Starting phenix.real_space_refine on Mon Dec 30 08:44:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnc_27563/12_2024/8dnc_27563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnc_27563/12_2024/8dnc_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_27563/12_2024/8dnc_27563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnc_27563/12_2024/8dnc_27563.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnc_27563/12_2024/8dnc_27563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnc_27563/12_2024/8dnc_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-5532/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: 6.52, per 1000 atoms: 0.61 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 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: 1.06 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: 3.29 Time building geometry restraints manager: 3.20 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.060 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.180 ------------------------------------------------------------------------------- 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 10951 Z= 0.232 Angle : 0.654 10.455 14818 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 *********************** 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 : 1.244 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: 0.2203 time to fit residues: 66.6649 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 : 1.208 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 10951 Z= 0.161 Angle : 0.591 10.558 14818 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 *********************** 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 : 1.248 Fit side-chains REVERT: A 19 ASP cc_start: 0.7963 (t0) cc_final: 0.7340 (m-30) REVERT: A 118 ILE cc_start: 0.8349 (mm) cc_final: 0.7999 (mt) REVERT: C 23 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6721 (tt0) REVERT: C 146 MET cc_start: 0.5421 (mtp) cc_final: 0.4041 (tpt) REVERT: C 205 LYS cc_start: 0.8548 (ptpp) cc_final: 0.7839 (mmmm) REVERT: C 353 MET cc_start: 0.5600 (ptp) cc_final: 0.5131 (ptm) REVERT: D 12 GLN cc_start: 0.7450 (mp10) cc_final: 0.7019 (mp10) outliers start: 14 outliers final: 8 residues processed: 186 average time/residue: 0.2191 time to fit residues: 58.4385 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 : 1.132 ------------------------------------------------------------------------------- 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 64 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 0.0170 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10951 Z= 0.213 Angle : 0.589 9.082 14818 Z= 0.295 Chirality : 0.043 0.241 1663 Planarity : 0.003 0.031 1815 Dihedral : 5.318 92.008 1467 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.90 % Allowed : 11.38 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1292 helix: 0.67 (0.22), residues: 619 sheet: -0.81 (0.38), residues: 209 loop : -1.84 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 26 HIS 0.004 0.001 HIS C 355 PHE 0.027 0.001 PHE B 92 TYR 0.021 0.001 TYR C 252 ARG 0.005 0.000 ARG B 11 *********************** 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 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.279 Fit side-chains REVERT: A 19 ASP cc_start: 0.7989 (t0) cc_final: 0.7329 (m-30) REVERT: B 23 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7928 (tt) REVERT: B 26 TRP cc_start: 0.8469 (t60) cc_final: 0.8072 (t-100) REVERT: C 23 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6720 (tt0) REVERT: C 205 LYS cc_start: 0.8575 (ptpp) cc_final: 0.7916 (mmmm) REVERT: C 260 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7301 (mmtt) REVERT: C 353 MET cc_start: 0.5557 (ptp) cc_final: 0.5192 (ptm) outliers start: 22 outliers final: 14 residues processed: 176 average time/residue: 0.2175 time to fit residues: 55.5666 Evaluate side-chains 167 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 156 MET 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 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10951 Z= 0.216 Angle : 0.577 9.333 14818 Z= 0.289 Chirality : 0.043 0.156 1663 Planarity : 0.003 0.032 1815 Dihedral : 5.281 90.711 1467 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.98 % Allowed : 13.79 % Favored : 84.22 % 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: 0.68 (0.22), residues: 619 sheet: -0.70 (0.41), residues: 191 loop : -1.87 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 26 HIS 0.004 0.001 HIS C 355 PHE 0.026 0.001 PHE B 92 TYR 0.018 0.001 TYR D 63 ARG 0.005 0.000 ARG B 11 *********************** 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 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.7951 (t0) cc_final: 0.7299 (m-30) REVERT: B 23 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8045 (tt) REVERT: B 26 TRP cc_start: 0.8512 (t60) cc_final: 0.8294 (t-100) REVERT: B 118 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7601 (tp) REVERT: B 205 MET cc_start: 0.7770 (mmm) cc_final: 0.7493 (mmm) REVERT: C 23 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6707 (tt0) REVERT: C 195 ILE cc_start: 0.8028 (mm) cc_final: 0.7787 (mt) REVERT: C 205 LYS cc_start: 0.8556 (ptpp) cc_final: 0.8099 (mmmm) REVERT: C 260 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7326 (mmtt) REVERT: D 3 LEU cc_start: 0.7730 (tt) cc_final: 0.7520 (tt) REVERT: D 12 GLN cc_start: 0.7349 (mp10) cc_final: 0.7012 (mp10) outliers start: 23 outliers final: 15 residues processed: 172 average time/residue: 0.2103 time to fit residues: 52.5803 Evaluate side-chains 165 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 156 MET 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 103 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10951 Z= 0.307 Angle : 0.622 10.722 14818 Z= 0.311 Chirality : 0.045 0.257 1663 Planarity : 0.004 0.033 1815 Dihedral : 5.497 95.208 1467 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.67 % Allowed : 14.74 % Favored : 82.59 % 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: -0.80 (0.24), residues: 1292 helix: 0.55 (0.22), residues: 619 sheet: -0.69 (0.39), residues: 202 loop : -1.86 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 181 HIS 0.004 0.001 HIS C 355 PHE 0.025 0.002 PHE B 92 TYR 0.023 0.002 TYR C 252 ARG 0.006 0.000 ARG B 11 *********************** 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 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.264 Fit side-chains REVERT: A 19 ASP cc_start: 0.8059 (t0) cc_final: 0.7805 (t0) REVERT: A 104 ILE cc_start: 0.8899 (mt) cc_final: 0.8616 (mt) REVERT: A 146 MET cc_start: 0.5889 (ptt) cc_final: 0.5636 (ptt) REVERT: B 23 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8111 (tt) REVERT: B 68 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 118 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7673 (tp) REVERT: B 205 MET cc_start: 0.7809 (mmm) cc_final: 0.7503 (mmm) REVERT: C 23 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6657 (tt0) REVERT: C 139 LEU cc_start: 0.6433 (tt) cc_final: 0.6147 (tt) REVERT: C 205 LYS cc_start: 0.8569 (ptpp) cc_final: 0.8104 (mmmm) REVERT: D 3 LEU cc_start: 0.7752 (tt) cc_final: 0.7534 (tt) outliers start: 31 outliers final: 20 residues processed: 183 average time/residue: 0.2300 time to fit residues: 61.2097 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 286 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 156 MET 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 0.3980 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10951 Z= 0.218 Angle : 0.592 9.959 14818 Z= 0.298 Chirality : 0.043 0.177 1663 Planarity : 0.003 0.033 1815 Dihedral : 5.382 93.529 1467 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.41 % Allowed : 15.95 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1292 helix: 0.69 (0.22), residues: 619 sheet: -0.65 (0.39), residues: 202 loop : -1.88 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 181 HIS 0.003 0.001 HIS C 355 PHE 0.024 0.001 PHE B 92 TYR 0.020 0.001 TYR C 252 ARG 0.007 0.000 ARG A 116 *********************** 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 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.154 Fit side-chains REVERT: A 19 ASP cc_start: 0.8011 (t0) cc_final: 0.7368 (m-30) REVERT: A 104 ILE cc_start: 0.8889 (mt) cc_final: 0.8597 (mt) REVERT: B 23 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8106 (tt) REVERT: B 68 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8672 (tt) REVERT: B 118 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7656 (tp) REVERT: B 177 GLN cc_start: 0.8597 (mp10) cc_final: 0.8286 (mt0) REVERT: B 205 MET cc_start: 0.7748 (mmm) cc_final: 0.7456 (mmm) REVERT: C 23 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6681 (tt0) REVERT: C 90 LEU cc_start: 0.4534 (mt) cc_final: 0.3854 (pp) REVERT: C 195 ILE cc_start: 0.7892 (mm) cc_final: 0.7667 (mt) REVERT: C 205 LYS cc_start: 0.8583 (ptpp) cc_final: 0.8203 (mttt) REVERT: C 250 ASN cc_start: 0.6683 (m-40) cc_final: 0.6431 (m110) REVERT: D 3 LEU cc_start: 0.7732 (tt) cc_final: 0.7511 (tt) REVERT: D 12 GLN cc_start: 0.7394 (mp10) cc_final: 0.7042 (mp10) outliers start: 28 outliers final: 20 residues processed: 177 average time/residue: 0.2230 time to fit residues: 57.0867 Evaluate side-chains 173 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 156 MET 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 123 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10951 Z= 0.196 Angle : 0.583 10.008 14818 Z= 0.292 Chirality : 0.042 0.152 1663 Planarity : 0.004 0.033 1815 Dihedral : 5.297 90.446 1467 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.98 % Allowed : 17.93 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1292 helix: 0.80 (0.22), residues: 619 sheet: -0.63 (0.39), residues: 201 loop : -1.82 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.023 0.001 PHE B 92 TYR 0.018 0.001 TYR C 252 ARG 0.007 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.243 Fit side-chains REVERT: A 19 ASP cc_start: 0.7993 (t0) cc_final: 0.7381 (m-30) REVERT: A 104 ILE cc_start: 0.8915 (mt) cc_final: 0.8625 (mt) REVERT: A 146 MET cc_start: 0.5329 (ptt) cc_final: 0.5084 (ptt) REVERT: B 68 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8687 (tt) REVERT: B 118 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7651 (tp) REVERT: B 205 MET cc_start: 0.7755 (mmm) cc_final: 0.7456 (mmm) REVERT: C 23 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6715 (tt0) REVERT: C 90 LEU cc_start: 0.4676 (mt) cc_final: 0.4037 (pp) REVERT: C 195 ILE cc_start: 0.7819 (mm) cc_final: 0.7609 (mt) REVERT: C 205 LYS cc_start: 0.8565 (ptpp) cc_final: 0.8251 (mttt) REVERT: D 3 LEU cc_start: 0.7720 (tt) cc_final: 0.7494 (tt) outliers start: 23 outliers final: 20 residues processed: 173 average time/residue: 0.2290 time to fit residues: 56.4978 Evaluate side-chains 172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 156 MET 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 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 D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10951 Z= 0.263 Angle : 0.613 10.353 14818 Z= 0.308 Chirality : 0.044 0.150 1663 Planarity : 0.004 0.034 1815 Dihedral : 5.412 92.009 1467 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.33 % Allowed : 17.93 % Favored : 79.74 % 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: 0.70 (0.22), residues: 619 sheet: -0.61 (0.39), residues: 202 loop : -1.83 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.023 0.002 PHE B 92 TYR 0.019 0.001 TYR D 63 ARG 0.008 0.000 ARG A 116 *********************** 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 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.226 Fit side-chains REVERT: A 19 ASP cc_start: 0.7993 (t0) cc_final: 0.7402 (m-30) REVERT: A 104 ILE cc_start: 0.8889 (mt) cc_final: 0.8594 (mt) REVERT: A 146 MET cc_start: 0.5530 (ptt) cc_final: 0.5286 (ptt) REVERT: B 68 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8692 (tt) REVERT: B 118 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7657 (tp) REVERT: B 205 MET cc_start: 0.7762 (mmm) cc_final: 0.7446 (mmm) REVERT: C 23 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6666 (tt0) REVERT: C 90 LEU cc_start: 0.4755 (mt) cc_final: 0.4107 (pp) REVERT: C 131 LEU cc_start: 0.4199 (mt) cc_final: 0.3615 (mt) REVERT: C 146 MET cc_start: 0.5324 (mtp) cc_final: 0.3919 (tpt) REVERT: C 195 ILE cc_start: 0.7866 (mm) cc_final: 0.7657 (mt) REVERT: C 201 MET cc_start: 0.4464 (ptp) cc_final: 0.3758 (ptp) REVERT: C 205 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8303 (mttt) REVERT: D 3 LEU cc_start: 0.7712 (tt) cc_final: 0.7488 (tt) REVERT: D 12 GLN cc_start: 0.7377 (mp10) cc_final: 0.7041 (mp10) outliers start: 27 outliers final: 22 residues processed: 174 average time/residue: 0.2230 time to fit residues: 55.9054 Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 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 156 MET 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10951 Z= 0.197 Angle : 0.588 10.495 14818 Z= 0.296 Chirality : 0.043 0.148 1663 Planarity : 0.004 0.036 1815 Dihedral : 5.299 89.676 1467 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.07 % Allowed : 18.53 % 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: -0.55 (0.24), residues: 1292 helix: 0.82 (0.22), residues: 619 sheet: -0.74 (0.38), residues: 207 loop : -1.77 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 26 HIS 0.003 0.001 HIS C 355 PHE 0.023 0.001 PHE B 92 TYR 0.027 0.001 TYR C 252 ARG 0.009 0.000 ARG A 116 *********************** 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 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.196 Fit side-chains REVERT: A 19 ASP cc_start: 0.7982 (t0) cc_final: 0.7365 (m-30) REVERT: A 104 ILE cc_start: 0.8869 (mt) cc_final: 0.8571 (mt) REVERT: B 68 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8669 (tt) REVERT: B 118 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7647 (tp) REVERT: B 177 GLN cc_start: 0.8603 (mp10) cc_final: 0.8320 (mt0) REVERT: B 205 MET cc_start: 0.7747 (mmm) cc_final: 0.7420 (mmm) REVERT: C 23 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6637 (tt0) REVERT: C 90 LEU cc_start: 0.4601 (mt) cc_final: 0.4009 (pp) REVERT: C 146 MET cc_start: 0.5269 (mtp) cc_final: 0.3899 (tpt) REVERT: C 195 ILE cc_start: 0.7822 (mm) cc_final: 0.7622 (mt) REVERT: C 201 MET cc_start: 0.4413 (ptp) cc_final: 0.3707 (ptp) REVERT: C 205 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8334 (mttt) REVERT: D 3 LEU cc_start: 0.7722 (tt) cc_final: 0.7495 (tt) REVERT: D 12 GLN cc_start: 0.7353 (mp10) cc_final: 0.7021 (mp10) outliers start: 24 outliers final: 19 residues processed: 172 average time/residue: 0.2227 time to fit residues: 55.3864 Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 156 MET 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 123 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN C 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10951 Z= 0.201 Angle : 0.601 10.306 14818 Z= 0.302 Chirality : 0.043 0.149 1663 Planarity : 0.004 0.038 1815 Dihedral : 5.249 87.554 1467 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.24 % Allowed : 18.88 % Favored : 78.88 % 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: -0.51 (0.24), residues: 1292 helix: 0.85 (0.22), residues: 619 sheet: -0.68 (0.38), residues: 209 loop : -1.76 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 26 HIS 0.003 0.001 HIS C 361 PHE 0.022 0.001 PHE B 92 TYR 0.026 0.001 TYR C 252 ARG 0.010 0.000 ARG B 11 ********************** 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 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.191 Fit side-chains REVERT: A 19 ASP cc_start: 0.7977 (t0) cc_final: 0.7368 (m-30) REVERT: A 104 ILE cc_start: 0.8786 (mt) cc_final: 0.8496 (mt) REVERT: B 11 ARG cc_start: 0.7406 (mtm110) cc_final: 0.7076 (mtm110) REVERT: B 68 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8677 (tt) REVERT: B 118 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7652 (tp) REVERT: B 177 GLN cc_start: 0.8587 (mp10) cc_final: 0.8311 (mt0) REVERT: B 205 MET cc_start: 0.7737 (mmm) cc_final: 0.7424 (mmm) REVERT: C 23 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6615 (tt0) REVERT: C 90 LEU cc_start: 0.4690 (mt) cc_final: 0.4119 (pp) REVERT: C 146 MET cc_start: 0.5414 (mtp) cc_final: 0.4025 (tpt) REVERT: C 195 ILE cc_start: 0.7851 (mm) cc_final: 0.7626 (mt) REVERT: C 201 MET cc_start: 0.4485 (ptp) cc_final: 0.3810 (ptp) REVERT: C 205 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8281 (mmmm) REVERT: D 3 LEU cc_start: 0.7722 (tt) cc_final: 0.7496 (tt) REVERT: D 12 GLN cc_start: 0.7351 (mp10) cc_final: 0.7016 (mp10) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.2268 time to fit residues: 57.7036 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 156 MET Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 123 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.182080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144461 restraints weight = 14433.913| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.68 r_work: 0.3364 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10951 Z= 0.235 Angle : 0.617 11.665 14818 Z= 0.309 Chirality : 0.044 0.304 1663 Planarity : 0.003 0.033 1815 Dihedral : 5.301 87.966 1467 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.16 % Allowed : 19.14 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1292 helix: 0.78 (0.22), residues: 619 sheet: -0.62 (0.39), residues: 203 loop : -1.78 (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 0.023 0.001 PHE C 389 TYR 0.023 0.001 TYR C 252 ARG 0.009 0.000 ARG B 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.21 seconds wall clock time: 41 minutes 4.21 seconds (2464.21 seconds total)