Starting phenix.real_space_refine on Wed Aug 5 15:02:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sws_55326/08_2026/9sws_55326.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sws_55326/08_2026/9sws_55326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sws_55326/08_2026/9sws_55326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sws_55326/08_2026/9sws_55326.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sws_55326/08_2026/9sws_55326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sws_55326/08_2026/9sws_55326.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 52 5.16 5 C 6416 2.51 5 N 1770 2.21 5 O 1792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10030 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2505 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 3 Chain: "D" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2510 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 3 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2505 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 3 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2510 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 3 Time building chain proxies: 2.52, per 1000 atoms: 0.25 Number of scatterers: 10030 At special positions: 0 Unit cell: (99.6, 104.912, 110.224, 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 52 16.00 O 1792 8.00 N 1770 7.00 C 6416 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 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 363.0 milliseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 64.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.515A pdb=" N VAL C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 70 removed outlier: 3.656A pdb=" N SER C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 54 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.611A pdb=" N ARG C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 97 through 100 Processing helix chain 'C' and resid 101 through 107 removed outlier: 4.000A pdb=" N PHE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 134 removed outlier: 3.781A pdb=" N ILE C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 152 removed outlier: 3.892A pdb=" N LYS C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 167 removed outlier: 4.243A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.752A pdb=" N TYR C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'C' and resid 263 through 272 removed outlier: 3.728A pdb=" N THR C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 6.110A pdb=" N GLN C 276 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 removed outlier: 3.620A pdb=" N GLU C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP C 301 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 removed outlier: 3.655A pdb=" N HIS C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 36 removed outlier: 3.570A pdb=" N VAL D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 70 removed outlier: 4.119A pdb=" N TYR D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 54 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.674A pdb=" N CYS D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 94 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 117 through 134 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 154 through 167 removed outlier: 3.966A pdb=" N GLY D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP D 161 " --> pdb=" O HIS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 186 Proline residue: D 173 - end of helix removed outlier: 4.419A pdb=" N GLN D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALA D 177 " --> pdb=" O PRO D 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 272 removed outlier: 3.679A pdb=" N THR D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 removed outlier: 6.280A pdb=" N GLN D 276 " --> pdb=" O GLN D 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY D 278 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 302 removed outlier: 4.096A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.943A pdb=" N GLU D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 36 removed outlier: 3.522A pdb=" N VAL A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.602A pdb=" N SER A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.543A pdb=" N CYS A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 118 through 134 removed outlier: 3.788A pdb=" N ILE A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.514A pdb=" N VAL A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 4.148A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.787A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.762A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 278 removed outlier: 3.503A pdb=" N GLY A 278 " --> pdb=" O SER A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 280 through 302 removed outlier: 3.604A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.521A pdb=" N HIS A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 36 removed outlier: 3.588A pdb=" N VAL B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 70 removed outlier: 4.237A pdb=" N TYR B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 54 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.511A pdb=" N CYS B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 94 Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 117 through 134 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 154 through 167 removed outlier: 4.003A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP B 161 " --> pdb=" O HIS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Proline residue: B 173 - end of helix removed outlier: 4.494A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.645A pdb=" N THR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 6.258A pdb=" N GLN B 276 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 278 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 302 removed outlier: 3.825A pdb=" N GLU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 324 through 336 removed outlier: 4.119A pdb=" N GLU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 219 through 224 removed outlier: 5.812A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE C 221 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU C 246 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 223 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER C 243 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C 259 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU C 249 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C 198 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE C 312 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE C 200 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TYR C 314 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 202 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 219 through 224 removed outlier: 6.776A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N SER D 243 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL D 258 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR D 245 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR D 256 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 247 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 224 removed outlier: 6.866A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N SER A 243 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 259 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 224 removed outlier: 6.725A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER B 243 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL B 258 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR B 245 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 256 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 247 " --> pdb=" O ALA B 254 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1494 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: 1.43 Time building geometry restraints manager: 1.19 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: 2715 1.33 - 1.45: 1740 1.45 - 1.57: 5727 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10246 Sorted by residual: bond pdb=" CA PRO D 39 " pdb=" C PRO D 39 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.88e+01 bond pdb=" N GLY B 15 " pdb=" CA GLY B 15 " ideal model delta sigma weight residual 1.442 1.475 -0.033 7.70e-03 1.69e+04 1.81e+01 bond pdb=" CA PRO B 39 " pdb=" C PRO B 39 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.76e+01 bond pdb=" CZ ARG D 293 " pdb=" NH2 ARG D 293 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.62e+00 bond pdb=" N GLY D 15 " pdb=" CA GLY D 15 " ideal model delta sigma weight residual 1.444 1.472 -0.028 9.10e-03 1.21e+04 9.61e+00 ... (remaining 10241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 11846 2.52 - 5.04: 1929 5.04 - 7.56: 116 7.56 - 10.09: 7 10.09 - 12.61: 2 Bond angle restraints: 13900 Sorted by residual: angle pdb=" CA PHE A 105 " pdb=" CB PHE A 105 " pdb=" CG PHE A 105 " ideal model delta sigma weight residual 113.80 123.52 -9.72 1.00e+00 1.00e+00 9.45e+01 angle pdb=" C LEU A 100 " pdb=" N LEU A 101 " pdb=" CA LEU A 101 " ideal model delta sigma weight residual 121.70 134.31 -12.61 1.80e+00 3.09e-01 4.91e+01 angle pdb=" C LEU C 100 " pdb=" N LEU C 101 " pdb=" CA LEU C 101 " ideal model delta sigma weight residual 121.70 134.14 -12.44 1.80e+00 3.09e-01 4.78e+01 angle pdb=" N PRO B 39 " pdb=" CA PRO B 39 " pdb=" CB PRO B 39 " ideal model delta sigma weight residual 103.19 106.53 -3.34 5.60e-01 3.19e+00 3.56e+01 angle pdb=" N PRO D 39 " pdb=" CA PRO D 39 " pdb=" CB PRO D 39 " ideal model delta sigma weight residual 103.19 106.47 -3.28 5.60e-01 3.19e+00 3.42e+01 ... (remaining 13895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5694 17.78 - 35.55: 365 35.55 - 53.33: 67 53.33 - 71.11: 15 71.11 - 88.89: 11 Dihedral angle restraints: 6152 sinusoidal: 2472 harmonic: 3680 Sorted by residual: dihedral pdb=" C LEU C 101 " pdb=" N LEU C 101 " pdb=" CA LEU C 101 " pdb=" CB LEU C 101 " ideal model delta harmonic sigma weight residual -122.60 -138.05 15.45 0 2.50e+00 1.60e-01 3.82e+01 dihedral pdb=" CA GLU B 304 " pdb=" C GLU B 304 " pdb=" N SER B 305 " pdb=" CA SER B 305 " ideal model delta harmonic sigma weight residual 180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" C LEU A 101 " pdb=" N LEU A 101 " pdb=" CA LEU A 101 " pdb=" CB LEU A 101 " ideal model delta harmonic sigma weight residual -122.60 -137.23 14.63 0 2.50e+00 1.60e-01 3.43e+01 ... (remaining 6149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1270 0.123 - 0.245: 267 0.245 - 0.368: 18 0.368 - 0.490: 5 0.490 - 0.613: 2 Chirality restraints: 1562 Sorted by residual: chirality pdb=" CA LEU C 101 " pdb=" N LEU C 101 " pdb=" C LEU C 101 " pdb=" CB LEU C 101 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.39e+00 chirality pdb=" CA LEU A 101 " pdb=" N LEU A 101 " pdb=" C LEU A 101 " pdb=" CB LEU A 101 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" CA TYR C 107 " pdb=" N TYR C 107 " pdb=" C TYR C 107 " pdb=" CB TYR C 107 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 1559 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 105 " 0.165 2.00e-02 2.50e+03 1.01e-01 1.80e+02 pdb=" CG PHE A 105 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 PHE A 105 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 PHE A 105 " -0.102 2.00e-02 2.50e+03 pdb=" CE1 PHE A 105 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 105 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 105 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 106 " -0.098 2.00e-02 2.50e+03 5.53e-02 6.11e+01 pdb=" CG TYR C 106 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 106 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR C 106 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR C 106 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR C 106 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR C 106 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR C 106 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 46 " 0.101 2.00e-02 2.50e+03 5.38e-02 5.79e+01 pdb=" CG TYR B 46 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 46 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR B 46 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR B 46 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 46 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 46 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 46 " 0.074 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 5041 3.03 - 3.50: 10481 3.50 - 3.96: 14561 3.96 - 4.43: 15853 4.43 - 4.90: 26387 Nonbonded interactions: 72323 Sorted by model distance: nonbonded pdb=" OE1 GLU C 69 " pdb=" OH TYR C 77 " model vdw 2.561 3.040 nonbonded pdb=" OD2 ASP B 216 " pdb=" OG SER B 326 " model vdw 2.576 3.040 nonbonded pdb=" OD2 ASP C 216 " pdb=" OG SER C 324 " model vdw 2.576 3.040 nonbonded pdb=" OD2 ASP D 216 " pdb=" OG SER D 326 " model vdw 2.581 3.040 nonbonded pdb=" OD2 ASP A 216 " pdb=" OG SER A 324 " model vdw 2.582 3.040 ... (remaining 72318 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 229 or resid 237 through 337)) selection = (chain 'B' and (resid 4 through 229 or resid 237 through 337)) selection = (chain 'C' and (resid 4 through 229 or resid 237 through 337)) selection = (chain 'D' and (resid 4 through 229 or resid 237 through 337)) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.470 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.012 0.040 10246 Z= 0.730 Angle : 1.781 12.608 13900 Z= 1.184 Chirality : 0.098 0.613 1562 Planarity : 0.014 0.116 1776 Dihedral : 13.052 88.886 3788 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 0.20 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.38 % Favored : 94.89 % Rotamer: Outliers : 1.67 % Allowed : 6.68 % Favored : 91.65 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.22), residues: 1232 helix: -1.42 (0.16), residues: 674 sheet: -0.75 (0.64), residues: 48 loop : -0.47 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 284 TYR 0.101 0.015 TYR B 46 PHE 0.165 0.016 PHE A 105 TRP 0.055 0.012 TRP A 82 HIS 0.010 0.002 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.01181 / 0.73 (10246) covalent geometry : angle 1.78099 / 1.18 (13900) hydrogen bonds : bond 0.22851 / 15.72 ( 512) hydrogen bonds : angle 7.51937 / 5.46 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: C 27 SER cc_start: 0.9417 (t) cc_final: 0.9129 (p) REVERT: C 120 MET cc_start: 0.9000 (tpp) cc_final: 0.8683 (tpp) REVERT: C 266 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8571 (mm-40) REVERT: C 271 MET cc_start: 0.9362 (ttt) cc_final: 0.8921 (ttp) REVERT: C 297 ASP cc_start: 0.9137 (m-30) cc_final: 0.8847 (m-30) REVERT: A 27 SER cc_start: 0.9426 (t) cc_final: 0.9146 (p) REVERT: A 120 MET cc_start: 0.8824 (tpp) cc_final: 0.8501 (tpp) REVERT: A 143 GLU cc_start: 0.8913 (tp30) cc_final: 0.8668 (mt-10) REVERT: A 271 MET cc_start: 0.9381 (ttt) cc_final: 0.8983 (ttp) REVERT: A 297 ASP cc_start: 0.9111 (m-30) cc_final: 0.8855 (m-30) REVERT: B 137 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8473 (mtpp) REVERT: B 283 ASP cc_start: 0.8733 (m-30) cc_final: 0.8501 (m-30) outliers start: 18 outliers final: 8 residues processed: 144 average time/residue: 0.0987 time to fit residues: 20.0447 Evaluate side-chains 96 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 HIS D 227 GLN D 252 GLN A 185 HIS B 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.062078 restraints weight = 23668.051| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.67 r_work: 0.2693 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10246 Z= 0.162 Angle : 0.737 11.301 13900 Z= 0.383 Chirality : 0.044 0.219 1562 Planarity : 0.005 0.046 1776 Dihedral : 6.064 46.799 1424 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.08 % Favored : 96.75 % Rotamer: Outliers : 1.67 % Allowed : 11.13 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1232 helix: 0.26 (0.19), residues: 682 sheet: -0.15 (0.67), residues: 48 loop : -0.16 (0.31), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 281 TYR 0.014 0.002 TYR C 261 PHE 0.051 0.002 PHE A 105 TRP 0.014 0.002 TRP D 119 HIS 0.006 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (10246) covalent geometry : angle 0.73732 / 0.38 (13900) hydrogen bonds : bond 0.06518 / 4.47 ( 512) hydrogen bonds : angle 4.90410 / 3.50 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.305 Fit side-chains REVERT: C 185 HIS cc_start: 0.8520 (t-90) cc_final: 0.8230 (t-170) REVERT: D 186 TYR cc_start: 0.8771 (t80) cc_final: 0.8457 (t80) REVERT: D 266 GLN cc_start: 0.9285 (tt0) cc_final: 0.8992 (mt0) REVERT: D 282 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7981 (tm-30) REVERT: D 283 ASP cc_start: 0.8688 (m-30) cc_final: 0.8455 (m-30) REVERT: A 44 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8651 (tm) REVERT: A 143 GLU cc_start: 0.9097 (tp30) cc_final: 0.8726 (mt-10) REVERT: B 137 LYS cc_start: 0.8996 (mmpt) cc_final: 0.8499 (mtmm) REVERT: B 283 ASP cc_start: 0.8836 (m-30) cc_final: 0.8490 (m-30) outliers start: 18 outliers final: 9 residues processed: 118 average time/residue: 0.0760 time to fit residues: 13.4988 Evaluate side-chains 96 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063372 restraints weight = 24011.031| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.83 r_work: 0.2720 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10246 Z= 0.119 Angle : 0.609 10.229 13900 Z= 0.307 Chirality : 0.040 0.204 1562 Planarity : 0.004 0.046 1776 Dihedral : 5.345 47.226 1420 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.92 % Favored : 96.92 % Rotamer: Outliers : 2.23 % Allowed : 11.04 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1232 helix: 0.92 (0.20), residues: 686 sheet: -0.23 (0.69), residues: 48 loop : -0.16 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 281 TYR 0.014 0.001 TYR B 186 PHE 0.019 0.001 PHE A 105 TRP 0.009 0.001 TRP D 119 HIS 0.002 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (10246) covalent geometry : angle 0.60851 / 0.31 (13900) hydrogen bonds : bond 0.04686 / 3.20 ( 512) hydrogen bonds : angle 4.32080 / 3.09 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: C 185 HIS cc_start: 0.8560 (t-90) cc_final: 0.8166 (t-170) REVERT: D 186 TYR cc_start: 0.8631 (t80) cc_final: 0.8370 (t80) REVERT: D 266 GLN cc_start: 0.9301 (tt0) cc_final: 0.9012 (mt0) REVERT: A 44 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8604 (tm) REVERT: A 143 GLU cc_start: 0.9172 (tp30) cc_final: 0.8837 (mt-10) REVERT: B 137 LYS cc_start: 0.8984 (mmpt) cc_final: 0.8489 (mtmm) REVERT: B 282 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 283 ASP cc_start: 0.8784 (m-30) cc_final: 0.8465 (m-30) outliers start: 24 outliers final: 17 residues processed: 121 average time/residue: 0.0723 time to fit residues: 13.2696 Evaluate side-chains 106 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 30 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.4916 > 50:) chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.059368 restraints weight = 24365.650| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.79 r_work: 0.2628 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10246 Z= 0.241 Angle : 0.655 9.729 13900 Z= 0.337 Chirality : 0.044 0.205 1562 Planarity : 0.005 0.047 1776 Dihedral : 5.482 51.789 1420 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.19 % Rotamer: Outliers : 3.34 % Allowed : 10.30 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1232 helix: 0.88 (0.20), residues: 682 sheet: 0.05 (0.55), residues: 74 loop : -0.20 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.011 0.001 TYR C 163 PHE 0.024 0.002 PHE A 105 TRP 0.007 0.001 TRP A 119 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (10246) covalent geometry : angle 0.65514 / 0.34 (13900) hydrogen bonds : bond 0.05889 / 4.02 ( 512) hydrogen bonds : angle 4.46390 / 3.19 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.376 Fit side-chains REVERT: C 159 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8779 (mp) REVERT: C 185 HIS cc_start: 0.8607 (t-90) cc_final: 0.8245 (t70) REVERT: C 266 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8913 (mm-40) REVERT: D 186 TYR cc_start: 0.8582 (t80) cc_final: 0.8319 (t80) REVERT: D 266 GLN cc_start: 0.9312 (tt0) cc_final: 0.8958 (mt0) REVERT: D 283 ASP cc_start: 0.8775 (m-30) cc_final: 0.8519 (m-30) REVERT: A 44 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8920 (tm) REVERT: A 143 GLU cc_start: 0.9193 (tp30) cc_final: 0.8822 (mt-10) REVERT: A 159 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 285 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8779 (tp) REVERT: B 84 THR cc_start: 0.8876 (m) cc_final: 0.8675 (m) REVERT: B 137 LYS cc_start: 0.9032 (mmpt) cc_final: 0.8696 (mtmt) REVERT: B 180 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8721 (mtm-85) REVERT: B 282 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 283 ASP cc_start: 0.8776 (m-30) cc_final: 0.8322 (m-30) outliers start: 36 outliers final: 20 residues processed: 126 average time/residue: 0.0875 time to fit residues: 16.1567 Evaluate side-chains 111 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 180 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.062150 restraints weight = 23778.241| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.79 r_work: 0.2694 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10246 Z= 0.117 Angle : 0.573 9.113 13900 Z= 0.287 Chirality : 0.039 0.195 1562 Planarity : 0.004 0.047 1776 Dihedral : 5.161 50.095 1420 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.92 % Favored : 96.92 % Rotamer: Outliers : 2.50 % Allowed : 11.41 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1232 helix: 1.15 (0.20), residues: 688 sheet: -0.34 (0.66), residues: 52 loop : -0.20 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 284 TYR 0.013 0.001 TYR B 186 PHE 0.020 0.001 PHE A 105 TRP 0.008 0.001 TRP A 119 HIS 0.002 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (10246) covalent geometry : angle 0.57321 / 0.29 (13900) hydrogen bonds : bond 0.04469 / 3.06 ( 512) hydrogen bonds : angle 4.15682 / 2.96 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.357 Fit side-chains REVERT: C 185 HIS cc_start: 0.8593 (t-90) cc_final: 0.8176 (t70) REVERT: D 186 TYR cc_start: 0.8382 (t80) cc_final: 0.8150 (t80) REVERT: D 266 GLN cc_start: 0.9312 (tt0) cc_final: 0.9025 (mt0) REVERT: D 283 ASP cc_start: 0.8693 (m-30) cc_final: 0.8449 (m-30) REVERT: A 44 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8744 (tm) REVERT: A 143 GLU cc_start: 0.9176 (tp30) cc_final: 0.8810 (mt-10) REVERT: A 296 GLU cc_start: 0.8977 (tt0) cc_final: 0.8772 (tm-30) REVERT: B 137 LYS cc_start: 0.8984 (mmpt) cc_final: 0.8633 (mtmt) REVERT: B 282 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 283 ASP cc_start: 0.8800 (m-30) cc_final: 0.8385 (m-30) outliers start: 27 outliers final: 19 residues processed: 118 average time/residue: 0.0772 time to fit residues: 13.6239 Evaluate side-chains 109 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.062795 restraints weight = 23959.064| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.80 r_work: 0.2720 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10246 Z= 0.108 Angle : 0.543 8.840 13900 Z= 0.271 Chirality : 0.038 0.192 1562 Planarity : 0.004 0.046 1776 Dihedral : 4.984 51.024 1420 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.68 % Favored : 97.16 % Rotamer: Outliers : 2.97 % Allowed : 11.22 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1232 helix: 1.43 (0.20), residues: 684 sheet: -0.18 (0.67), residues: 52 loop : -0.20 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.008 0.001 TYR A 261 PHE 0.019 0.001 PHE A 105 TRP 0.008 0.001 TRP A 119 HIS 0.001 0.000 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (10246) covalent geometry : angle 0.54338 / 0.27 (13900) hydrogen bonds : bond 0.03897 / 2.66 ( 512) hydrogen bonds : angle 3.96533 / 2.84 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.278 Fit side-chains REVERT: C 185 HIS cc_start: 0.8629 (t-90) cc_final: 0.8283 (t70) REVERT: D 186 TYR cc_start: 0.8391 (t80) cc_final: 0.8123 (t80) REVERT: D 266 GLN cc_start: 0.9316 (tt0) cc_final: 0.9036 (mt0) REVERT: D 283 ASP cc_start: 0.8700 (m-30) cc_final: 0.8470 (m-30) REVERT: A 44 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8622 (tm) REVERT: A 143 GLU cc_start: 0.9161 (tp30) cc_final: 0.8804 (mt-10) REVERT: A 185 HIS cc_start: 0.8749 (t-90) cc_final: 0.8508 (t70) REVERT: B 137 LYS cc_start: 0.8978 (mmpt) cc_final: 0.8568 (mtmt) REVERT: B 180 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8750 (mtm-85) REVERT: B 282 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8212 (tm-30) REVERT: B 283 ASP cc_start: 0.8777 (m-30) cc_final: 0.8373 (m-30) outliers start: 32 outliers final: 24 residues processed: 130 average time/residue: 0.0821 time to fit residues: 15.5779 Evaluate side-chains 121 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.062349 restraints weight = 23957.828| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.73 r_work: 0.2707 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10246 Z= 0.123 Angle : 0.562 8.958 13900 Z= 0.278 Chirality : 0.039 0.190 1562 Planarity : 0.004 0.045 1776 Dihedral : 4.957 52.042 1420 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 3.06 % Allowed : 11.78 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1232 helix: 1.49 (0.20), residues: 684 sheet: -0.13 (0.65), residues: 52 loop : -0.17 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.015 0.001 TYR B 186 PHE 0.020 0.002 PHE A 105 TRP 0.007 0.001 TRP A 119 HIS 0.002 0.000 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10246) covalent geometry : angle 0.56207 / 0.28 (13900) hydrogen bonds : bond 0.04068 / 2.76 ( 512) hydrogen bonds : angle 3.92943 / 2.82 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.386 Fit side-chains REVERT: C 185 HIS cc_start: 0.8705 (t-90) cc_final: 0.8378 (t70) REVERT: D 180 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9071 (mtm-85) REVERT: D 186 TYR cc_start: 0.8426 (t80) cc_final: 0.8131 (t80) REVERT: D 266 GLN cc_start: 0.9305 (tt0) cc_final: 0.9014 (mt0) REVERT: D 283 ASP cc_start: 0.8672 (m-30) cc_final: 0.8453 (m-30) REVERT: A 44 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8614 (tm) REVERT: A 143 GLU cc_start: 0.9154 (tp30) cc_final: 0.8789 (mt-10) REVERT: A 185 HIS cc_start: 0.8797 (t-90) cc_final: 0.8552 (t70) REVERT: B 137 LYS cc_start: 0.8953 (mmpt) cc_final: 0.8720 (mtpt) REVERT: B 180 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8731 (mtm-85) REVERT: B 282 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 283 ASP cc_start: 0.8749 (m-30) cc_final: 0.8360 (m-30) outliers start: 33 outliers final: 23 residues processed: 126 average time/residue: 0.0869 time to fit residues: 15.9908 Evaluate side-chains 119 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 26 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.091573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063410 restraints weight = 23919.187| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.76 r_work: 0.2722 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10246 Z= 0.131 Angle : 0.578 12.646 13900 Z= 0.284 Chirality : 0.039 0.215 1562 Planarity : 0.004 0.045 1776 Dihedral : 4.954 52.526 1420 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.00 % Favored : 96.83 % Rotamer: Outliers : 2.78 % Allowed : 12.24 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1232 helix: 1.57 (0.20), residues: 682 sheet: -0.17 (0.64), residues: 52 loop : -0.15 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.015 0.001 TYR C 107 PHE 0.024 0.001 PHE A 105 TRP 0.007 0.001 TRP A 119 HIS 0.002 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10246) covalent geometry : angle 0.57756 / 0.28 (13900) hydrogen bonds : bond 0.04111 / 2.79 ( 512) hydrogen bonds : angle 3.92863 / 2.81 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.303 Fit side-chains REVERT: C 185 HIS cc_start: 0.8715 (t-90) cc_final: 0.8384 (t70) REVERT: D 180 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.9042 (mtm-85) REVERT: D 186 TYR cc_start: 0.8432 (t80) cc_final: 0.8145 (t80) REVERT: D 266 GLN cc_start: 0.9322 (tt0) cc_final: 0.9037 (mt0) REVERT: D 283 ASP cc_start: 0.8730 (m-30) cc_final: 0.8524 (m-30) REVERT: A 44 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8666 (tm) REVERT: A 143 GLU cc_start: 0.9184 (tp30) cc_final: 0.8837 (mt-10) REVERT: A 185 HIS cc_start: 0.8809 (t-90) cc_final: 0.8552 (t70) REVERT: B 180 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8686 (mtm-85) REVERT: B 282 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8229 (tm-30) REVERT: B 283 ASP cc_start: 0.8793 (m-30) cc_final: 0.8376 (m-30) outliers start: 30 outliers final: 22 residues processed: 123 average time/residue: 0.0928 time to fit residues: 16.5864 Evaluate side-chains 117 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.092167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.064076 restraints weight = 23885.818| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.78 r_work: 0.2745 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10246 Z= 0.110 Angle : 0.577 11.156 13900 Z= 0.281 Chirality : 0.039 0.219 1562 Planarity : 0.004 0.045 1776 Dihedral : 4.874 52.649 1420 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 2.69 % Allowed : 12.24 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1232 helix: 1.68 (0.20), residues: 682 sheet: 0.03 (0.65), residues: 52 loop : -0.11 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 284 TYR 0.016 0.001 TYR B 186 PHE 0.021 0.001 PHE A 105 TRP 0.008 0.001 TRP D 119 HIS 0.004 0.000 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10246) covalent geometry : angle 0.57735 / 0.28 (13900) hydrogen bonds : bond 0.03734 / 2.53 ( 512) hydrogen bonds : angle 3.83468 / 2.75 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.380 Fit side-chains REVERT: C 185 HIS cc_start: 0.8720 (t-90) cc_final: 0.8376 (t70) REVERT: D 180 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.9037 (mtm-85) REVERT: D 186 TYR cc_start: 0.8427 (t80) cc_final: 0.8120 (t80) REVERT: D 266 GLN cc_start: 0.9320 (tt0) cc_final: 0.9043 (mt0) REVERT: D 283 ASP cc_start: 0.8724 (m-30) cc_final: 0.8518 (m-30) REVERT: A 143 GLU cc_start: 0.9173 (tp30) cc_final: 0.8827 (mt-10) REVERT: A 185 HIS cc_start: 0.8763 (t-90) cc_final: 0.8509 (t70) REVERT: B 180 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8669 (mtm-85) REVERT: B 282 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8273 (tm-30) REVERT: B 283 ASP cc_start: 0.8783 (m-30) cc_final: 0.8381 (m-30) outliers start: 29 outliers final: 23 residues processed: 122 average time/residue: 0.0836 time to fit residues: 14.8593 Evaluate side-chains 118 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 84 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.061397 restraints weight = 23943.270| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.77 r_work: 0.2692 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10246 Z= 0.204 Angle : 0.651 12.209 13900 Z= 0.318 Chirality : 0.042 0.217 1562 Planarity : 0.004 0.045 1776 Dihedral : 4.934 53.745 1418 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 2.41 % Allowed : 12.62 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1232 helix: 1.56 (0.20), residues: 686 sheet: -0.28 (0.60), residues: 52 loop : -0.24 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.014 0.001 TYR C 107 PHE 0.024 0.002 PHE A 105 TRP 0.006 0.001 TRP D 119 HIS 0.004 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (10246) covalent geometry : angle 0.65138 / 0.32 (13900) hydrogen bonds : bond 0.04747 / 3.22 ( 512) hydrogen bonds : angle 4.03132 / 2.89 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.317 Fit side-chains REVERT: C 185 HIS cc_start: 0.8757 (t-90) cc_final: 0.8451 (t70) REVERT: D 180 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8944 (mtm-85) REVERT: D 186 TYR cc_start: 0.8478 (t80) cc_final: 0.8180 (t80) REVERT: D 266 GLN cc_start: 0.9343 (tt0) cc_final: 0.9043 (mt0) REVERT: A 143 GLU cc_start: 0.9200 (tp30) cc_final: 0.8853 (mt-10) REVERT: A 185 HIS cc_start: 0.8827 (t-90) cc_final: 0.8608 (t70) REVERT: B 180 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8689 (mtm-85) REVERT: B 282 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 283 ASP cc_start: 0.8756 (m-30) cc_final: 0.8347 (m-30) REVERT: B 297 ASP cc_start: 0.9117 (m-30) cc_final: 0.8885 (m-30) outliers start: 26 outliers final: 22 residues processed: 116 average time/residue: 0.0842 time to fit residues: 14.1323 Evaluate side-chains 113 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 0.0070 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.064742 restraints weight = 23672.061| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.75 r_work: 0.2745 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10246 Z= 0.112 Angle : 0.606 12.444 13900 Z= 0.291 Chirality : 0.039 0.242 1562 Planarity : 0.004 0.047 1776 Dihedral : 4.779 53.248 1418 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 2.41 % Allowed : 12.89 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1232 helix: 1.72 (0.20), residues: 686 sheet: -0.04 (0.63), residues: 52 loop : -0.21 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 284 TYR 0.016 0.001 TYR B 186 PHE 0.020 0.001 PHE A 105 TRP 0.007 0.001 TRP D 119 HIS 0.004 0.000 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10246) covalent geometry : angle 0.60597 / 0.29 (13900) hydrogen bonds : bond 0.03764 / 2.56 ( 512) hydrogen bonds : angle 3.87137 / 2.77 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1896.76 seconds wall clock time: 33 minutes 12.98 seconds (1992.98 seconds total)