Starting phenix.real_space_refine on Fri Jul 3 03:34:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o12_12687/07_2026/7o12_12687.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o12_12687/07_2026/7o12_12687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7o12_12687/07_2026/7o12_12687.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o12_12687/07_2026/7o12_12687.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o12_12687/07_2026/7o12_12687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o12_12687/07_2026/7o12_12687.map" model { file = "/net/cci-nas-00/data/ceres_data/7o12_12687/07_2026/7o12_12687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o12_12687/07_2026/7o12_12687.cif" } resolution = 3.7 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= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 36 5.16 5 C 7471 2.51 5 N 2047 2.21 5 O 2128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11691 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3140 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain: "E" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1880 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain breaks: 3 Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.62, per 1000 atoms: 0.22 Number of scatterers: 11691 At special positions: 0 Unit cell: (83.106, 168.264, 134.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 3 11.99 O 2128 8.00 N 2047 7.00 C 7471 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: 0.68 Conformation dependent library (CDL) restraints added in 563.5 milliseconds 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 48.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.532A pdb=" N MET B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 103 removed outlier: 3.707A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.777A pdb=" N LEU B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 143 removed outlier: 4.001A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.530A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.094A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.784A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.776A pdb=" N GLU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.563A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.671A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.572A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 117 removed outlier: 4.741A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.635A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.775A pdb=" N THR C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.560A pdb=" N MET C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.516A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.503A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.652A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.527A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.817A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.575A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.633A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.593A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.507A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 208 through 213 removed outlier: 3.535A pdb=" N LEU E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 248 through 272 removed outlier: 3.815A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.049A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.524A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.743A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.538A pdb=" N TYR D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.794A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 3.914A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.591A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.560A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.834A pdb=" N MET D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 244 removed outlier: 4.017A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.848A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 26 removed outlier: 5.365A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.282A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 201 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 35 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.787A pdb=" N ILE B 255 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 223 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.787A pdb=" N ILE B 255 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26 removed outlier: 5.978A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 7 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 254 through 258 removed outlier: 3.659A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 37 through 40 removed outlier: 8.000A pdb=" N ARG A 44 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.734A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR A 94 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 199 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.550A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR A 226 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 288 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 252 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE A 290 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASN A 254 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS A 286 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS A 311 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 288 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.541A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 172 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.248A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1476 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: 1.75 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3661 1.33 - 1.45: 2211 1.45 - 1.57: 5972 1.57 - 1.69: 6 1.69 - 1.81: 62 Bond restraints: 11912 Sorted by residual: bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.529 0.171 2.00e-02 2.50e+03 7.30e+01 bond pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 1.700 1.532 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 1.795 1.679 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.680 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" O5' ANP B 402 " pdb=" PA ANP B 402 " ideal model delta sigma weight residual 1.655 1.557 0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 11907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 16012 4.68 - 9.35: 152 9.35 - 14.03: 14 14.03 - 18.70: 5 18.70 - 23.38: 2 Bond angle restraints: 16185 Sorted by residual: angle pdb=" PB ANP C 402 " pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 126.95 103.57 23.38 3.00e+00 1.11e-01 6.07e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 105.67 21.28 3.00e+00 1.11e-01 5.03e+01 angle pdb=" CG1 VAL B 31 " pdb=" CB VAL B 31 " pdb=" CG2 VAL B 31 " ideal model delta sigma weight residual 110.80 99.06 11.74 2.20e+00 2.07e-01 2.85e+01 angle pdb=" PA ANP B 402 " pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 125.41 109.66 15.75 3.00e+00 1.11e-01 2.75e+01 angle pdb=" PA ANP C 402 " pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 125.41 110.62 14.79 3.00e+00 1.11e-01 2.43e+01 ... (remaining 16180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 6532 22.39 - 44.77: 421 44.77 - 67.15: 55 67.15 - 89.54: 2 89.54 - 111.92: 2 Dihedral angle restraints: 7012 sinusoidal: 2753 harmonic: 4259 Sorted by residual: dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU E 73 " pdb=" C LEU E 73 " pdb=" N ALA E 74 " pdb=" CA ALA E 74 " ideal model delta harmonic sigma weight residual 180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA SER D 240 " pdb=" C SER D 240 " pdb=" N LEU D 241 " pdb=" CA LEU D 241 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 7009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1620 0.102 - 0.203: 216 0.203 - 0.305: 22 0.305 - 0.407: 6 0.407 - 0.508: 1 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" CB VAL C 187 " pdb=" CA VAL C 187 " pdb=" CG1 VAL C 187 " pdb=" CG2 VAL C 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE B 255 " pdb=" CA ILE B 255 " pdb=" CG1 ILE B 255 " pdb=" CG2 ILE B 255 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1862 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 187 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C VAL B 187 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL B 187 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 188 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO D 67 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 97 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C GLU A 97 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 97 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP A 98 " 0.017 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 31 2.37 - 3.00: 5864 3.00 - 3.63: 18585 3.63 - 4.27: 28575 4.27 - 4.90: 46732 Nonbonded interactions: 99787 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 1.734 2.170 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 1.944 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G ANP B 402 " model vdw 2.095 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2B ANP B 402 " model vdw 2.106 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G ANP C 402 " model vdw 2.107 2.170 ... (remaining 99782 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 132 or resid 136 through \ 228 or resid 245 through 274)) selection = chain 'E' } 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 group one per residue 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.850 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 0.171 11912 Z= 0.536 Angle : 1.294 23.378 16185 Z= 0.647 Chirality : 0.073 0.508 1865 Planarity : 0.008 0.076 2060 Dihedral : 14.582 111.922 4296 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.82 % Allowed : 9.50 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -5.32 (0.15), residues: 1493 helix: -4.25 (0.09), residues: 639 sheet: -3.34 (0.30), residues: 194 loop : -2.63 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 360 TYR 0.026 0.003 TYR E 93 PHE 0.022 0.003 PHE A 56 TRP 0.040 0.003 TRP A 45 HIS 0.010 0.002 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.01173 / 0.54 (11912) covalent geometry : angle 1.29443 / 0.65 (16185) hydrogen bonds : bond 0.29050 / 19.46 ( 523) hydrogen bonds : angle 10.67804 / 7.48 ( 1476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8580 (tmm) cc_final: 0.8304 (tmm) REVERT: B 61 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8748 (tppt) REVERT: B 200 ILE cc_start: 0.9798 (mt) cc_final: 0.9536 (tt) REVERT: C 46 MET cc_start: 0.9251 (mtm) cc_final: 0.9048 (mtm) REVERT: C 83 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8828 (p) REVERT: C 295 MET cc_start: 0.8078 (mmm) cc_final: 0.7064 (mmm) REVERT: A 62 MET cc_start: 0.8065 (mmp) cc_final: 0.7818 (mmm) REVERT: A 103 THR cc_start: 0.9281 (p) cc_final: 0.9081 (p) REVERT: A 235 LYS cc_start: 0.9338 (mmtt) cc_final: 0.9002 (tppt) REVERT: A 334 LYS cc_start: 0.9540 (tttt) cc_final: 0.8928 (ttmm) REVERT: E 66 MET cc_start: 0.9390 (mmm) cc_final: 0.9083 (mpp) REVERT: E 138 MET cc_start: 0.8877 (tpt) cc_final: 0.8568 (tpp) REVERT: E 171 LYS cc_start: 0.9204 (tttt) cc_final: 0.8974 (tmmt) REVERT: E 213 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9256 (mm) REVERT: E 255 CYS cc_start: 0.9128 (t) cc_final: 0.8716 (t) REVERT: D 82 ASP cc_start: 0.8899 (t70) cc_final: 0.8611 (t0) REVERT: D 83 GLU cc_start: 0.9154 (pt0) cc_final: 0.8734 (pp20) REVERT: D 138 MET cc_start: 0.8849 (tmm) cc_final: 0.8294 (tmm) REVERT: D 171 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8941 (ttmm) REVERT: D 219 ASP cc_start: 0.9182 (m-30) cc_final: 0.8977 (m-30) outliers start: 10 outliers final: 3 residues processed: 104 average time/residue: 0.1116 time to fit residues: 16.9181 Evaluate side-chains 69 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 131 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 HIS B 115 GLN B 283 HIS C 207 GLN A 53 GLN A 77 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS A 179 ASN A 190 ASN A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 373 ASN A 417 HIS D 225 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.044760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034351 restraints weight = 74621.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035547 restraints weight = 38208.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036307 restraints weight = 24847.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036852 restraints weight = 18672.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037185 restraints weight = 15275.420| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11912 Z= 0.129 Angle : 0.625 9.859 16185 Z= 0.319 Chirality : 0.042 0.175 1865 Planarity : 0.005 0.068 2060 Dihedral : 7.665 130.025 1653 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.13 % Allowed : 13.43 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.00 (0.19), residues: 1493 helix: -1.52 (0.17), residues: 663 sheet: -3.04 (0.31), residues: 199 loop : -1.96 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 269 TYR 0.011 0.001 TYR E 221 PHE 0.009 0.001 PHE E 157 TRP 0.011 0.001 TRP D 253 HIS 0.005 0.001 HIS D 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (11912) covalent geometry : angle 0.62451 / 0.32 (16185) hydrogen bonds : bond 0.04205 / 2.80 ( 523) hydrogen bonds : angle 5.47391 / 3.75 ( 1476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8802 (tppt) REVERT: B 200 ILE cc_start: 0.9691 (mt) cc_final: 0.9453 (tt) REVERT: C 37 HIS cc_start: 0.8138 (m-70) cc_final: 0.7484 (m90) REVERT: C 112 LEU cc_start: 0.9737 (OUTLIER) cc_final: 0.9398 (mm) REVERT: C 268 LEU cc_start: 0.9603 (mt) cc_final: 0.9382 (mt) REVERT: C 295 MET cc_start: 0.8138 (mmm) cc_final: 0.7247 (mmm) REVERT: A 231 MET cc_start: 0.9187 (mtp) cc_final: 0.8933 (mtp) REVERT: A 235 LYS cc_start: 0.9284 (mmtt) cc_final: 0.8998 (tppt) REVERT: A 334 LYS cc_start: 0.9486 (tttt) cc_final: 0.9159 (tttp) REVERT: E 143 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8950 (m-10) REVERT: E 212 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8873 (mp) REVERT: E 213 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9303 (mm) REVERT: E 255 CYS cc_start: 0.8790 (t) cc_final: 0.8505 (t) REVERT: D 82 ASP cc_start: 0.8809 (t70) cc_final: 0.8601 (t0) REVERT: D 83 GLU cc_start: 0.8996 (pt0) cc_final: 0.8597 (pp20) REVERT: D 114 LEU cc_start: 0.8944 (tt) cc_final: 0.8534 (mp) REVERT: D 138 MET cc_start: 0.8844 (tmm) cc_final: 0.8379 (tmm) REVERT: D 170 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: D 255 CYS cc_start: 0.9228 (t) cc_final: 0.8778 (t) outliers start: 26 outliers final: 12 residues processed: 110 average time/residue: 0.0897 time to fit residues: 14.8714 Evaluate side-chains 83 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 122 optimal weight: 0.2980 chunk 141 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 GLN C 214 GLN A 63 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.044091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.033671 restraints weight = 77166.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034822 restraints weight = 40088.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035580 restraints weight = 26441.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.036118 restraints weight = 19979.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.036480 restraints weight = 16414.032| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11912 Z= 0.194 Angle : 0.639 10.843 16185 Z= 0.318 Chirality : 0.042 0.160 1865 Planarity : 0.004 0.038 2060 Dihedral : 6.775 122.469 1652 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.05 % Allowed : 14.91 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.64 (0.22), residues: 1493 helix: 0.10 (0.20), residues: 663 sheet: -2.82 (0.33), residues: 204 loop : -1.69 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 269 TYR 0.008 0.001 TYR E 93 PHE 0.014 0.001 PHE E 157 TRP 0.008 0.001 TRP A 45 HIS 0.002 0.001 HIS D 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (11912) covalent geometry : angle 0.63925 / 0.32 (16185) hydrogen bonds : bond 0.03595 / 2.37 ( 523) hydrogen bonds : angle 4.82066 / 3.31 ( 1476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8798 (tppt) REVERT: C 37 HIS cc_start: 0.8165 (m-70) cc_final: 0.7674 (m90) REVERT: C 112 LEU cc_start: 0.9741 (OUTLIER) cc_final: 0.9395 (mm) REVERT: C 268 LEU cc_start: 0.9625 (mt) cc_final: 0.9412 (mt) REVERT: C 295 MET cc_start: 0.8428 (mmm) cc_final: 0.7269 (mmm) REVERT: A 235 LYS cc_start: 0.9290 (mmtt) cc_final: 0.9082 (tppt) REVERT: A 334 LYS cc_start: 0.9517 (tttt) cc_final: 0.9183 (tttp) REVERT: E 143 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8900 (m-10) REVERT: E 212 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8906 (mp) REVERT: E 219 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8543 (t0) REVERT: E 255 CYS cc_start: 0.8743 (t) cc_final: 0.8363 (t) REVERT: D 82 ASP cc_start: 0.8779 (t70) cc_final: 0.8560 (t0) REVERT: D 83 GLU cc_start: 0.8954 (pt0) cc_final: 0.8570 (pp20) REVERT: D 114 LEU cc_start: 0.9002 (tt) cc_final: 0.8589 (mp) REVERT: D 138 MET cc_start: 0.8869 (tmm) cc_final: 0.8412 (tmm) REVERT: D 201 GLU cc_start: 0.8254 (mp0) cc_final: 0.7981 (mp0) REVERT: D 255 CYS cc_start: 0.9239 (t) cc_final: 0.8853 (t) outliers start: 25 outliers final: 18 residues processed: 94 average time/residue: 0.0883 time to fit residues: 12.8372 Evaluate side-chains 83 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 HIS A 30 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.043953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033781 restraints weight = 76993.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.034929 restraints weight = 40487.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.035569 restraints weight = 26864.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036118 restraints weight = 21049.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.036484 restraints weight = 17278.503| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11912 Z= 0.229 Angle : 0.653 11.373 16185 Z= 0.321 Chirality : 0.043 0.153 1865 Planarity : 0.004 0.037 2060 Dihedral : 6.595 121.641 1650 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.03 % Allowed : 15.72 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.12 (0.22), residues: 1493 helix: 0.69 (0.21), residues: 663 sheet: -2.63 (0.34), residues: 199 loop : -1.61 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.007 0.001 TYR C 293 PHE 0.015 0.001 PHE E 157 TRP 0.009 0.001 TRP A 45 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (11912) covalent geometry : angle 0.65278 / 0.32 (16185) hydrogen bonds : bond 0.03421 / 2.25 ( 523) hydrogen bonds : angle 4.63459 / 3.19 ( 1476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8854 (tppt) REVERT: C 112 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9403 (mm) REVERT: C 133 MET cc_start: 0.9093 (mtm) cc_final: 0.8755 (ptp) REVERT: C 261 ASN cc_start: 0.8466 (t0) cc_final: 0.8258 (t0) REVERT: C 268 LEU cc_start: 0.9631 (mt) cc_final: 0.9410 (mt) REVERT: A 231 MET cc_start: 0.9279 (mtp) cc_final: 0.8808 (mtp) REVERT: A 334 LYS cc_start: 0.9536 (tttt) cc_final: 0.9220 (tttp) REVERT: E 143 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8956 (m-10) REVERT: E 219 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8604 (t0) REVERT: E 252 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9029 (tp) REVERT: E 255 CYS cc_start: 0.8762 (t) cc_final: 0.8397 (t) REVERT: D 11 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8031 (mm-30) REVERT: D 82 ASP cc_start: 0.8826 (t70) cc_final: 0.8573 (t0) REVERT: D 83 GLU cc_start: 0.8956 (pt0) cc_final: 0.8608 (pp20) REVERT: D 114 LEU cc_start: 0.9049 (tt) cc_final: 0.8640 (mp) REVERT: D 138 MET cc_start: 0.8882 (tmm) cc_final: 0.8423 (tmm) REVERT: D 201 GLU cc_start: 0.8338 (mp0) cc_final: 0.8061 (mp0) REVERT: D 255 CYS cc_start: 0.9250 (t) cc_final: 0.8893 (t) outliers start: 37 outliers final: 19 residues processed: 99 average time/residue: 0.0858 time to fit residues: 13.3397 Evaluate side-chains 80 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 HIS ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.044727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.034641 restraints weight = 75558.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035823 restraints weight = 39677.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036614 restraints weight = 26167.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037089 restraints weight = 19699.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.037471 restraints weight = 16332.595| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11912 Z= 0.126 Angle : 0.581 9.511 16185 Z= 0.286 Chirality : 0.041 0.159 1865 Planarity : 0.003 0.039 2060 Dihedral : 6.385 119.829 1648 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.29 % Allowed : 17.53 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.78 (0.23), residues: 1493 helix: 0.95 (0.21), residues: 668 sheet: -2.35 (0.35), residues: 197 loop : -1.47 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 269 TYR 0.007 0.001 TYR E 221 PHE 0.011 0.001 PHE E 157 TRP 0.007 0.001 TRP C 236 HIS 0.014 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11912) covalent geometry : angle 0.58108 / 0.29 (16185) hydrogen bonds : bond 0.03119 / 2.04 ( 523) hydrogen bonds : angle 4.34232 / 2.98 ( 1476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8835 (tppt) REVERT: C 112 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9371 (mm) REVERT: C 133 MET cc_start: 0.9120 (mtm) cc_final: 0.8678 (ptp) REVERT: C 268 LEU cc_start: 0.9607 (mt) cc_final: 0.9394 (mt) REVERT: A 334 LYS cc_start: 0.9501 (tttt) cc_final: 0.9194 (tttp) REVERT: E 35 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8857 (tt) REVERT: E 219 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8584 (t0) REVERT: E 255 CYS cc_start: 0.8770 (t) cc_final: 0.8403 (t) REVERT: D 11 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8042 (mm-30) REVERT: D 82 ASP cc_start: 0.8765 (t70) cc_final: 0.8528 (t0) REVERT: D 83 GLU cc_start: 0.8928 (pt0) cc_final: 0.8588 (pp20) REVERT: D 114 LEU cc_start: 0.8969 (tt) cc_final: 0.8570 (mp) REVERT: D 138 MET cc_start: 0.8891 (tmm) cc_final: 0.8531 (tmm) REVERT: D 201 GLU cc_start: 0.8326 (mp0) cc_final: 0.8043 (mp0) REVERT: D 255 CYS cc_start: 0.9204 (t) cc_final: 0.8863 (t) outliers start: 28 outliers final: 15 residues processed: 90 average time/residue: 0.0739 time to fit residues: 10.7586 Evaluate side-chains 79 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 37 HIS C 283 HIS ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.043463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.033405 restraints weight = 77433.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.034538 restraints weight = 41138.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.035261 restraints weight = 27295.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.035770 restraints weight = 20851.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.036115 restraints weight = 17191.654| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11912 Z= 0.260 Angle : 0.685 11.177 16185 Z= 0.333 Chirality : 0.043 0.157 1865 Planarity : 0.004 0.034 2060 Dihedral : 6.360 119.139 1648 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.62 % Allowed : 18.35 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.65 (0.23), residues: 1493 helix: 1.12 (0.21), residues: 669 sheet: -2.27 (0.34), residues: 212 loop : -1.45 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 269 TYR 0.011 0.001 TYR C 293 PHE 0.016 0.002 PHE E 157 TRP 0.009 0.001 TRP A 45 HIS 0.018 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.26 (11912) covalent geometry : angle 0.68510 / 0.33 (16185) hydrogen bonds : bond 0.03353 / 2.20 ( 523) hydrogen bonds : angle 4.46195 / 3.07 ( 1476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8859 (tppt) REVERT: B 295 MET cc_start: 0.8319 (mmm) cc_final: 0.7914 (mtp) REVERT: C 46 MET cc_start: 0.9375 (ptp) cc_final: 0.8916 (ptp) REVERT: C 112 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9412 (mm) REVERT: C 133 MET cc_start: 0.9146 (mtm) cc_final: 0.8712 (ptp) REVERT: C 268 LEU cc_start: 0.9619 (mt) cc_final: 0.9400 (mt) REVERT: C 295 MET cc_start: 0.8009 (mmm) cc_final: 0.7770 (mmm) REVERT: A 62 MET cc_start: 0.7994 (mmp) cc_final: 0.7783 (mmm) REVERT: A 334 LYS cc_start: 0.9537 (tttt) cc_final: 0.9214 (tttp) REVERT: E 35 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8808 (tt) REVERT: E 219 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8645 (t0) REVERT: E 255 CYS cc_start: 0.8796 (t) cc_final: 0.8436 (t) REVERT: D 11 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8028 (mm-30) REVERT: D 83 GLU cc_start: 0.8994 (pt0) cc_final: 0.8664 (pp20) REVERT: D 114 LEU cc_start: 0.9051 (tt) cc_final: 0.8648 (mp) REVERT: D 138 MET cc_start: 0.8949 (tmm) cc_final: 0.8544 (tmm) REVERT: D 201 GLU cc_start: 0.8527 (mp0) cc_final: 0.8188 (mp0) REVERT: D 255 CYS cc_start: 0.9221 (t) cc_final: 0.8888 (t) outliers start: 32 outliers final: 25 residues processed: 91 average time/residue: 0.0795 time to fit residues: 11.7496 Evaluate side-chains 87 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** 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 = 0.3208 r_free = 0.3208 target = 0.044197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.033805 restraints weight = 77599.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034965 restraints weight = 40477.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035720 restraints weight = 26775.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036261 restraints weight = 20282.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.036624 restraints weight = 16697.390| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11912 Z= 0.227 Angle : 0.654 10.937 16185 Z= 0.318 Chirality : 0.043 0.157 1865 Planarity : 0.004 0.034 2060 Dihedral : 6.312 120.393 1648 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.11 % Allowed : 18.67 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.45 (0.23), residues: 1493 helix: 1.27 (0.21), residues: 669 sheet: -2.06 (0.34), residues: 217 loop : -1.38 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.018 0.001 TYR D 221 PHE 0.014 0.001 PHE E 157 TRP 0.008 0.001 TRP C 240 HIS 0.008 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (11912) covalent geometry : angle 0.65446 / 0.32 (16185) hydrogen bonds : bond 0.03224 / 2.12 ( 523) hydrogen bonds : angle 4.37110 / 3.01 ( 1476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8832 (tppt) REVERT: B 295 MET cc_start: 0.8457 (mmm) cc_final: 0.8149 (mtp) REVERT: C 46 MET cc_start: 0.9363 (ptp) cc_final: 0.8897 (ptp) REVERT: C 83 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9006 (t) REVERT: C 112 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9396 (mm) REVERT: C 133 MET cc_start: 0.9241 (mtm) cc_final: 0.8703 (ptp) REVERT: C 268 LEU cc_start: 0.9629 (mt) cc_final: 0.9418 (mt) REVERT: A 62 MET cc_start: 0.8030 (mmp) cc_final: 0.7796 (mmm) REVERT: A 334 LYS cc_start: 0.9541 (tttt) cc_final: 0.9159 (tttp) REVERT: E 35 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8783 (tt) REVERT: E 138 MET cc_start: 0.8878 (tpt) cc_final: 0.8596 (tpp) REVERT: E 219 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8663 (t0) REVERT: E 255 CYS cc_start: 0.8773 (t) cc_final: 0.8419 (t) REVERT: D 11 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8099 (mm-30) REVERT: D 83 GLU cc_start: 0.8893 (pt0) cc_final: 0.8649 (pp20) REVERT: D 114 LEU cc_start: 0.8997 (tt) cc_final: 0.8612 (mp) REVERT: D 138 MET cc_start: 0.8989 (tmm) cc_final: 0.8595 (tmm) REVERT: D 201 GLU cc_start: 0.8575 (mp0) cc_final: 0.8202 (mp0) REVERT: D 255 CYS cc_start: 0.9234 (t) cc_final: 0.8907 (t) outliers start: 38 outliers final: 27 residues processed: 98 average time/residue: 0.0835 time to fit residues: 13.4294 Evaluate side-chains 91 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 126 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.043801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033733 restraints weight = 77495.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.034865 restraints weight = 41284.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035591 restraints weight = 27565.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.036106 restraints weight = 21060.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036458 restraints weight = 17364.925| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11912 Z= 0.208 Angle : 0.650 10.620 16185 Z= 0.314 Chirality : 0.042 0.165 1865 Planarity : 0.003 0.035 2060 Dihedral : 6.267 120.664 1648 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.95 % Allowed : 19.41 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.36 (0.23), residues: 1493 helix: 1.36 (0.21), residues: 670 sheet: -2.04 (0.35), residues: 209 loop : -1.35 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.008 0.001 TYR B 293 PHE 0.014 0.001 PHE E 157 TRP 0.009 0.001 TRP C 240 HIS 0.004 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (11912) covalent geometry : angle 0.64968 / 0.31 (16185) hydrogen bonds : bond 0.03158 / 2.08 ( 523) hydrogen bonds : angle 4.31257 / 2.98 ( 1476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 MET cc_start: 0.8309 (mmm) cc_final: 0.7910 (mtp) REVERT: C 46 MET cc_start: 0.9298 (ptp) cc_final: 0.8860 (ptp) REVERT: C 83 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8999 (t) REVERT: C 112 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9395 (mm) REVERT: C 133 MET cc_start: 0.9142 (mtm) cc_final: 0.8691 (ptp) REVERT: C 268 LEU cc_start: 0.9613 (mt) cc_final: 0.9404 (mt) REVERT: A 62 MET cc_start: 0.7962 (mmp) cc_final: 0.7736 (mmm) REVERT: A 334 LYS cc_start: 0.9540 (tttt) cc_final: 0.9191 (tttp) REVERT: E 35 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8844 (tt) REVERT: E 138 MET cc_start: 0.8809 (tpt) cc_final: 0.8531 (tpp) REVERT: E 219 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8615 (t0) REVERT: E 255 CYS cc_start: 0.8790 (t) cc_final: 0.8440 (t) REVERT: D 11 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8079 (mm-30) REVERT: D 83 GLU cc_start: 0.8848 (pt0) cc_final: 0.8609 (pp20) REVERT: D 114 LEU cc_start: 0.9005 (tt) cc_final: 0.8617 (mp) REVERT: D 138 MET cc_start: 0.8951 (tmm) cc_final: 0.8560 (tmm) REVERT: D 201 GLU cc_start: 0.8551 (mp0) cc_final: 0.8172 (mp0) REVERT: D 255 CYS cc_start: 0.9201 (t) cc_final: 0.8892 (t) outliers start: 36 outliers final: 30 residues processed: 97 average time/residue: 0.0837 time to fit residues: 13.3431 Evaluate side-chains 94 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 6.9990 chunk 93 optimal weight: 0.2980 chunk 82 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN C 11 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.045446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.035386 restraints weight = 75541.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.036575 restraints weight = 39001.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.037348 restraints weight = 25536.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037817 restraints weight = 19231.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.038242 restraints weight = 15972.678| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11912 Z= 0.103 Angle : 0.604 11.338 16185 Z= 0.290 Chirality : 0.042 0.159 1865 Planarity : 0.003 0.042 2060 Dihedral : 6.107 118.507 1648 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.21 % Allowed : 20.15 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.31 (0.23), residues: 1493 helix: 1.41 (0.21), residues: 685 sheet: -1.93 (0.36), residues: 207 loop : -1.45 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.009 0.001 TYR B 291 PHE 0.008 0.001 PHE D 157 TRP 0.008 0.001 TRP C 236 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (11912) covalent geometry : angle 0.60421 / 0.29 (16185) hydrogen bonds : bond 0.02925 / 1.94 ( 523) hydrogen bonds : angle 4.08841 / 2.81 ( 1476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 MET cc_start: 0.9258 (ptp) cc_final: 0.8818 (ptp) REVERT: C 83 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.8996 (t) REVERT: C 112 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9354 (mm) REVERT: C 133 MET cc_start: 0.9112 (mtm) cc_final: 0.8684 (ptp) REVERT: A 62 MET cc_start: 0.7985 (mmp) cc_final: 0.7746 (mmm) REVERT: A 334 LYS cc_start: 0.9487 (tttt) cc_final: 0.9025 (ttmm) REVERT: E 35 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8794 (tt) REVERT: E 81 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8164 (mm-30) REVERT: E 138 MET cc_start: 0.8802 (tpt) cc_final: 0.8533 (tpp) REVERT: E 219 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8551 (t0) REVERT: E 255 CYS cc_start: 0.8701 (t) cc_final: 0.8345 (t) REVERT: D 11 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8051 (mm-30) REVERT: D 83 GLU cc_start: 0.8794 (pt0) cc_final: 0.8557 (pp20) REVERT: D 114 LEU cc_start: 0.8842 (tt) cc_final: 0.8481 (mt) REVERT: D 138 MET cc_start: 0.8913 (tmm) cc_final: 0.8530 (tmm) REVERT: D 201 GLU cc_start: 0.8452 (mp0) cc_final: 0.8042 (mp0) REVERT: D 255 CYS cc_start: 0.9216 (t) cc_final: 0.8893 (t) outliers start: 27 outliers final: 18 residues processed: 88 average time/residue: 0.0800 time to fit residues: 11.6184 Evaluate side-chains 83 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 105 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 186 HIS ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.045420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035311 restraints weight = 75492.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.036506 restraints weight = 39213.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037286 restraints weight = 25704.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037763 restraints weight = 19326.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038144 restraints weight = 16026.633| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11912 Z= 0.127 Angle : 0.608 11.062 16185 Z= 0.293 Chirality : 0.042 0.186 1865 Planarity : 0.003 0.042 2060 Dihedral : 5.995 115.938 1648 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.21 % Allowed : 20.15 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.23 (0.23), residues: 1493 helix: 1.47 (0.21), residues: 685 sheet: -1.90 (0.35), residues: 209 loop : -1.39 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.009 0.001 TYR C 291 PHE 0.010 0.001 PHE E 157 TRP 0.009 0.001 TRP A 98 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (11912) covalent geometry : angle 0.60793 / 0.29 (16185) hydrogen bonds : bond 0.02954 / 1.94 ( 523) hydrogen bonds : angle 4.09204 / 2.80 ( 1476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.9202 (mmm) cc_final: 0.8971 (mmm) REVERT: C 46 MET cc_start: 0.9194 (ptp) cc_final: 0.8769 (ptp) REVERT: C 83 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8954 (t) REVERT: C 112 LEU cc_start: 0.9767 (OUTLIER) cc_final: 0.9370 (mm) REVERT: C 133 MET cc_start: 0.8992 (mtm) cc_final: 0.8649 (ptp) REVERT: A 62 MET cc_start: 0.7866 (mmp) cc_final: 0.7629 (mmm) REVERT: A 279 MET cc_start: 0.8099 (ppp) cc_final: 0.7783 (ppp) REVERT: A 334 LYS cc_start: 0.9471 (tttt) cc_final: 0.9190 (tttp) REVERT: E 35 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8860 (tt) REVERT: E 81 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8072 (mm-30) REVERT: E 138 MET cc_start: 0.8734 (tpt) cc_final: 0.8420 (tpp) REVERT: E 219 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8590 (t0) REVERT: E 255 CYS cc_start: 0.8718 (t) cc_final: 0.8388 (t) REVERT: D 11 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7978 (mm-30) REVERT: D 83 GLU cc_start: 0.8782 (pt0) cc_final: 0.8563 (pp20) REVERT: D 114 LEU cc_start: 0.8862 (tt) cc_final: 0.8505 (mt) REVERT: D 138 MET cc_start: 0.8903 (tmm) cc_final: 0.8530 (tmm) REVERT: D 201 GLU cc_start: 0.8419 (mp0) cc_final: 0.8017 (mp0) REVERT: D 255 CYS cc_start: 0.9175 (t) cc_final: 0.8892 (t) outliers start: 27 outliers final: 20 residues processed: 84 average time/residue: 0.0746 time to fit residues: 10.3265 Evaluate side-chains 84 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 109 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.044538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034399 restraints weight = 77686.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.035565 restraints weight = 40677.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036335 restraints weight = 26890.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.036858 restraints weight = 20331.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037033 restraints weight = 16772.275| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11912 Z= 0.210 Angle : 0.657 10.782 16185 Z= 0.320 Chirality : 0.043 0.182 1865 Planarity : 0.003 0.038 2060 Dihedral : 6.023 115.373 1648 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.05 % Allowed : 20.23 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.16 (0.23), residues: 1493 helix: 1.55 (0.21), residues: 684 sheet: -1.89 (0.36), residues: 209 loop : -1.37 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 17 TYR 0.010 0.001 TYR C 291 PHE 0.014 0.001 PHE E 157 TRP 0.006 0.001 TRP A 45 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (11912) covalent geometry : angle 0.65668 / 0.32 (16185) hydrogen bonds : bond 0.03145 / 2.05 ( 523) hydrogen bonds : angle 4.20704 / 2.89 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.26 seconds wall clock time: 30 minutes 15.00 seconds (1815.00 seconds total)