Starting phenix.real_space_refine on Thu May 15 01:39:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dku_27491/05_2025/8dku_27491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dku_27491/05_2025/8dku_27491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dku_27491/05_2025/8dku_27491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dku_27491/05_2025/8dku_27491.map" model { file = "/net/cci-nas-00/data/ceres_data/8dku_27491/05_2025/8dku_27491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dku_27491/05_2025/8dku_27491.cif" } resolution = 3.2 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= 0.095 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 7089 2.51 5 N 1666 2.21 5 O 1857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 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: 10644 Number of models: 1 Model: "" Number of chains: 5 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: "F" 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 Time building chain proxies: 6.49, per 1000 atoms: 0.61 Number of scatterers: 10644 At special positions: 0 Unit cell: (91.8, 100.44, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1857 8.00 N 1666 7.00 C 7089 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 F 1 " - " UBO F 2 " ?1-3 " UBO F 2 " - " UBH F 3 " Time building additional restraints: 2.69 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: 50 helices and 11 sheets defined 49.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 removed outlier: 4.451A 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 129 removed outlier: 5.060A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.666A pdb=" N THR A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.859A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.953A pdb=" N VAL A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.591A pdb=" N LYS A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.727A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.739A 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 43 removed outlier: 3.605A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 83 removed outlier: 3.608A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix removed outlier: 3.792A pdb=" N ILE B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.659A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 4.046A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.712A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.746A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.639A 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: 3.860A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.050A 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 195 through 202 removed outlier: 3.803A pdb=" N LEU B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) 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: 4.633A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 4.173A pdb=" N ARG C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 114 through 130 removed outlier: 5.092A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 167 through 171 removed outlier: 4.141A pdb=" N ALA C 170 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.960A 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 174 through 188 removed outlier: 4.076A pdb=" N LYS C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 240 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 23 through 43 removed outlier: 3.835A pdb=" N TRP D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix removed outlier: 3.522A pdb=" N LEU D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.901A pdb=" N LEU D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 88 removed outlier: 3.693A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.840A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.053A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.945A 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: 3.754A pdb=" N ILE D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 163 removed outlier: 4.166A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 removed outlier: 4.314A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.819A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 225 through 248 removed outlier: 3.737A pdb=" N GLY D 229 " --> pdb=" O TYR D 225 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 249 through 256 removed outlier: 4.543A pdb=" N ALA D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.660A pdb=" N GLU A 32 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 13 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.660A pdb=" N GLU A 32 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 13 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 165 removed outlier: 6.280A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 49 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 212 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 51 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU A 214 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 53 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU A 221 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 259 removed outlier: 4.339A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 282 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 257 through 259 removed outlier: 4.339A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 327 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 276 removed outlier: 3.500A pdb=" N ASN A 372 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 276 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE A 374 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 363 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU A 349 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASN A 365 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL A 347 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 297 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN A 313 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 299 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY A 311 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 301 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 392 removed outlier: 3.697A pdb=" N LEU C 329 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR C 279 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER C 266 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 281 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 264 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU C 283 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL C 262 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP C 285 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.528A pdb=" N ILE C 2 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 84 through 86 removed outlier: 7.313A pdb=" N VAL C 85 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE C 163 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 197 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE C 165 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU C 50 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 313 removed outlier: 3.506A pdb=" N GLY C 298 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 341 through 342 469 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2806 1.33 - 1.45: 2038 1.45 - 1.57: 6026 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 10922 Sorted by residual: bond pdb=" C LYS A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.331 1.372 -0.041 1.21e-02 6.83e+03 1.15e+01 bond pdb=" C4 UBO F 2 " pdb=" O4 UBO F 2 " ideal model delta sigma weight residual 1.430 1.367 0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" N GLU D 132 " pdb=" CA GLU D 132 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.52e+00 bond pdb=" N ILE B 127 " pdb=" CA ILE B 127 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.17e-02 7.31e+03 7.35e+00 bond pdb=" N MET C 353 " pdb=" CA MET C 353 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.19e-02 7.06e+03 6.61e+00 ... (remaining 10917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 14562 2.27 - 4.54: 177 4.54 - 6.80: 27 6.80 - 9.07: 4 9.07 - 11.34: 3 Bond angle restraints: 14773 Sorted by residual: angle pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" C VAL D 22 " ideal model delta sigma weight residual 112.96 108.31 4.65 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C LEU B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta sigma weight residual 122.54 115.64 6.90 1.65e+00 3.67e-01 1.75e+01 angle pdb=" C5 UBO F 2 " pdb=" C4 UBO F 2 " pdb=" O4 UBO F 2 " ideal model delta sigma weight residual 111.37 100.03 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 109.94 115.80 -5.86 1.57e+00 4.06e-01 1.40e+01 angle pdb=" CA TYR C 360 " pdb=" C TYR C 360 " pdb=" O TYR C 360 " ideal model delta sigma weight residual 120.82 117.09 3.73 1.05e+00 9.07e-01 1.26e+01 ... (remaining 14768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 5694 16.78 - 33.57: 594 33.57 - 50.35: 108 50.35 - 67.13: 26 67.13 - 83.92: 8 Dihedral angle restraints: 6430 sinusoidal: 2650 harmonic: 3780 Sorted by residual: 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 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA HIS C 361 " pdb=" C HIS C 361 " pdb=" N TRP C 362 " pdb=" CA TRP C 362 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN B 16 " pdb=" C ASN B 16 " pdb=" N ARG B 17 " pdb=" CA ARG B 17 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1465 0.070 - 0.139: 189 0.139 - 0.209: 1 0.209 - 0.279: 2 0.279 - 0.349: 2 Chirality restraints: 1659 Sorted by residual: chirality pdb=" C3 UBO F 2 " pdb=" C2 UBO F 2 " pdb=" C4 UBO F 2 " pdb=" O3 UBO F 2 " both_signs ideal model delta sigma weight residual False 2.39 2.74 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C5 UBH F 3 " pdb=" C4 UBH F 3 " pdb=" C6 UBH F 3 " pdb=" O5 UBH F 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.22 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2 XXR F 1 " pdb=" C1 XXR F 1 " pdb=" C3 XXR F 1 " pdb=" O2 XXR F 1 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1656 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 28 " -0.032 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A 29 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 274 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 275 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 275 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 275 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 95 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 96 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " 0.022 5.00e-02 4.00e+02 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 888 2.74 - 3.28: 10341 3.28 - 3.82: 16866 3.82 - 4.36: 19536 4.36 - 4.90: 35545 Nonbonded interactions: 83176 Sorted by model distance: nonbonded pdb=" OG SER C 114 " pdb=" OE1 GLU C 117 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 252 " pdb=" OD2 ASP A 364 " model vdw 2.259 3.040 nonbonded pdb=" O THR D 40 " pdb=" OG SER D 44 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLU C 186 " pdb=" NZ LYS C 190 " model vdw 2.272 3.120 nonbonded pdb=" O VAL B 36 " pdb=" OG1 THR B 40 " model vdw 2.282 3.040 ... (remaining 83171 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' 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: 0.900 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.950 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 0.063 10924 Z= 0.200 Angle : 0.641 11.341 14779 Z= 0.353 Chirality : 0.045 0.349 1659 Planarity : 0.003 0.050 1814 Dihedral : 14.084 83.918 4014 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -0.86 (0.24), residues: 1292 helix: 0.60 (0.22), residues: 603 sheet: -0.52 (0.42), residues: 177 loop : -2.02 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 26 HIS 0.007 0.001 HIS A 355 PHE 0.020 0.001 PHE B 179 TYR 0.014 0.001 TYR D 63 ARG 0.012 0.001 ARG C 3 Details of bonding type rmsd hydrogen bonds : bond 0.14573 ( 462) hydrogen bonds : angle 5.96974 ( 1350) glycosidic custom : bond 0.04487 ( 2) glycosidic custom : angle 4.40534 ( 6) covalent geometry : bond 0.00392 (10922) covalent geometry : angle 0.63480 (14773) *********************** 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 206 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7826 (m-30) cc_final: 0.7459 (m-30) REVERT: B 11 ARG cc_start: 0.7711 (mtm110) cc_final: 0.6667 (mmt180) REVERT: B 13 GLU cc_start: 0.7440 (tp30) cc_final: 0.7165 (tp30) REVERT: C 263 ARG cc_start: 0.7399 (mtm110) cc_final: 0.7012 (mtm110) REVERT: D 110 GLU cc_start: 0.7595 (tp30) cc_final: 0.7225 (tp30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2383 time to fit residues: 67.1879 Evaluate side-chains 162 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 0.0770 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN C 215 HIS D 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.192540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132448 restraints weight = 12611.827| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.56 r_work: 0.3422 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10924 Z= 0.117 Angle : 0.546 10.262 14779 Z= 0.282 Chirality : 0.042 0.161 1659 Planarity : 0.004 0.038 1814 Dihedral : 4.101 23.537 1456 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.69 % Allowed : 8.53 % Favored : 90.78 % 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: 0.91 (0.22), residues: 599 sheet: -0.36 (0.43), residues: 175 loop : -1.95 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 26 HIS 0.004 0.001 HIS C 268 PHE 0.031 0.001 PHE B 92 TYR 0.019 0.001 TYR C 384 ARG 0.003 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 462) hydrogen bonds : angle 4.61290 ( 1350) glycosidic custom : bond 0.00006 ( 2) glycosidic custom : angle 1.65474 ( 6) covalent geometry : bond 0.00267 (10922) covalent geometry : angle 0.54518 (14773) *********************** 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 192 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7826 (m-30) cc_final: 0.7436 (m-30) REVERT: A 122 LEU cc_start: 0.7265 (tt) cc_final: 0.6949 (tp) REVERT: A 273 ASN cc_start: 0.8434 (t0) cc_final: 0.8116 (t0) REVERT: A 372 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7365 (p0) REVERT: B 11 ARG cc_start: 0.7799 (mtm110) cc_final: 0.6499 (mmt180) REVERT: C 117 GLU cc_start: 0.8628 (mp0) cc_final: 0.8300 (mp0) REVERT: C 128 PHE cc_start: 0.7247 (t80) cc_final: 0.7034 (t80) REVERT: C 190 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7019 (pptt) REVERT: C 289 LYS cc_start: 0.7292 (mmtm) cc_final: 0.7011 (mmtm) REVERT: D 110 GLU cc_start: 0.8053 (tp30) cc_final: 0.7637 (tp30) outliers start: 8 outliers final: 4 residues processed: 189 average time/residue: 0.2214 time to fit residues: 58.9883 Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.190536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130122 restraints weight = 12858.346| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.61 r_work: 0.3395 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10924 Z= 0.141 Angle : 0.531 10.195 14779 Z= 0.277 Chirality : 0.042 0.159 1659 Planarity : 0.003 0.038 1814 Dihedral : 4.052 21.768 1456 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.47 % Allowed : 11.29 % Favored : 87.24 % 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: -0.47 (0.24), residues: 1292 helix: 0.96 (0.22), residues: 602 sheet: -0.29 (0.43), residues: 175 loop : -1.88 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 26 HIS 0.004 0.001 HIS C 268 PHE 0.026 0.001 PHE B 92 TYR 0.022 0.001 TYR D 243 ARG 0.003 0.000 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 462) hydrogen bonds : angle 4.38729 ( 1350) glycosidic custom : bond 0.00079 ( 2) glycosidic custom : angle 1.50564 ( 6) covalent geometry : bond 0.00341 (10922) covalent geometry : angle 0.53016 (14773) *********************** 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 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7984 (m-30) cc_final: 0.7534 (m-30) REVERT: A 122 LEU cc_start: 0.7381 (tt) cc_final: 0.7181 (tp) REVERT: B 8 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7699 (tp30) REVERT: B 11 ARG cc_start: 0.7794 (mtm110) cc_final: 0.6492 (mmt180) REVERT: B 224 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7740 (mp) REVERT: C 16 LYS cc_start: 0.7021 (tttt) cc_final: 0.6812 (tttp) REVERT: C 117 GLU cc_start: 0.8413 (mp0) cc_final: 0.8154 (mp0) REVERT: C 182 ARG cc_start: 0.8467 (ptm-80) cc_final: 0.7920 (ptt-90) REVERT: C 190 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7009 (pptt) REVERT: C 236 MET cc_start: 0.7713 (ttp) cc_final: 0.7329 (tpp) REVERT: C 289 LYS cc_start: 0.7281 (mmtm) cc_final: 0.7071 (mmtm) REVERT: D 110 GLU cc_start: 0.8143 (tp30) cc_final: 0.7706 (tp30) outliers start: 17 outliers final: 11 residues processed: 178 average time/residue: 0.2319 time to fit residues: 59.2204 Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS 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 19 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN C 215 HIS C 268 HIS D 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.185025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123997 restraints weight = 12813.755| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.56 r_work: 0.3320 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 10924 Z= 0.265 Angle : 0.634 11.595 14779 Z= 0.326 Chirality : 0.045 0.155 1659 Planarity : 0.004 0.046 1814 Dihedral : 4.448 21.237 1456 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.50 % Allowed : 13.79 % Favored : 83.71 % 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: -0.90 (0.24), residues: 1292 helix: 0.44 (0.22), residues: 612 sheet: -0.71 (0.40), residues: 188 loop : -1.84 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 26 HIS 0.006 0.001 HIS C 268 PHE 0.029 0.002 PHE B 180 TYR 0.022 0.002 TYR D 243 ARG 0.003 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 462) hydrogen bonds : angle 4.51464 ( 1350) glycosidic custom : bond 0.00245 ( 2) glycosidic custom : angle 1.65669 ( 6) covalent geometry : bond 0.00662 (10922) covalent geometry : angle 0.63338 (14773) *********************** 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 199 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7844 (m-80) cc_final: 0.7490 (m-80) REVERT: A 119 ASP cc_start: 0.8086 (m-30) cc_final: 0.7883 (m-30) REVERT: A 358 GLU cc_start: 0.7308 (tp30) cc_final: 0.7027 (tp30) REVERT: A 372 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7185 (p0) REVERT: B 8 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7646 (tp30) REVERT: B 13 GLU cc_start: 0.7945 (tp30) cc_final: 0.7654 (tp30) REVERT: C 3 ARG cc_start: 0.6305 (tmt170) cc_final: 0.5930 (tpt90) REVERT: C 117 GLU cc_start: 0.8485 (mp0) cc_final: 0.8154 (mp0) REVERT: C 190 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7004 (pptt) REVERT: C 236 MET cc_start: 0.7703 (ttp) cc_final: 0.7285 (tpp) REVERT: C 289 LYS cc_start: 0.7369 (mmtm) cc_final: 0.6842 (mmtm) REVERT: D 110 GLU cc_start: 0.8253 (tp30) cc_final: 0.7784 (tp30) outliers start: 29 outliers final: 21 residues processed: 188 average time/residue: 0.2213 time to fit residues: 59.1967 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 174 VAL 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 96 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 0.0270 chunk 127 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.188919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130592 restraints weight = 12677.770| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.91 r_work: 0.3328 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10924 Z= 0.111 Angle : 0.522 12.099 14779 Z= 0.271 Chirality : 0.041 0.160 1659 Planarity : 0.003 0.045 1814 Dihedral : 4.140 18.889 1456 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.98 % Allowed : 14.57 % Favored : 83.45 % 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: 0.86 (0.22), residues: 599 sheet: -0.52 (0.41), residues: 186 loop : -1.83 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 26 HIS 0.002 0.001 HIS B 212 PHE 0.027 0.001 PHE B 92 TYR 0.023 0.001 TYR D 243 ARG 0.001 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 462) hydrogen bonds : angle 4.26475 ( 1350) glycosidic custom : bond 0.00055 ( 2) glycosidic custom : angle 1.16907 ( 6) covalent geometry : bond 0.00256 (10922) covalent geometry : angle 0.52150 (14773) *********************** 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 184 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7769 (m-80) cc_final: 0.7377 (m-80) REVERT: A 137 LYS cc_start: 0.7918 (mppt) cc_final: 0.7629 (mptt) REVERT: A 274 PHE cc_start: 0.7788 (m-10) cc_final: 0.7501 (m-10) REVERT: A 358 GLU cc_start: 0.7183 (tp30) cc_final: 0.6905 (tp30) REVERT: B 8 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7632 (tp30) REVERT: B 13 GLU cc_start: 0.7786 (tp30) cc_final: 0.7480 (tp30) REVERT: C 117 GLU cc_start: 0.8370 (mp0) cc_final: 0.8067 (mp0) REVERT: C 190 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7111 (pptt) REVERT: C 236 MET cc_start: 0.7784 (ttp) cc_final: 0.7299 (tpp) REVERT: C 289 LYS cc_start: 0.7317 (mmtm) cc_final: 0.6757 (mmtm) REVERT: D 247 LYS cc_start: 0.7682 (tppt) cc_final: 0.7174 (tppt) outliers start: 23 outliers final: 16 residues processed: 176 average time/residue: 0.2121 time to fit residues: 53.6969 Evaluate side-chains 170 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 1 optimal weight: 0.0170 overall best weight: 2.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122583 restraints weight = 12990.693| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.59 r_work: 0.3300 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 10924 Z= 0.310 Angle : 0.669 12.909 14779 Z= 0.344 Chirality : 0.047 0.153 1659 Planarity : 0.004 0.051 1814 Dihedral : 4.569 21.003 1456 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.28 % Allowed : 15.17 % Favored : 81.55 % 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 (0.23), residues: 1292 helix: 0.40 (0.22), residues: 600 sheet: -0.87 (0.40), residues: 189 loop : -1.84 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 26 HIS 0.005 0.001 HIS C 215 PHE 0.029 0.002 PHE B 180 TYR 0.023 0.002 TYR D 243 ARG 0.003 0.000 ARG D 166 Details of bonding type rmsd hydrogen bonds : bond 0.05331 ( 462) hydrogen bonds : angle 4.54196 ( 1350) glycosidic custom : bond 0.00258 ( 2) glycosidic custom : angle 1.67592 ( 6) covalent geometry : bond 0.00780 (10922) covalent geometry : angle 0.66792 (14773) *********************** 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 199 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7916 (m-80) cc_final: 0.7372 (m-80) REVERT: A 137 LYS cc_start: 0.8125 (mppt) cc_final: 0.7793 (mptt) REVERT: A 274 PHE cc_start: 0.7979 (m-10) cc_final: 0.7745 (m-10) REVERT: A 372 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7077 (p0) REVERT: B 8 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7653 (tp30) REVERT: B 13 GLU cc_start: 0.7759 (tp30) cc_final: 0.7474 (tp30) REVERT: B 137 PHE cc_start: 0.8309 (t80) cc_final: 0.8076 (t80) REVERT: C 117 GLU cc_start: 0.8492 (mp0) cc_final: 0.8075 (mp0) REVERT: C 190 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7135 (pptt) REVERT: C 236 MET cc_start: 0.7773 (ttp) cc_final: 0.7298 (tpp) REVERT: C 289 LYS cc_start: 0.7426 (mmtm) cc_final: 0.6954 (mmtm) REVERT: D 110 GLU cc_start: 0.8287 (tp30) cc_final: 0.7915 (tp30) REVERT: D 170 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6938 (mp0) outliers start: 38 outliers final: 28 residues processed: 186 average time/residue: 0.2158 time to fit residues: 57.2801 Evaluate side-chains 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128245 restraints weight = 12959.284| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.85 r_work: 0.3288 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10924 Z= 0.144 Angle : 0.551 9.434 14779 Z= 0.287 Chirality : 0.042 0.158 1659 Planarity : 0.004 0.046 1814 Dihedral : 4.324 19.109 1456 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.24 % Allowed : 16.47 % 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: -0.79 (0.24), residues: 1292 helix: 0.63 (0.22), residues: 599 sheet: -0.82 (0.41), residues: 189 loop : -1.79 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 26 HIS 0.004 0.001 HIS C 215 PHE 0.027 0.001 PHE B 92 TYR 0.024 0.001 TYR D 243 ARG 0.004 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 462) hydrogen bonds : angle 4.34346 ( 1350) glycosidic custom : bond 0.00075 ( 2) glycosidic custom : angle 1.39398 ( 6) covalent geometry : bond 0.00350 (10922) covalent geometry : angle 0.55041 (14773) *********************** 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 188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7822 (m-80) cc_final: 0.7215 (m-80) REVERT: A 97 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7858 (pm20) REVERT: A 137 LYS cc_start: 0.8029 (mppt) cc_final: 0.7777 (mptt) REVERT: A 274 PHE cc_start: 0.7889 (m-10) cc_final: 0.7639 (m-10) REVERT: B 8 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7606 (tp30) REVERT: C 117 GLU cc_start: 0.8404 (mp0) cc_final: 0.8001 (mp0) REVERT: C 190 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7183 (pptt) REVERT: C 236 MET cc_start: 0.7829 (ttp) cc_final: 0.7289 (tpp) REVERT: C 289 LYS cc_start: 0.7378 (mmtm) cc_final: 0.6875 (mmtm) REVERT: D 247 LYS cc_start: 0.7673 (tppt) cc_final: 0.7134 (tppt) outliers start: 26 outliers final: 21 residues processed: 178 average time/residue: 0.2161 time to fit residues: 54.8768 Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 100 optimal weight: 0.0970 chunk 58 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.189096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131207 restraints weight = 12743.620| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.84 r_work: 0.3331 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10924 Z= 0.106 Angle : 0.515 11.705 14779 Z= 0.269 Chirality : 0.041 0.159 1659 Planarity : 0.003 0.040 1814 Dihedral : 4.093 18.924 1456 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.72 % Allowed : 17.41 % Favored : 80.86 % 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: -0.54 (0.24), residues: 1292 helix: 0.91 (0.23), residues: 597 sheet: -0.58 (0.42), residues: 189 loop : -1.82 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 26 HIS 0.004 0.001 HIS C 215 PHE 0.026 0.001 PHE B 92 TYR 0.024 0.001 TYR D 243 ARG 0.002 0.000 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 462) hydrogen bonds : angle 4.17002 ( 1350) glycosidic custom : bond 0.00087 ( 2) glycosidic custom : angle 1.27865 ( 6) covalent geometry : bond 0.00247 (10922) covalent geometry : angle 0.51485 (14773) *********************** 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 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 1.214 Fit side-chains REVERT: A 30 PHE cc_start: 0.7824 (m-80) cc_final: 0.7272 (m-80) REVERT: A 137 LYS cc_start: 0.8027 (mppt) cc_final: 0.7763 (mptt) REVERT: A 372 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6859 (p0) REVERT: B 8 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7635 (tp30) REVERT: C 117 GLU cc_start: 0.8419 (mp0) cc_final: 0.8149 (mp0) REVERT: C 190 LYS cc_start: 0.7903 (mtmm) cc_final: 0.7179 (pptt) REVERT: C 236 MET cc_start: 0.7832 (ttp) cc_final: 0.7114 (tpp) REVERT: C 285 ASP cc_start: 0.6685 (m-30) cc_final: 0.6383 (m-30) REVERT: C 289 LYS cc_start: 0.7372 (mmtm) cc_final: 0.6911 (mmtm) REVERT: D 247 LYS cc_start: 0.7717 (tppt) cc_final: 0.7229 (tppt) outliers start: 20 outliers final: 17 residues processed: 182 average time/residue: 0.2166 time to fit residues: 57.7547 Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN D 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.185149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123174 restraints weight = 12921.820| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.90 r_work: 0.3264 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10924 Z= 0.222 Angle : 0.609 13.846 14779 Z= 0.314 Chirality : 0.044 0.166 1659 Planarity : 0.004 0.044 1814 Dihedral : 4.336 21.830 1456 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.24 % Allowed : 17.76 % Favored : 80.00 % 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: -0.79 (0.24), residues: 1292 helix: 0.63 (0.22), residues: 599 sheet: -0.79 (0.41), residues: 191 loop : -1.81 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 26 HIS 0.005 0.001 HIS C 215 PHE 0.039 0.002 PHE B 152 TYR 0.023 0.001 TYR D 243 ARG 0.002 0.000 ARG D 166 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 462) hydrogen bonds : angle 4.35016 ( 1350) glycosidic custom : bond 0.00135 ( 2) glycosidic custom : angle 1.51932 ( 6) covalent geometry : bond 0.00558 (10922) covalent geometry : angle 0.60852 (14773) *********************** 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 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7829 (m-80) cc_final: 0.7167 (m-80) REVERT: A 137 LYS cc_start: 0.7956 (mppt) cc_final: 0.7667 (mptt) REVERT: A 372 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.6510 (p0) REVERT: B 8 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7610 (tp30) REVERT: B 13 GLU cc_start: 0.7814 (tp30) cc_final: 0.7487 (tp30) REVERT: C 13 TYR cc_start: 0.6913 (m-10) cc_final: 0.6599 (m-10) REVERT: C 117 GLU cc_start: 0.8407 (mp0) cc_final: 0.8073 (mp0) REVERT: C 190 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7207 (pptt) REVERT: C 236 MET cc_start: 0.7891 (ttp) cc_final: 0.7451 (tpp) REVERT: C 289 LYS cc_start: 0.7445 (mmtm) cc_final: 0.7007 (mmtm) REVERT: D 247 LYS cc_start: 0.7698 (tppt) cc_final: 0.7210 (tppt) outliers start: 26 outliers final: 22 residues processed: 178 average time/residue: 0.2066 time to fit residues: 52.4699 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 : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 174 VAL 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 121 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 42 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.187876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129758 restraints weight = 12782.540| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.90 r_work: 0.3322 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10924 Z= 0.113 Angle : 0.535 13.722 14779 Z= 0.277 Chirality : 0.041 0.159 1659 Planarity : 0.003 0.041 1814 Dihedral : 4.113 20.215 1456 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.90 % Allowed : 17.84 % Favored : 80.26 % 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: -0.62 (0.24), residues: 1292 helix: 0.74 (0.22), residues: 610 sheet: -0.59 (0.41), residues: 192 loop : -1.79 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 26 HIS 0.004 0.001 HIS C 215 PHE 0.026 0.001 PHE B 152 TYR 0.023 0.001 TYR D 243 ARG 0.002 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 462) hydrogen bonds : angle 4.18792 ( 1350) glycosidic custom : bond 0.00083 ( 2) glycosidic custom : angle 1.27043 ( 6) covalent geometry : bond 0.00267 (10922) covalent geometry : angle 0.53404 (14773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7847 (m-80) cc_final: 0.7215 (m-80) REVERT: A 137 LYS cc_start: 0.7992 (mppt) cc_final: 0.7725 (mptt) REVERT: B 8 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7605 (tp30) REVERT: C 117 GLU cc_start: 0.8434 (mp0) cc_final: 0.8119 (mp0) REVERT: C 190 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7218 (pptt) REVERT: C 236 MET cc_start: 0.7831 (ttp) cc_final: 0.7372 (tpp) REVERT: C 285 ASP cc_start: 0.6649 (m-30) cc_final: 0.6331 (m-30) REVERT: C 289 LYS cc_start: 0.7436 (mmtm) cc_final: 0.6776 (mmtm) REVERT: C 323 LEU cc_start: 0.7524 (mt) cc_final: 0.7135 (mt) REVERT: D 247 LYS cc_start: 0.7698 (tppt) cc_final: 0.7210 (tppt) outliers start: 22 outliers final: 20 residues processed: 178 average time/residue: 0.2622 time to fit residues: 67.7869 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL 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 27 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN D 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.190294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136139 restraints weight = 12772.686| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.61 r_work: 0.3400 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10924 Z= 0.111 Angle : 0.528 14.063 14779 Z= 0.272 Chirality : 0.041 0.160 1659 Planarity : 0.003 0.039 1814 Dihedral : 4.011 19.174 1456 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.90 % Allowed : 18.10 % Favored : 80.00 % 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: 0.86 (0.22), residues: 610 sheet: -0.52 (0.41), residues: 192 loop : -1.78 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 26 HIS 0.004 0.001 HIS C 215 PHE 0.025 0.001 PHE B 152 TYR 0.023 0.001 TYR D 243 ARG 0.001 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 462) hydrogen bonds : angle 4.09305 ( 1350) glycosidic custom : bond 0.00062 ( 2) glycosidic custom : angle 1.28548 ( 6) covalent geometry : bond 0.00264 (10922) covalent geometry : angle 0.52739 (14773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5729.99 seconds wall clock time: 100 minutes 10.58 seconds (6010.58 seconds total)