Starting phenix.real_space_refine on Mon Dec 30 07:22:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dku_27491/12_2024/8dku_27491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dku_27491/12_2024/8dku_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_27491/12_2024/8dku_27491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dku_27491/12_2024/8dku_27491.map" model { file = "/net/cci-nas-00/data/ceres_data/8dku_27491/12_2024/8dku_27491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dku_27491/12_2024/8dku_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-5532/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: 6.72, per 1000 atoms: 0.63 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: 3.10 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: 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: 1.21 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: 3.56 Time building geometry restraints manager: 3.26 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: 1.040 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.880 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.700 ------------------------------------------------------------------------------- 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 10922 Z= 0.255 Angle : 0.635 11.341 14773 Z= 0.352 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 *********************** 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 : 1.257 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: 0.2564 time to fit residues: 72.2127 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 : 1.278 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 10922 Z= 0.173 Angle : 0.545 10.262 14773 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 *********************** 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 : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7677 (m-30) cc_final: 0.7320 (m-30) REVERT: A 122 LEU cc_start: 0.7499 (tt) cc_final: 0.7229 (tp) REVERT: A 273 ASN cc_start: 0.8215 (t0) cc_final: 0.7910 (t0) REVERT: A 372 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7453 (p0) REVERT: B 11 ARG cc_start: 0.7705 (mtm110) cc_final: 0.6680 (mmt180) REVERT: C 190 LYS cc_start: 0.7365 (mtmm) cc_final: 0.6843 (pptt) REVERT: C 289 LYS cc_start: 0.7393 (mmtm) cc_final: 0.7155 (mmtm) REVERT: D 110 GLU cc_start: 0.7536 (tp30) cc_final: 0.7147 (tp30) outliers start: 8 outliers final: 4 residues processed: 189 average time/residue: 0.2351 time to fit residues: 62.8690 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 : 1.312 ------------------------------------------------------------------------------- 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 64 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 93 optimal weight: 5.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS B 177 GLN C 215 HIS D 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 10922 Z= 0.639 Angle : 0.755 10.816 14773 Z= 0.389 Chirality : 0.050 0.169 1659 Planarity : 0.005 0.054 1814 Dihedral : 4.787 23.022 1456 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.59 % Allowed : 11.72 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1292 helix: 0.23 (0.22), residues: 592 sheet: -0.91 (0.41), residues: 187 loop : -2.00 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 181 HIS 0.005 0.002 HIS A 350 PHE 0.035 0.003 PHE B 180 TYR 0.023 0.002 TYR B 150 ARG 0.006 0.001 ARG B 17 *********************** 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 196 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7810 (m-80) cc_final: 0.7464 (m-80) REVERT: A 119 ASP cc_start: 0.7886 (m-30) cc_final: 0.7459 (m-30) REVERT: C 74 ASP cc_start: 0.7210 (m-30) cc_final: 0.7007 (m-30) REVERT: C 152 PHE cc_start: 0.7806 (t80) cc_final: 0.7564 (t80) REVERT: C 190 LYS cc_start: 0.7337 (mtmm) cc_final: 0.6832 (pptt) REVERT: C 289 LYS cc_start: 0.7575 (mmtm) cc_final: 0.7263 (mmtm) REVERT: D 110 GLU cc_start: 0.7893 (tp30) cc_final: 0.7474 (tp30) REVERT: D 170 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6546 (mp0) outliers start: 30 outliers final: 24 residues processed: 183 average time/residue: 0.2378 time to fit residues: 60.8162 Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 141 THR 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 86 THR 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 124 ILE Chi-restraints excluded: chain B residue 175 PHE 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 331 THR Chi-restraints excluded: chain D residue 68 ILE 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 170 GLU Chi-restraints excluded: chain D residue 174 VAL 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: 0.7980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10922 Z= 0.199 Angle : 0.537 7.491 14773 Z= 0.282 Chirality : 0.041 0.160 1659 Planarity : 0.004 0.048 1814 Dihedral : 4.310 19.316 1456 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.72 % Allowed : 13.97 % Favored : 84.31 % 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: -0.84 (0.24), residues: 1292 helix: 0.58 (0.22), residues: 600 sheet: -0.77 (0.41), residues: 187 loop : -1.85 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 26 HIS 0.004 0.001 HIS C 268 PHE 0.027 0.001 PHE B 92 TYR 0.023 0.001 TYR D 243 ARG 0.004 0.000 ARG D 166 *********************** 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 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7764 (m-80) cc_final: 0.7463 (m-80) REVERT: A 119 ASP cc_start: 0.7877 (m-30) cc_final: 0.7568 (m-30) REVERT: A 372 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7304 (p0) REVERT: B 224 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7567 (mp) REVERT: C 190 LYS cc_start: 0.7368 (mtmm) cc_final: 0.6879 (pptt) REVERT: C 289 LYS cc_start: 0.7486 (mmtm) cc_final: 0.7011 (mmtm) REVERT: D 247 LYS cc_start: 0.7862 (tppt) cc_final: 0.7497 (tppt) outliers start: 20 outliers final: 13 residues processed: 177 average time/residue: 0.2330 time to fit residues: 58.5382 Evaluate side-chains 166 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 175 PHE 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 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 D residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 HIS C 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10922 Z= 0.238 Angle : 0.543 10.137 14773 Z= 0.284 Chirality : 0.042 0.159 1659 Planarity : 0.004 0.043 1814 Dihedral : 4.249 21.719 1456 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.07 % Allowed : 15.34 % 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: -0.75 (0.24), residues: 1292 helix: 0.68 (0.22), residues: 600 sheet: -0.70 (0.41), residues: 186 loop : -1.86 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 26 HIS 0.007 0.001 HIS C 268 PHE 0.027 0.001 PHE B 92 TYR 0.022 0.001 TYR D 243 ARG 0.003 0.000 ARG B 17 *********************** 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 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7895 (m-80) cc_final: 0.7555 (m-80) REVERT: A 274 PHE cc_start: 0.8293 (m-80) cc_final: 0.8054 (m-10) REVERT: B 172 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7386 (tp) REVERT: C 190 LYS cc_start: 0.7381 (mtmm) cc_final: 0.6898 (pptt) REVERT: C 289 LYS cc_start: 0.7537 (mmtm) cc_final: 0.7045 (mmtm) REVERT: D 195 PHE cc_start: 0.7891 (t80) cc_final: 0.7589 (t80) REVERT: D 247 LYS cc_start: 0.7886 (tppt) cc_final: 0.7509 (tppt) outliers start: 24 outliers final: 18 residues processed: 179 average time/residue: 0.2162 time to fit residues: 55.7215 Evaluate side-chains 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 172 ILE 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 D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10922 Z= 0.299 Angle : 0.577 13.054 14773 Z= 0.297 Chirality : 0.043 0.155 1659 Planarity : 0.004 0.042 1814 Dihedral : 4.305 18.403 1456 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.84 % Allowed : 16.03 % Favored : 81.12 % 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: -0.82 (0.24), residues: 1292 helix: 0.63 (0.22), residues: 600 sheet: -0.83 (0.40), residues: 189 loop : -1.84 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 26 HIS 0.003 0.001 HIS C 187 PHE 0.026 0.002 PHE B 92 TYR 0.022 0.001 TYR D 243 ARG 0.002 0.000 ARG B 17 *********************** 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 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7889 (m-80) cc_final: 0.7495 (m-80) REVERT: A 372 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7286 (p0) REVERT: B 68 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8698 (tt) REVERT: B 172 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7466 (tp) REVERT: C 3 ARG cc_start: 0.6515 (tmt170) cc_final: 0.6315 (tmt-80) REVERT: C 190 LYS cc_start: 0.7395 (mtmm) cc_final: 0.6916 (pptt) REVERT: C 289 LYS cc_start: 0.7533 (mmtm) cc_final: 0.7071 (mmtm) REVERT: D 195 PHE cc_start: 0.7954 (t80) cc_final: 0.7703 (t80) REVERT: D 247 LYS cc_start: 0.7883 (tppt) cc_final: 0.7556 (tppt) outliers start: 33 outliers final: 22 residues processed: 186 average time/residue: 0.2238 time to fit residues: 59.8360 Evaluate side-chains 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 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 86 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 172 ILE 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 D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU 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 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 119 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 77 optimal weight: 0.0020 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10922 Z= 0.166 Angle : 0.515 11.963 14773 Z= 0.268 Chirality : 0.041 0.159 1659 Planarity : 0.003 0.040 1814 Dihedral : 4.129 20.707 1456 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.07 % Allowed : 16.90 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1292 helix: 0.73 (0.22), residues: 612 sheet: -0.64 (0.41), residues: 186 loop : -1.81 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 26 HIS 0.002 0.001 HIS B 212 PHE 0.026 0.001 PHE B 92 TYR 0.023 0.001 TYR D 243 ARG 0.003 0.000 ARG B 17 *********************** 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 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7884 (m-80) cc_final: 0.7489 (m-80) REVERT: B 172 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7277 (tp) REVERT: C 190 LYS cc_start: 0.7374 (mtmm) cc_final: 0.6908 (pptt) REVERT: C 289 LYS cc_start: 0.7521 (mmtm) cc_final: 0.7032 (mmtm) REVERT: D 247 LYS cc_start: 0.7883 (tppt) cc_final: 0.7564 (tppt) outliers start: 24 outliers final: 20 residues processed: 181 average time/residue: 0.2357 time to fit residues: 61.3442 Evaluate side-chains 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 172 ILE 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 D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.0670 chunk 73 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10922 Z= 0.189 Angle : 0.531 13.784 14773 Z= 0.272 Chirality : 0.041 0.159 1659 Planarity : 0.003 0.040 1814 Dihedral : 4.080 18.099 1456 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.72 % Allowed : 17.76 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1292 helix: 0.78 (0.22), residues: 611 sheet: -0.61 (0.42), residues: 184 loop : -1.80 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 26 HIS 0.002 0.001 HIS B 212 PHE 0.024 0.001 PHE B 92 TYR 0.023 0.001 TYR D 243 ARG 0.001 0.000 ARG B 80 *********************** 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 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7855 (m-80) cc_final: 0.7386 (m-80) REVERT: B 172 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7290 (tp) REVERT: C 190 LYS cc_start: 0.7392 (mtmm) cc_final: 0.6889 (pptt) REVERT: C 289 LYS cc_start: 0.7529 (mmtm) cc_final: 0.7070 (mmtm) REVERT: D 247 LYS cc_start: 0.7880 (tppt) cc_final: 0.7578 (tppt) outliers start: 20 outliers final: 17 residues processed: 180 average time/residue: 0.2278 time to fit residues: 58.5260 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 123 LEU Chi-restraints excluded: chain B residue 172 ILE 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 D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 0.0670 chunk 114 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10922 Z= 0.169 Angle : 0.520 13.195 14773 Z= 0.269 Chirality : 0.041 0.160 1659 Planarity : 0.003 0.040 1814 Dihedral : 3.999 18.442 1456 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.98 % Allowed : 18.10 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1292 helix: 0.84 (0.22), residues: 610 sheet: -0.58 (0.42), residues: 184 loop : -1.77 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 26 HIS 0.002 0.001 HIS C 187 PHE 0.024 0.001 PHE B 92 TYR 0.023 0.001 TYR D 243 ARG 0.002 0.000 ARG A 115 *********************** 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 192 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7888 (m-80) cc_final: 0.7403 (m-80) REVERT: A 358 GLU cc_start: 0.7212 (tp30) cc_final: 0.7009 (tp30) REVERT: A 372 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7386 (p0) REVERT: B 172 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7225 (tp) REVERT: C 190 LYS cc_start: 0.7433 (mtmm) cc_final: 0.6968 (pptt) REVERT: C 236 MET cc_start: 0.7278 (tmm) cc_final: 0.6981 (tpp) REVERT: C 289 LYS cc_start: 0.7513 (mmtm) cc_final: 0.7111 (mmtm) REVERT: C 323 LEU cc_start: 0.7106 (mt) cc_final: 0.6798 (mt) REVERT: D 247 LYS cc_start: 0.7891 (tppt) cc_final: 0.7617 (tppt) outliers start: 23 outliers final: 16 residues processed: 186 average time/residue: 0.2221 time to fit residues: 59.5708 Evaluate side-chains 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 372 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 172 ILE 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 D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL 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: 5.9990 chunk 57 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10922 Z= 0.341 Angle : 0.608 14.484 14773 Z= 0.312 Chirality : 0.044 0.156 1659 Planarity : 0.004 0.040 1814 Dihedral : 4.285 21.490 1456 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.81 % Allowed : 18.45 % 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: -0.79 (0.24), residues: 1292 helix: 0.58 (0.22), residues: 612 sheet: -0.72 (0.41), residues: 184 loop : -1.81 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 26 HIS 0.005 0.001 HIS C 215 PHE 0.024 0.002 PHE B 92 TYR 0.023 0.001 TYR D 243 ARG 0.004 0.000 ARG C 182 ********************** 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 184 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7928 (m-80) cc_final: 0.7358 (m-80) REVERT: A 358 GLU cc_start: 0.7247 (tp30) cc_final: 0.7037 (tp30) REVERT: B 172 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7477 (tp) REVERT: C 190 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7005 (pptt) REVERT: C 289 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7221 (mmtm) REVERT: C 323 LEU cc_start: 0.7089 (mt) cc_final: 0.6750 (mt) REVERT: D 247 LYS cc_start: 0.7915 (tppt) cc_final: 0.7585 (tppt) outliers start: 21 outliers final: 17 residues processed: 179 average time/residue: 0.2324 time to fit residues: 59.6165 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 123 LEU Chi-restraints excluded: chain B residue 172 ILE 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 D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL 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: 1.9990 chunk 93 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129300 restraints weight = 12687.236| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.59 r_work: 0.3375 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10922 Z= 0.190 Angle : 0.556 14.206 14773 Z= 0.286 Chirality : 0.041 0.159 1659 Planarity : 0.003 0.041 1814 Dihedral : 4.119 20.163 1456 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.72 % Allowed : 18.97 % Favored : 79.31 % 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: -0.65 (0.24), residues: 1292 helix: 0.74 (0.22), residues: 609 sheet: -0.65 (0.41), residues: 187 loop : -1.82 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 26 HIS 0.005 0.001 HIS C 215 PHE 0.025 0.001 PHE B 92 TYR 0.023 0.001 TYR D 243 ARG 0.003 0.000 ARG B 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.42 seconds wall clock time: 44 minutes 4.63 seconds (2644.63 seconds total)