sheet: -0.59 (0.39), residues: 203 loop : -1.77 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 26 HIS 0.004 0.001 HIS A 187 PHE 0.023 0.002 PHE B 92 TYR 0.026 0.002 TYR D 63 ARG 0.008 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 490) hydrogen bonds : angle 4.43926 ( 1419) glycosidic custom : bond 0.00393 ( 2) glycosidic custom : angle 1.36321 ( 6) covalent geometry : bond 0.00522 (10951) covalent geometry : angle 0.64196 (14818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8378 (t0) cc_final: 0.7547 (m-30) REVERT: A 30 PHE cc_start: 0.7698 (m-10) cc_final: 0.7317 (m-10) REVERT: A 104 ILE cc_start: 0.8836 (mt) cc_final: 0.8529 (mt) REVERT: A 133 ASP cc_start: 0.8827 (p0) cc_final: 0.8624 (p0) REVERT: A 146 MET cc_start: 0.6379 (ptt) cc_final: 0.6152 (ptt) REVERT: B 68 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B 118 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7729 (tp) REVERT: B 205 MET cc_start: 0.8210 (mmm) cc_final: 0.7837 (mmm) REVERT: C 23 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6545 (tt0) REVERT: C 201 MET cc_start: 0.5336 (ptp) cc_final: 0.4392 (ptp) REVERT: C 205 LYS cc_start: 0.8734 (ptpp) cc_final: 0.8311 (mmmm) REVERT: D 3 LEU cc_start: 0.7706 (tt) cc_final: 0.7487 (tt) REVERT: D 17 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7322 (mtm110) REVERT: D 124 ILE cc_start: 0.8020 (mm) cc_final: 0.7812 (mt) outliers start: 25 outliers final: 20 residues processed: 176 average time/residue: 0.2285 time to fit residues: 57.6226 Evaluate side-chains 176 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN C 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.189415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150759 restraints weight = 14470.142| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.49 r_work: 0.3492 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10953 Z= 0.136 Angle : 0.605 10.509 14824 Z= 0.303 Chirality : 0.043 0.147 1663 Planarity : 0.003 0.032 1815 Dihedral : 4.582 35.278 1467 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.81 % Allowed : 17.84 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1292 helix: 0.92 (0.22), residues: 619 sheet: -0.62 (0.39), residues: 202 loop : -1.72 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.024 0.001 PHE B 175 TYR 0.024 0.001 TYR C 252 ARG 0.009 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 490) hydrogen bonds : angle 4.35930 ( 1419) glycosidic custom : bond 0.00174 ( 2) glycosidic custom : angle 1.01809 ( 6) covalent geometry : bond 0.00324 (10951) covalent geometry : angle 0.60480 (14818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5471.94 seconds wall clock time: 98 minutes 9.56 seconds (5889.56 seconds total)