Starting phenix.real_space_refine on Thu May 15 04:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnc_27563/05_2025/8dnc_27563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnc_27563/05_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_27563/05_2025/8dnc_27563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnc_27563/05_2025/8dnc_27563.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnc_27563/05_2025/8dnc_27563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnc_27563/05_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-5687/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: 6.80, per 1000 atoms: 0.64 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: 2.81 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: 1.23 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: 3.57 Time building geometry restraints manager: 3.25 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: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.260 Find NCS groups from input model: 0.370 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- 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 : 1.309 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: 0.2182 time to fit residues: 65.8347 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 : 1.112 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.184974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140334 restraints weight = 14319.658| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.41 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: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10953 Z= 0.116 Angle : 0.592 10.558 14824 Z= 0.298 Chirality : 0.043 0.163 1663 Planarity : 0.004 0.035 1815 Dihedral : 5.348 93.530 1467 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.22 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 0.017 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 0.04190 ( 490) hydrogen bonds : angle 4.79234 ( 1419) glycosidic custom : bond 0.00166 ( 2) glycosidic custom : angle 1.32362 ( 6) covalent geometry : bond 0.00257 (10951) covalent geometry : angle 0.59114 (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 : 1.194 Fit side-chains REVERT: A 19 ASP cc_start: 0.8184 (t0) cc_final: 0.7319 (m-30) REVERT: A 118 ILE cc_start: 0.8139 (mm) cc_final: 0.7782 (mt) REVERT: A 119 ASP cc_start: 0.7767 (m-30) cc_final: 0.7540 (m-30) REVERT: A 129 SER cc_start: 0.8313 (t) cc_final: 0.8036 (p) REVERT: A 285 ASP cc_start: 0.7046 (m-30) cc_final: 0.6792 (t0) REVERT: A 322 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6818 (mp0) REVERT: C 23 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6661 (tt0) REVERT: C 146 MET cc_start: 0.5324 (mtp) cc_final: 0.3892 (tpt) REVERT: C 205 LYS cc_start: 0.8735 (ptpp) cc_final: 0.7892 (mmmm) REVERT: C 330 PHE cc_start: 0.7636 (m-10) cc_final: 0.7341 (m-80) REVERT: C 353 MET cc_start: 0.5767 (ptp) cc_final: 0.5273 (ptm) REVERT: D 12 GLN cc_start: 0.7639 (mp10) cc_final: 0.7240 (mp10) outliers start: 14 outliers final: 8 residues processed: 186 average time/residue: 0.2101 time to fit residues: 56.3778 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 : 1.283 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 108 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.186664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150250 restraints weight = 14670.743| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.67 r_work: 0.3448 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10953 Z= 0.114 Angle : 0.569 8.998 14824 Z= 0.284 Chirality : 0.042 0.215 1663 Planarity : 0.003 0.030 1815 Dihedral : 5.161 87.610 1467 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.90 % Allowed : 11.12 % Favored : 86.98 % 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: -0.64 (0.24), residues: 1292 helix: 0.75 (0.22), residues: 619 sheet: -0.83 (0.38), residues: 205 loop : -1.80 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 26 HIS 0.004 0.001 HIS C 355 PHE 0.028 0.001 PHE B 92 TYR 0.021 0.001 TYR C 252 ARG 0.005 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 490) hydrogen bonds : angle 4.55822 ( 1419) glycosidic custom : bond 0.00189 ( 2) glycosidic custom : angle 1.19941 ( 6) covalent geometry : bond 0.00259 (10951) covalent geometry : angle 0.56889 (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 190 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.254 Fit side-chains REVERT: A 19 ASP cc_start: 0.8229 (t0) cc_final: 0.7300 (m-30) REVERT: A 118 ILE cc_start: 0.8166 (mm) cc_final: 0.7842 (mt) REVERT: A 119 ASP cc_start: 0.7895 (m-30) cc_final: 0.7688 (m-30) REVERT: A 129 SER cc_start: 0.8297 (t) cc_final: 0.8048 (p) REVERT: A 285 ASP cc_start: 0.7080 (m-30) cc_final: 0.6704 (t0) REVERT: B 23 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7380 (tt) REVERT: B 26 TRP cc_start: 0.8356 (t60) cc_final: 0.7960 (t-100) REVERT: B 221 ASP cc_start: 0.8097 (p0) cc_final: 0.7839 (p0) REVERT: C 23 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6571 (tt0) REVERT: C 205 LYS cc_start: 0.8752 (ptpp) cc_final: 0.7971 (mmmm) REVERT: C 260 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7519 (mmtt) REVERT: C 353 MET cc_start: 0.5653 (ptp) cc_final: 0.5256 (ptm) REVERT: D 17 ARG cc_start: 0.7116 (mtm110) cc_final: 0.6910 (mtm110) outliers start: 22 outliers final: 11 residues processed: 181 average time/residue: 0.2113 time to fit residues: 55.5592 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 : 1.325 ------------------------------------------------------------------------------- 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: 0.0980 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.182122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145214 restraints weight = 14397.693| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.93 r_work: 0.3345 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10953 Z= 0.179 Angle : 0.606 9.424 14824 Z= 0.304 Chirality : 0.044 0.156 1663 Planarity : 0.004 0.033 1815 Dihedral : 5.355 90.638 1467 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.81 % Allowed : 13.53 % Favored : 84.66 % 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: -0.74 (0.24), residues: 1292 helix: 0.65 (0.22), residues: 619 sheet: -0.67 (0.41), residues: 191 loop : -1.90 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 26 HIS 0.005 0.001 HIS A 355 PHE 0.025 0.002 PHE B 92 TYR 0.024 0.002 TYR D 63 ARG 0.006 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 490) hydrogen bonds : angle 4.54603 ( 1419) glycosidic custom : bond 0.00369 ( 2) glycosidic custom : angle 1.42355 ( 6) covalent geometry : bond 0.00438 (10951) covalent geometry : angle 0.60586 (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 184 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.321 Fit side-chains REVERT: A 19 ASP cc_start: 0.8267 (t0) cc_final: 0.7369 (m-30) REVERT: A 285 ASP cc_start: 0.7310 (m-30) cc_final: 0.6995 (t0) REVERT: B 23 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7744 (tt) REVERT: B 26 TRP cc_start: 0.8437 (t60) cc_final: 0.8203 (t-100) REVERT: B 118 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7666 (tp) REVERT: B 205 MET cc_start: 0.8248 (mmm) cc_final: 0.7932 (mmm) REVERT: B 221 ASP cc_start: 0.8121 (p0) cc_final: 0.7824 (p0) REVERT: C 23 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6609 (tt0) REVERT: C 139 LEU cc_start: 0.6905 (tt) cc_final: 0.6627 (tt) REVERT: C 205 LYS cc_start: 0.8738 (ptpp) cc_final: 0.8136 (mmmm) REVERT: C 250 ASN cc_start: 0.7291 (m-40) cc_final: 0.6921 (m110) REVERT: C 330 PHE cc_start: 0.7750 (m-10) cc_final: 0.7465 (m-80) REVERT: C 353 MET cc_start: 0.5812 (ptp) cc_final: 0.5461 (ptm) REVERT: D 3 LEU cc_start: 0.7724 (tt) cc_final: 0.7508 (tt) REVERT: D 17 ARG cc_start: 0.7422 (mtm110) cc_final: 0.7187 (mtm110) outliers start: 21 outliers final: 14 residues processed: 175 average time/residue: 0.2200 time to fit residues: 55.6848 Evaluate side-chains 165 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 23 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 56 ASN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 321 VAL 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: 10.0000 chunk 30 optimal weight: 0.2980 chunk 66 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.182895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144912 restraints weight = 14465.232| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.58 r_work: 0.3383 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1774 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= 0.128 Angle : 0.566 9.709 14824 Z= 0.284 Chirality : 0.042 0.155 1663 Planarity : 0.003 0.032 1815 Dihedral : 5.224 88.297 1467 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.50 % Allowed : 13.97 % Favored : 83.53 % 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: -0.63 (0.24), residues: 1292 helix: 0.78 (0.22), residues: 619 sheet: -0.74 (0.40), residues: 196 loop : -1.85 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 181 HIS 0.004 0.001 HIS C 355 PHE 0.026 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 0.03972 ( 490) hydrogen bonds : angle 4.44396 ( 1419) glycosidic custom : bond 0.00185 ( 2) glycosidic custom : angle 1.12212 ( 6) covalent geometry : bond 0.00302 (10951) covalent geometry : angle 0.56524 (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 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.252 Fit side-chains REVERT: A 19 ASP cc_start: 0.8318 (t0) cc_final: 0.7441 (m-30) REVERT: A 30 PHE cc_start: 0.7561 (m-10) cc_final: 0.7151 (m-10) REVERT: A 104 ILE cc_start: 0.8946 (mt) cc_final: 0.8633 (mt) REVERT: A 285 ASP cc_start: 0.7237 (m-30) cc_final: 0.6854 (t0) REVERT: B 23 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7746 (tt) REVERT: B 68 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8724 (tt) REVERT: B 118 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7670 (tp) REVERT: B 205 MET cc_start: 0.8138 (mmm) cc_final: 0.7826 (mmm) REVERT: B 221 ASP cc_start: 0.8058 (p0) cc_final: 0.7781 (p0) REVERT: C 23 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6614 (tt0) REVERT: C 205 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8166 (mmmm) REVERT: C 250 ASN cc_start: 0.7144 (m-40) cc_final: 0.6750 (m110) REVERT: C 260 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7507 (mmtt) REVERT: C 360 TYR cc_start: 0.7604 (m-80) cc_final: 0.7208 (m-80) REVERT: D 3 LEU cc_start: 0.7689 (tt) cc_final: 0.7477 (tt) REVERT: D 12 GLN cc_start: 0.7616 (mp10) cc_final: 0.7340 (mp10) REVERT: D 17 ARG cc_start: 0.7425 (mtm110) cc_final: 0.7167 (mtm110) REVERT: D 87 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7288 (tp30) REVERT: D 224 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8402 (tt) outliers start: 29 outliers final: 17 residues processed: 177 average time/residue: 0.2163 time to fit residues: 55.7145 Evaluate side-chains 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 23 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 53 VAL 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 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: 3.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.183724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145947 restraints weight = 14505.597| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.56 r_work: 0.3373 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10953 Z= 0.132 Angle : 0.583 11.255 14824 Z= 0.291 Chirality : 0.043 0.304 1663 Planarity : 0.003 0.033 1815 Dihedral : 5.152 85.557 1467 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.16 % Allowed : 15.60 % Favored : 82.24 % 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: -0.57 (0.24), residues: 1292 helix: 0.83 (0.22), residues: 619 sheet: -0.67 (0.41), residues: 192 loop : -1.84 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 181 HIS 0.003 0.001 HIS C 355 PHE 0.024 0.001 PHE B 92 TYR 0.019 0.001 TYR C 252 ARG 0.007 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 490) hydrogen bonds : angle 4.40747 ( 1419) glycosidic custom : bond 0.00201 ( 2) glycosidic custom : angle 1.12894 ( 6) covalent geometry : bond 0.00314 (10951) covalent geometry : angle 0.58232 (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 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.156 Fit side-chains REVERT: A 19 ASP cc_start: 0.8316 (t0) cc_final: 0.7414 (m-30) REVERT: A 30 PHE cc_start: 0.7551 (m-10) cc_final: 0.7180 (m-10) REVERT: A 285 ASP cc_start: 0.7194 (m-30) cc_final: 0.6868 (t0) REVERT: B 23 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7707 (tt) REVERT: B 68 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8719 (tt) REVERT: B 118 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7652 (tp) REVERT: B 205 MET cc_start: 0.8125 (mmm) cc_final: 0.7809 (mmm) REVERT: B 221 ASP cc_start: 0.8016 (p0) cc_final: 0.7739 (p0) REVERT: C 23 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6557 (tt0) REVERT: C 90 LEU cc_start: 0.4765 (mt) cc_final: 0.3918 (pp) REVERT: C 205 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8248 (mttt) REVERT: C 250 ASN cc_start: 0.7157 (m-40) cc_final: 0.6760 (m110) REVERT: C 260 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7681 (mmmt) REVERT: C 360 TYR cc_start: 0.7703 (m-80) cc_final: 0.7225 (m-80) REVERT: D 3 LEU cc_start: 0.7697 (tt) cc_final: 0.7481 (tt) REVERT: D 17 ARG cc_start: 0.7417 (mtm110) cc_final: 0.7125 (mtm110) REVERT: D 224 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8420 (tt) outliers start: 25 outliers final: 18 residues processed: 170 average time/residue: 0.2114 time to fit residues: 51.9684 Evaluate side-chains 169 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 23 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 53 VAL Chi-restraints excluded: chain C residue 56 ASN 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 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: 7.9990 chunk 82 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.181248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145036 restraints weight = 14487.617| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.55 r_work: 0.3380 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10953 Z= 0.154 Angle : 0.596 9.982 14824 Z= 0.297 Chirality : 0.043 0.209 1663 Planarity : 0.003 0.033 1815 Dihedral : 5.236 86.900 1467 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.33 % Allowed : 16.38 % Favored : 81.29 % 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: -0.58 (0.24), residues: 1292 helix: 0.80 (0.22), residues: 619 sheet: -0.64 (0.41), residues: 192 loop : -1.83 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 26 HIS 0.003 0.001 HIS A 187 PHE 0.023 0.001 PHE B 92 TYR 0.018 0.001 TYR C 252 ARG 0.008 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 490) hydrogen bonds : angle 4.41464 ( 1419) glycosidic custom : bond 0.00262 ( 2) glycosidic custom : angle 1.17255 ( 6) covalent geometry : bond 0.00372 (10951) covalent geometry : angle 0.59543 (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 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8278 (t0) cc_final: 0.7385 (m-30) REVERT: A 30 PHE cc_start: 0.7619 (m-10) cc_final: 0.7238 (m-10) REVERT: A 104 ILE cc_start: 0.8872 (mt) cc_final: 0.8576 (mt) REVERT: A 146 MET cc_start: 0.5832 (ptt) cc_final: 0.5576 (ptt) REVERT: A 285 ASP cc_start: 0.7194 (m-30) cc_final: 0.6856 (t0) REVERT: B 68 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8727 (tt) REVERT: B 118 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7670 (tp) REVERT: B 205 MET cc_start: 0.8148 (mmm) cc_final: 0.7812 (mmm) REVERT: B 221 ASP cc_start: 0.8002 (p0) cc_final: 0.7704 (p0) REVERT: C 23 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6533 (tt0) REVERT: C 90 LEU cc_start: 0.4739 (mt) cc_final: 0.3796 (pp) REVERT: C 205 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8322 (mttt) REVERT: C 250 ASN cc_start: 0.7297 (m-40) cc_final: 0.7035 (m110) REVERT: C 260 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7637 (mmmt) REVERT: C 360 TYR cc_start: 0.7756 (m-80) cc_final: 0.7293 (m-80) REVERT: D 3 LEU cc_start: 0.7705 (tt) cc_final: 0.7482 (tt) REVERT: D 12 GLN cc_start: 0.7547 (mp10) cc_final: 0.7220 (mp10) REVERT: D 17 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7325 (mtm110) REVERT: D 224 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8415 (tt) outliers start: 27 outliers final: 21 residues processed: 174 average time/residue: 0.2184 time to fit residues: 54.2866 Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 123 GLU Chi-restraints excluded: chain C residue 295 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 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: 0.8980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 0.4980 chunk 36 optimal weight: 0.2980 chunk 66 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.183325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145643 restraints weight = 14430.493| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.49 r_work: 0.3399 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2046 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= 0.121 Angle : 0.575 10.383 14824 Z= 0.288 Chirality : 0.042 0.149 1663 Planarity : 0.003 0.037 1815 Dihedral : 5.037 80.579 1467 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.98 % Allowed : 17.41 % Favored : 80.60 % 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: -0.43 (0.24), residues: 1292 helix: 0.96 (0.22), residues: 619 sheet: -0.62 (0.41), residues: 191 loop : -1.79 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.022 0.001 PHE B 92 TYR 0.018 0.001 TYR C 252 ARG 0.008 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 490) hydrogen bonds : angle 4.32664 ( 1419) glycosidic custom : bond 0.00131 ( 2) glycosidic custom : angle 0.97644 ( 6) covalent geometry : bond 0.00283 (10951) covalent geometry : angle 0.57522 (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 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8299 (t0) cc_final: 0.7434 (m-30) REVERT: A 30 PHE cc_start: 0.7516 (m-10) cc_final: 0.7183 (m-10) REVERT: A 104 ILE cc_start: 0.8867 (mt) cc_final: 0.8560 (mt) REVERT: A 285 ASP cc_start: 0.7043 (m-30) cc_final: 0.6823 (t0) REVERT: B 11 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7512 (mtm110) REVERT: B 68 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8688 (tt) REVERT: B 118 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7566 (tp) REVERT: B 177 GLN cc_start: 0.8858 (mp10) cc_final: 0.8573 (mt0) REVERT: B 205 MET cc_start: 0.8120 (mmm) cc_final: 0.7774 (mmm) REVERT: C 23 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6652 (tt0) REVERT: C 90 LEU cc_start: 0.4850 (mt) cc_final: 0.4126 (pp) REVERT: C 131 LEU cc_start: 0.4208 (mt) cc_final: 0.3791 (mt) REVERT: C 201 MET cc_start: 0.5246 (ptp) cc_final: 0.4282 (ptp) REVERT: C 205 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8373 (mttt) REVERT: C 249 GLN cc_start: 0.7282 (mp10) cc_final: 0.6950 (mp10) REVERT: C 260 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7660 (mmmt) REVERT: C 330 PHE cc_start: 0.7697 (m-10) cc_final: 0.7437 (m-80) REVERT: C 360 TYR cc_start: 0.7734 (m-80) cc_final: 0.7278 (m-80) REVERT: D 3 LEU cc_start: 0.7678 (tt) cc_final: 0.7459 (tt) REVERT: D 17 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7270 (mtm110) REVERT: D 58 TYR cc_start: 0.7649 (m-80) cc_final: 0.7447 (m-80) REVERT: D 224 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8404 (tt) outliers start: 23 outliers final: 19 residues processed: 171 average time/residue: 0.1995 time to fit residues: 49.5707 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 : 1.149 ------------------------------------------------------------------------------- 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 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 317 MET Chi-restraints excluded: chain C residue 361 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145060 restraints weight = 14632.980| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.65 r_work: 0.3389 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10953 Z= 0.133 Angle : 0.584 10.157 14824 Z= 0.293 Chirality : 0.043 0.157 1663 Planarity : 0.003 0.033 1815 Dihedral : 5.007 75.283 1467 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.24 % Allowed : 17.33 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1292 helix: 0.97 (0.22), residues: 619 sheet: -0.63 (0.41), residues: 191 loop : -1.76 (0.27), residues: 482 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 0.029 0.001 PHE D 92 TYR 0.027 0.001 TYR C 252 ARG 0.007 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 490) hydrogen bonds : angle 4.33895 ( 1419) glycosidic custom : bond 0.00190 ( 2) glycosidic custom : angle 1.04693 ( 6) covalent geometry : bond 0.00316 (10951) covalent geometry : angle 0.58337 (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 184 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8288 (t0) cc_final: 0.7429 (m-30) REVERT: A 30 PHE cc_start: 0.7546 (m-10) cc_final: 0.7115 (m-10) REVERT: A 104 ILE cc_start: 0.8863 (mt) cc_final: 0.8558 (mt) REVERT: A 146 MET cc_start: 0.5740 (ptt) cc_final: 0.5469 (ptt) REVERT: A 285 ASP cc_start: 0.6952 (m-30) cc_final: 0.6731 (t0) REVERT: B 68 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8680 (tt) REVERT: B 118 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7614 (tp) REVERT: B 205 MET cc_start: 0.8128 (mmm) cc_final: 0.7790 (mmm) REVERT: C 16 LYS cc_start: 0.6352 (pttt) cc_final: 0.6141 (pttt) REVERT: C 23 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6601 (tt0) REVERT: C 90 LEU cc_start: 0.4863 (mt) cc_final: 0.4084 (pp) REVERT: C 131 LEU cc_start: 0.4242 (mt) cc_final: 0.3866 (mt) REVERT: C 201 MET cc_start: 0.5270 (ptp) cc_final: 0.4356 (ptp) REVERT: C 205 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8299 (mmmm) REVERT: C 260 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7659 (mmmt) REVERT: C 330 PHE cc_start: 0.7650 (m-10) cc_final: 0.7418 (m-80) REVERT: C 360 TYR cc_start: 0.7734 (m-80) cc_final: 0.7252 (m-80) REVERT: D 3 LEU cc_start: 0.7684 (tt) cc_final: 0.7473 (tt) REVERT: D 12 GLN cc_start: 0.7582 (mp10) cc_final: 0.7321 (mp10) REVERT: D 17 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7273 (mtm110) REVERT: D 58 TYR cc_start: 0.7694 (m-80) cc_final: 0.7480 (m-80) REVERT: D 224 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8441 (tt) outliers start: 26 outliers final: 19 residues processed: 172 average time/residue: 0.2205 time to fit residues: 55.0576 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 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 317 MET Chi-restraints excluded: chain C residue 361 HIS 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: 7.9990 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.180945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142766 restraints weight = 14495.188| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.64 r_work: 0.3341 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10953 Z= 0.192 Angle : 0.636 10.861 14824 Z= 0.321 Chirality : 0.045 0.147 1663 Planarity : 0.004 0.034 1815 Dihedral : 5.291 79.191 1467 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.07 % Allowed : 18.02 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.24), residues: 1292 helix: 0.60 (0.22), residues: 631 sheet: -0.68 (0.40), residues: 192 loop : -1.85 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 26 HIS 0.004 0.001 HIS A 187 PHE 0.023 0.002 PHE D 92 TYR 0.026 0.001 TYR C 252 ARG 0.010 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 490) hydrogen bonds : angle 4.47439 ( 1419) glycosidic custom : bond 0.00334 ( 2) glycosidic custom : angle 1.27085 ( 6) covalent geometry : bond 0.00469 (10951) covalent geometry : angle 0.63596 (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 183 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8321 (t0) cc_final: 0.7463 (m-30) REVERT: A 30 PHE cc_start: 0.7738 (m-10) cc_final: 0.7254 (m-10) REVERT: A 104 ILE cc_start: 0.8908 (mt) cc_final: 0.8600 (mt) REVERT: A 146 MET cc_start: 0.6235 (ptt) cc_final: 0.5995 (ptt) REVERT: A 285 ASP cc_start: 0.7046 (m-30) cc_final: 0.6832 (t0) REVERT: B 11 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7496 (mtm110) REVERT: B 68 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 118 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7693 (tp) REVERT: B 205 MET cc_start: 0.8169 (mmm) cc_final: 0.7808 (mmm) REVERT: C 23 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6549 (tt0) REVERT: C 90 LEU cc_start: 0.5076 (mt) cc_final: 0.4221 (pp) REVERT: C 201 MET cc_start: 0.5283 (ptp) cc_final: 0.4255 (ptp) REVERT: C 205 LYS cc_start: 0.8740 (ptpp) cc_final: 0.8391 (mttt) REVERT: C 360 TYR cc_start: 0.7819 (m-80) cc_final: 0.7282 (m-80) REVERT: D 3 LEU cc_start: 0.7682 (tt) cc_final: 0.7456 (tt) REVERT: D 12 GLN cc_start: 0.7627 (mp10) cc_final: 0.7239 (mp10) REVERT: D 17 ARG cc_start: 0.7641 (mtm110) cc_final: 0.7347 (mtm110) outliers start: 24 outliers final: 19 residues processed: 173 average time/residue: 0.2092 time to fit residues: 52.6199 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 286 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 317 MET Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.183837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145992 restraints weight = 14489.514| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.49 r_work: 0.3391 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10953 Z= 0.128 Angle : 0.600 10.640 14824 Z= 0.302 Chirality : 0.043 0.148 1663 Planarity : 0.003 0.032 1815 Dihedral : 5.020 71.566 1467 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.81 % Allowed : 18.79 % Favored : 79.40 % 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: -0.56 (0.24), residues: 1292 helix: 0.79 (0.22), residues: 631 sheet: -0.72 (0.40), residues: 191 loop : -1.80 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.025 0.001 PHE B 175 TYR 0.026 0.001 TYR C 252 ARG 0.008 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 490) hydrogen bonds : angle 4.37378 ( 1419) glycosidic custom : bond 0.00140 ( 2) glycosidic custom : angle 0.96733 ( 6) covalent geometry : bond 0.00307 (10951) covalent geometry : angle 0.59996 (14818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4826.39 seconds wall clock time: 84 minutes 39.92 seconds (5079.92 seconds total)