Starting phenix.real_space_refine on Sat Sep 12 11:34:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3j8a_6124/09_2026/3j8a_6124.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j8a_6124/09_2026/3j8a_6124.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/3j8a_6124/09_2026/3j8a_6124.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3j8a_6124/09_2026/3j8a_6124.cif" model { file = "/net/cci-nas-00/data/ceres_data/3j8a_6124/09_2026/3j8a_6124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j8a_6124/09_2026/3j8a_6124.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j8a_6124/09_2026/3j8a_6124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j8a_6124/09_2026/3j8a_6124.map" } 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 ------------------------------------------------------------------------------- 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= 0.038 sd= 1.493 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 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9925 2.51 5 N 2700 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.54, per 1000 atoms: 0.22 Number of scatterers: 15800 At special positions: 0 Unit cell: (103.04, 97.44, 207.2, 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 100 16.00 P 10 15.00 Mg 5 11.99 O 3060 8.00 N 2700 7.00 C 9925 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: 1.28 Conformation dependent library (CDL) restraints added in 609.6 milliseconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 0 sheets defined 52.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'F' and resid 97 through 231 removed outlier: 3.829A pdb=" N UNK F 129 " --> pdb=" O UNK F 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK F 143 " --> pdb=" O UNK F 139 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK F 164 " --> pdb=" O UNK F 160 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N UNK F 170 " --> pdb=" O UNK F 166 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK F 177 " --> pdb=" O UNK F 173 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK F 178 " --> pdb=" O UNK F 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK F 205 " --> pdb=" O UNK F 201 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK F 209 " --> pdb=" O UNK F 205 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK F 220 " --> pdb=" O UNK F 216 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N UNK F 223 " --> pdb=" O UNK F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 231 removed outlier: 3.577A pdb=" N UNK G 123 " --> pdb=" O UNK G 119 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK G 129 " --> pdb=" O UNK G 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK G 143 " --> pdb=" O UNK G 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK G 164 " --> pdb=" O UNK G 160 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK G 198 " --> pdb=" O UNK G 194 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N UNK G 219 " --> pdb=" O UNK G 215 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK G 226 " --> pdb=" O UNK G 222 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK G 227 " --> pdb=" O UNK G 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.613A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.888A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 141' Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.753A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.557A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 4.209A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.922A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.507A pdb=" N LEU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.687A pdb=" N ILE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.577A pdb=" N ASP A 363 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.637A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.657A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 4.052A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.920A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.741A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.638A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.562A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.768A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 205 through 215 removed outlier: 3.711A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 4.444A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.994A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.509A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.542A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.756A pdb=" N ILE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.683A pdb=" N ASP C 363 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.622A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.697A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.959A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 removed outlier: 4.250A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 273 through 283 removed outlier: 3.909A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 310 through 321 removed outlier: 3.606A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.696A pdb=" N ILE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.691A pdb=" N ASP D 363 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.516A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 127 Processing helix chain 'E' and resid 137 through 141 removed outlier: 3.871A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 141' Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.764A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.728A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 removed outlier: 4.401A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.816A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.847A pdb=" N ILE E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 359 through 363 removed outlier: 3.705A pdb=" N ASP E 363 " --> pdb=" O GLN E 360 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.72 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: 5092 1.33 - 1.45: 2089 1.45 - 1.57: 8736 1.57 - 1.69: 16 1.69 - 1.81: 180 Bond restraints: 16113 Sorted by residual: bond pdb=" NE2 HIC A 73 " pdb=" CZ HIC A 73 " ideal model delta sigma weight residual 1.444 1.273 0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" NE2 HIC B 73 " pdb=" CZ HIC B 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" NE2 HIC D 73 " pdb=" CZ HIC D 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" NE2 HIC C 73 " pdb=" CZ HIC C 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" NE2 HIC E 73 " pdb=" CZ HIC E 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.20e+01 ... (remaining 16108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 20765 2.62 - 5.24: 1056 5.24 - 7.86: 101 7.86 - 10.48: 11 10.48 - 13.10: 1 Bond angle restraints: 21934 Sorted by residual: angle pdb=" C GLN E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta sigma weight residual 119.84 109.99 9.85 1.25e+00 6.40e-01 6.21e+01 angle pdb=" N VAL E 201 " pdb=" CA VAL E 201 " pdb=" C VAL E 201 " ideal model delta sigma weight residual 110.62 118.31 -7.69 1.02e+00 9.61e-01 5.69e+01 angle pdb=" N LEU A 236 " pdb=" CA LEU A 236 " pdb=" C LEU A 236 " ideal model delta sigma weight residual 112.72 104.27 8.45 1.14e+00 7.69e-01 5.49e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 110.62 117.99 -7.37 1.02e+00 9.61e-01 5.22e+01 angle pdb=" N LEU D 236 " pdb=" CA LEU D 236 " pdb=" C LEU D 236 " ideal model delta sigma weight residual 112.72 104.70 8.02 1.14e+00 7.69e-01 4.95e+01 ... (remaining 21929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 8963 21.37 - 42.74: 579 42.74 - 64.11: 125 64.11 - 85.48: 1 85.48 - 106.85: 10 Dihedral angle restraints: 9678 sinusoidal: 3570 harmonic: 6108 Sorted by residual: dihedral pdb=" CA HIS C 101 " pdb=" C HIS C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 -166.86 106.85 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 -163.67 103.66 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 9675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1645 0.038 - 0.075: 522 0.075 - 0.113: 232 0.113 - 0.150: 90 0.150 - 0.188: 16 Chirality restraints: 2505 Sorted by residual: chirality pdb=" CA VAL B 54 " pdb=" N VAL B 54 " pdb=" C VAL B 54 " pdb=" CB VAL B 54 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA GLN E 263 " pdb=" N GLN E 263 " pdb=" C GLN E 263 " pdb=" CB GLN E 263 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA VAL D 54 " pdb=" N VAL D 54 " pdb=" C VAL D 54 " pdb=" CB VAL D 54 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 2502 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 263 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" CD GLN A 263 " 0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN A 263 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN A 263 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 102 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 102 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.024 5.00e-02 4.00e+02 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 741 2.70 - 3.25: 16846 3.25 - 3.80: 24089 3.80 - 4.35: 32022 4.35 - 4.90: 49075 Nonbonded interactions: 122773 Sorted by model distance: nonbonded pdb=" OD2 ASP A 286 " pdb=" NH2 ARG C 39 " model vdw 2.145 3.120 nonbonded pdb=" OG SER B 52 " pdb=" NZ LYS B 84 " model vdw 2.153 3.120 nonbonded pdb=" OD2 ASP D 286 " pdb=" NH2 ARG E 39 " model vdw 2.169 3.120 nonbonded pdb=" O PRO C 332 " pdb=" NH1 ARG C 335 " model vdw 2.213 3.120 nonbonded pdb=" O LEU E 221 " pdb=" NZ LYS E 315 " model vdw 2.220 3.120 ... (remaining 122768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 0.120 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.750 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.006 0.171 16113 Z= 0.376 Angle : 1.270 13.096 21934 Z= 0.851 Chirality : 0.049 0.188 2505 Planarity : 0.005 0.047 2828 Dihedral : 14.877 106.855 5748 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 1.38 % Allowed : 11.22 % Favored : 87.40 % Rotamer: Outliers : 6.28 % Allowed : 15.08 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -5.31 (0.15), residues: 1810 helix: -4.21 (0.10), residues: 670 sheet: -2.64 (0.32), residues: 200 loop : -3.20 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 254 TYR 0.013 0.002 TYR A 169 PHE 0.016 0.002 PHE D 255 TRP 0.013 0.002 TRP D 340 HIS 0.016 0.002 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.38 (16113) covalent geometry : angle 1.27050 / 0.85 (21934) hydrogen bonds : bond 0.22471 / 12.64 ( 577) hydrogen bonds : angle 9.19302 / 4.63 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 535 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9725 (OUTLIER) cc_final: 0.9510 (m) REVERT: A 10 CYS cc_start: 0.9116 (t) cc_final: 0.8703 (p) REVERT: A 100 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: A 111 ASN cc_start: 0.9228 (t0) cc_final: 0.9027 (t0) REVERT: A 123 MET cc_start: 0.8236 (ttt) cc_final: 0.8010 (ttp) REVERT: B 47 MET cc_start: 0.7148 (ptm) cc_final: 0.6928 (ptp) REVERT: B 100 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: B 132 MET cc_start: 0.8873 (tpp) cc_final: 0.8606 (tpt) REVERT: B 153 LEU cc_start: 0.9330 (tp) cc_final: 0.9105 (tp) REVERT: B 162 ASN cc_start: 0.9274 (t0) cc_final: 0.8758 (t0) REVERT: B 183 ARG cc_start: 0.9271 (mtt-85) cc_final: 0.8834 (ttm-80) REVERT: B 196 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8607 (mtt90) REVERT: B 199 SER cc_start: 0.9005 (p) cc_final: 0.8804 (p) REVERT: B 256 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8771 (ttm-80) REVERT: B 334 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8452 (pt0) REVERT: B 337 TYR cc_start: 0.9183 (m-10) cc_final: 0.8952 (m-10) REVERT: B 345 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9192 (mt) REVERT: C 61 LYS cc_start: 0.9140 (mttt) cc_final: 0.8926 (mttt) REVERT: C 103 THR cc_start: 0.9462 (t) cc_final: 0.9253 (t) REVERT: C 111 ASN cc_start: 0.9108 (t0) cc_final: 0.8847 (t0) REVERT: C 121 GLN cc_start: 0.9326 (tt0) cc_final: 0.9117 (tm-30) REVERT: C 248 ILE cc_start: 0.9426 (mt) cc_final: 0.9129 (tt) REVERT: C 277 THR cc_start: 0.9439 (p) cc_final: 0.8962 (t) REVERT: C 325 MET cc_start: 0.9064 (tpp) cc_final: 0.8660 (tpt) REVERT: C 328 LYS cc_start: 0.8830 (mttt) cc_final: 0.8575 (mptt) REVERT: C 334 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: D 16 LEU cc_start: 0.9610 (mm) cc_final: 0.9405 (mp) REVERT: D 44 MET cc_start: 0.8567 (ttt) cc_final: 0.8086 (tmm) REVERT: D 115 ASN cc_start: 0.9107 (t0) cc_final: 0.8510 (t0) REVERT: D 132 MET cc_start: 0.8977 (tpp) cc_final: 0.8557 (mmm) REVERT: D 154 ASP cc_start: 0.8857 (t0) cc_final: 0.8523 (t0) REVERT: D 183 ARG cc_start: 0.9279 (mtt-85) cc_final: 0.8740 (tpp80) REVERT: D 213 LYS cc_start: 0.9555 (tttt) cc_final: 0.9221 (tttm) REVERT: D 280 ASN cc_start: 0.9269 (t0) cc_final: 0.9069 (t0) REVERT: D 316 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: D 336 LYS cc_start: 0.9428 (tttt) cc_final: 0.9202 (tttp) REVERT: D 340 TRP cc_start: 0.9250 (t60) cc_final: 0.8831 (t60) REVERT: D 345 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9258 (mt) REVERT: E 132 MET cc_start: 0.9093 (tpp) cc_final: 0.8847 (tpp) REVERT: E 167 GLU cc_start: 0.9056 (tt0) cc_final: 0.8816 (tm-30) REVERT: E 280 ASN cc_start: 0.9446 (t0) cc_final: 0.9238 (t0) REVERT: E 288 ASP cc_start: 0.9296 (t0) cc_final: 0.8999 (t0) REVERT: E 289 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9348 (mm) REVERT: E 329 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9295 (mp) REVERT: E 334 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8673 (pt0) outliers start: 97 outliers final: 33 residues processed: 590 average time/residue: 0.1065 time to fit residues: 97.0837 Evaluate side-chains 467 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 422 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 60.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN C 92 ASN C 263 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 115 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.100469 restraints weight = 31725.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103003 restraints weight = 15027.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104808 restraints weight = 8699.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106015 restraints weight = 5580.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106766 restraints weight = 3909.177| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 16113 Z= 0.225 Angle : 0.815 7.854 21934 Z= 0.418 Chirality : 0.045 0.178 2505 Planarity : 0.005 0.054 2828 Dihedral : 10.117 95.326 2421 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.69 % Favored : 92.49 % Rotamer: Outliers : 7.44 % Allowed : 20.78 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % 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: -3.79 (0.17), residues: 1810 helix: -2.96 (0.15), residues: 655 sheet: -1.74 (0.34), residues: 200 loop : -2.34 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 335 TYR 0.017 0.001 TYR D 169 PHE 0.011 0.002 PHE D 255 TRP 0.036 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (16113) covalent geometry : angle 0.81524 / 0.42 (21934) hydrogen bonds : bond 0.05839 / 3.27 ( 577) hydrogen bonds : angle 5.22916 / 2.63 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 432 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9413 (OUTLIER) cc_final: 0.9173 (m) REVERT: A 10 CYS cc_start: 0.8851 (t) cc_final: 0.8372 (p) REVERT: A 328 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8264 (mttp) REVERT: B 18 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8989 (mmtm) REVERT: B 162 ASN cc_start: 0.8807 (t0) cc_final: 0.8293 (t0) REVERT: B 256 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8459 (ttm110) REVERT: B 313 MET cc_start: 0.8536 (tpp) cc_final: 0.8315 (tpp) REVERT: B 329 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9010 (mm) REVERT: B 369 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8853 (mm) REVERT: C 18 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9151 (mmtp) REVERT: C 115 ASN cc_start: 0.9295 (t0) cc_final: 0.8378 (t0) REVERT: C 121 GLN cc_start: 0.9399 (tm-30) cc_final: 0.9074 (tm-30) REVERT: C 161 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.8356 (m-70) REVERT: C 205 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 246 GLN cc_start: 0.9222 (tp-100) cc_final: 0.8649 (tm-30) REVERT: C 248 ILE cc_start: 0.9560 (mt) cc_final: 0.9281 (tt) REVERT: C 300 SER cc_start: 0.9339 (m) cc_final: 0.8861 (p) REVERT: C 325 MET cc_start: 0.8827 (tpp) cc_final: 0.8550 (tpt) REVERT: D 44 MET cc_start: 0.8486 (ttt) cc_final: 0.8261 (ttp) REVERT: D 100 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: D 115 ASN cc_start: 0.8900 (t0) cc_final: 0.8427 (t0) REVERT: D 242 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8718 (mp) REVERT: D 340 TRP cc_start: 0.8775 (t60) cc_final: 0.8014 (t60) REVERT: E 39 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8277 (ptt180) REVERT: E 59 GLN cc_start: 0.9434 (tp40) cc_final: 0.9014 (mm-40) REVERT: E 263 GLN cc_start: 0.8788 (mt0) cc_final: 0.8563 (mt0) outliers start: 115 outliers final: 67 residues processed: 501 average time/residue: 0.1029 time to fit residues: 80.6153 Evaluate side-chains 458 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 382 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 14 optimal weight: 110.0000 chunk 67 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 115 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100779 restraints weight = 32243.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103280 restraints weight = 15271.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104849 restraints weight = 8853.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106153 restraints weight = 5937.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107008 restraints weight = 4093.401| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 16113 Z= 0.202 Angle : 0.762 8.409 21934 Z= 0.380 Chirality : 0.045 0.185 2505 Planarity : 0.005 0.039 2828 Dihedral : 9.608 90.406 2394 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.69 % Favored : 92.49 % Rotamer: Outliers : 7.38 % Allowed : 22.33 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % 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: -3.19 (0.18), residues: 1810 helix: -2.39 (0.17), residues: 650 sheet: -1.45 (0.42), residues: 150 loop : -2.04 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.029 0.001 TYR B 279 PHE 0.012 0.002 PHE E 255 TRP 0.055 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (16113) covalent geometry : angle 0.76211 / 0.38 (21934) hydrogen bonds : bond 0.05078 / 2.83 ( 577) hydrogen bonds : angle 4.78496 / 2.41 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 400 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8844 (t) cc_final: 0.8410 (p) REVERT: A 39 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8535 (ptt180) REVERT: A 105 LEU cc_start: 0.9023 (mt) cc_final: 0.8799 (mt) REVERT: A 328 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8026 (mttp) REVERT: B 121 GLN cc_start: 0.9203 (tt0) cc_final: 0.8872 (tm-30) REVERT: B 124 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: B 162 ASN cc_start: 0.8752 (t0) cc_final: 0.8287 (t0) REVERT: B 256 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8450 (ttm110) REVERT: B 313 MET cc_start: 0.8594 (tpp) cc_final: 0.8330 (tpp) REVERT: B 329 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9030 (mm) REVERT: B 340 TRP cc_start: 0.8700 (t60) cc_final: 0.8150 (t60) REVERT: C 18 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9145 (mmtp) REVERT: C 39 ARG cc_start: 0.8791 (ptp-170) cc_final: 0.8449 (ptp-170) REVERT: C 121 GLN cc_start: 0.9386 (tm-30) cc_final: 0.9037 (tm-30) REVERT: C 246 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8596 (tm-30) REVERT: C 259 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8745 (tm-30) REVERT: C 325 MET cc_start: 0.8750 (tpp) cc_final: 0.8475 (tpt) REVERT: D 115 ASN cc_start: 0.8974 (t0) cc_final: 0.8536 (t0) REVERT: D 242 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8712 (mp) REVERT: D 325 MET cc_start: 0.9051 (tpp) cc_final: 0.8297 (tpp) REVERT: D 340 TRP cc_start: 0.8716 (t60) cc_final: 0.8025 (t60) REVERT: E 39 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8332 (ptt180) REVERT: E 121 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.8812 (tm-30) REVERT: E 263 GLN cc_start: 0.8814 (mt0) cc_final: 0.8354 (mt0) REVERT: E 270 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8019 (mt-10) outliers start: 114 outliers final: 72 residues processed: 469 average time/residue: 0.1029 time to fit residues: 75.0047 Evaluate side-chains 454 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 374 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 32 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 21 optimal weight: 220.0000 chunk 108 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.100924 restraints weight = 32174.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103483 restraints weight = 15274.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105247 restraints weight = 8779.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106451 restraints weight = 5632.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107208 restraints weight = 3938.507| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16113 Z= 0.207 Angle : 0.750 8.133 21934 Z= 0.371 Chirality : 0.045 0.190 2505 Planarity : 0.005 0.061 2828 Dihedral : 9.213 88.153 2384 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.96 % Favored : 92.21 % Rotamer: Outliers : 8.41 % Allowed : 22.46 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % 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: -2.98 (0.18), residues: 1810 helix: -2.20 (0.17), residues: 675 sheet: -1.39 (0.42), residues: 150 loop : -1.88 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.021 0.001 TYR A 362 PHE 0.022 0.002 PHE D 200 TRP 0.056 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (16113) covalent geometry : angle 0.74975 / 0.37 (21934) hydrogen bonds : bond 0.04735 / 2.62 ( 577) hydrogen bonds : angle 4.61044 / 2.32 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 388 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8822 (t) cc_final: 0.8326 (p) REVERT: A 39 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8598 (ptt180) REVERT: A 153 LEU cc_start: 0.9198 (tp) cc_final: 0.8971 (tp) REVERT: A 328 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8052 (mttp) REVERT: B 121 GLN cc_start: 0.9178 (tt0) cc_final: 0.8875 (tm-30) REVERT: B 124 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: B 154 ASP cc_start: 0.8538 (t0) cc_final: 0.8330 (t0) REVERT: B 162 ASN cc_start: 0.8747 (t0) cc_final: 0.8261 (t0) REVERT: B 256 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8585 (ttm110) REVERT: B 313 MET cc_start: 0.8592 (tpp) cc_final: 0.8296 (tpp) REVERT: B 329 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9034 (mm) REVERT: B 334 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: B 340 TRP cc_start: 0.8655 (t60) cc_final: 0.8073 (t60) REVERT: C 39 ARG cc_start: 0.8776 (ptp-170) cc_final: 0.8344 (ptp-170) REVERT: C 121 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9143 (tm-30) REVERT: C 202 THR cc_start: 0.8800 (t) cc_final: 0.8250 (t) REVERT: C 246 GLN cc_start: 0.9205 (tp-100) cc_final: 0.8523 (tm-30) REVERT: C 259 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8710 (tm-30) REVERT: C 283 MET cc_start: 0.8594 (mtp) cc_final: 0.8350 (tpp) REVERT: C 325 MET cc_start: 0.8694 (tpp) cc_final: 0.8396 (tpt) REVERT: D 115 ASN cc_start: 0.9009 (t0) cc_final: 0.8570 (t0) REVERT: D 242 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8665 (mp) REVERT: E 39 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8342 (ptt180) REVERT: E 121 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8846 (tm-30) REVERT: E 263 GLN cc_start: 0.8838 (mt0) cc_final: 0.8481 (mt0) REVERT: E 270 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8162 (mt-10) outliers start: 130 outliers final: 82 residues processed: 464 average time/residue: 0.1011 time to fit residues: 74.1779 Evaluate side-chains 463 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 374 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 17 optimal weight: 90.0000 chunk 200 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** 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 = 0.3428 r_free = 0.3428 target = 0.118783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101809 restraints weight = 31844.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104382 restraints weight = 15010.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106239 restraints weight = 8726.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107403 restraints weight = 5644.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108186 restraints weight = 3962.320| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16113 Z= 0.188 Angle : 0.737 9.090 21934 Z= 0.360 Chirality : 0.045 0.191 2505 Planarity : 0.005 0.039 2828 Dihedral : 8.970 86.381 2381 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.02 % Favored : 93.15 % Rotamer: Outliers : 7.90 % Allowed : 23.30 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % 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: -2.84 (0.19), residues: 1810 helix: -1.99 (0.18), residues: 675 sheet: -2.40 (0.34), residues: 205 loop : -1.58 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.016 0.001 TYR A 198 PHE 0.016 0.002 PHE D 200 TRP 0.072 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (16113) covalent geometry : angle 0.73730 / 0.36 (21934) hydrogen bonds : bond 0.04474 / 2.48 ( 577) hydrogen bonds : angle 4.44118 / 2.24 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 409 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8783 (t) cc_final: 0.8238 (p) REVERT: A 39 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8553 (ptt180) REVERT: A 100 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: A 153 LEU cc_start: 0.9151 (tp) cc_final: 0.8928 (tp) REVERT: A 328 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8264 (mttp) REVERT: B 44 MET cc_start: 0.8288 (ttp) cc_final: 0.7891 (ttm) REVERT: B 121 GLN cc_start: 0.9186 (tt0) cc_final: 0.8884 (tm-30) REVERT: B 124 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: B 162 ASN cc_start: 0.8750 (t0) cc_final: 0.8277 (t0) REVERT: B 167 GLU cc_start: 0.8522 (tt0) cc_final: 0.8310 (tt0) REVERT: B 313 MET cc_start: 0.8574 (tpp) cc_final: 0.8291 (tpp) REVERT: B 329 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9034 (mm) REVERT: B 334 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: B 340 TRP cc_start: 0.8528 (t60) cc_final: 0.7836 (t60) REVERT: C 18 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9072 (mmtp) REVERT: C 161 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8442 (m-70) REVERT: C 246 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8520 (tm-30) REVERT: C 259 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8489 (tm-30) REVERT: C 263 GLN cc_start: 0.9315 (tt0) cc_final: 0.9025 (pt0) REVERT: C 283 MET cc_start: 0.8516 (mtp) cc_final: 0.8218 (tpp) REVERT: C 325 MET cc_start: 0.8685 (tpp) cc_final: 0.8392 (tpt) REVERT: C 359 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9024 (mtpp) REVERT: D 115 ASN cc_start: 0.8988 (t0) cc_final: 0.8564 (t0) REVERT: D 124 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: D 242 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8642 (mp) REVERT: D 325 MET cc_start: 0.9021 (tpp) cc_final: 0.8138 (tpp) REVERT: E 39 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8534 (ptt180) REVERT: E 100 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: E 121 GLN cc_start: 0.9250 (tm-30) cc_final: 0.8991 (tm-30) REVERT: E 125 GLU cc_start: 0.8014 (pt0) cc_final: 0.7744 (pt0) REVERT: E 263 GLN cc_start: 0.8855 (mt0) cc_final: 0.8583 (mt0) REVERT: E 275 HIS cc_start: 0.9563 (OUTLIER) cc_final: 0.8995 (p-80) outliers start: 122 outliers final: 76 residues processed: 485 average time/residue: 0.1020 time to fit residues: 77.6528 Evaluate side-chains 468 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 378 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 90.0000 chunk 55 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103973 restraints weight = 31556.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106499 restraints weight = 14988.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108451 restraints weight = 8750.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109660 restraints weight = 5560.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110453 restraints weight = 3848.043| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16113 Z= 0.149 Angle : 0.719 8.841 21934 Z= 0.350 Chirality : 0.045 0.185 2505 Planarity : 0.004 0.067 2828 Dihedral : 8.464 84.286 2375 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.19 % Favored : 93.98 % Rotamer: Outliers : 6.93 % Allowed : 24.85 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.52 (0.19), residues: 1810 helix: -1.74 (0.18), residues: 670 sheet: -2.27 (0.34), residues: 205 loop : -1.37 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 183 TYR 0.016 0.001 TYR A 198 PHE 0.012 0.001 PHE D 255 TRP 0.072 0.002 TRP A 340 HIS 0.013 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16113) covalent geometry : angle 0.71897 / 0.35 (21934) hydrogen bonds : bond 0.04203 / 2.31 ( 577) hydrogen bonds : angle 4.25597 / 2.15 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 405 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8587 (t) cc_final: 0.8193 (p) REVERT: A 39 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8546 (ptt180) REVERT: A 153 LEU cc_start: 0.9149 (tp) cc_final: 0.8928 (tp) REVERT: A 328 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8265 (mttp) REVERT: B 44 MET cc_start: 0.8279 (ttp) cc_final: 0.7966 (ttm) REVERT: B 121 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8842 (tm-30) REVERT: B 124 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: B 162 ASN cc_start: 0.8654 (t0) cc_final: 0.8167 (t0) REVERT: B 167 GLU cc_start: 0.8529 (tt0) cc_final: 0.8326 (tt0) REVERT: B 283 MET cc_start: 0.9085 (mtm) cc_final: 0.8832 (mtm) REVERT: B 299 MET cc_start: 0.8480 (mtm) cc_final: 0.8228 (mtm) REVERT: B 313 MET cc_start: 0.8549 (tpp) cc_final: 0.8308 (tpp) REVERT: B 329 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9040 (mm) REVERT: B 334 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: B 340 TRP cc_start: 0.8557 (t60) cc_final: 0.7891 (t60) REVERT: B 364 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: C 115 ASN cc_start: 0.9162 (t0) cc_final: 0.8788 (t0) REVERT: C 161 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8406 (m-70) REVERT: C 325 MET cc_start: 0.8714 (tpp) cc_final: 0.8430 (tpt) REVERT: C 354 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8718 (mt0) REVERT: D 100 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: D 124 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: D 242 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8592 (mp) REVERT: D 275 HIS cc_start: 0.9501 (OUTLIER) cc_final: 0.9274 (p-80) REVERT: D 325 MET cc_start: 0.8942 (tpp) cc_final: 0.8036 (tpp) REVERT: E 39 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8448 (ptt180) REVERT: E 121 GLN cc_start: 0.9237 (tt0) cc_final: 0.8798 (tm-30) REVERT: E 125 GLU cc_start: 0.7964 (pt0) cc_final: 0.7667 (pt0) REVERT: E 263 GLN cc_start: 0.8834 (mt0) cc_final: 0.8583 (mt0) REVERT: E 275 HIS cc_start: 0.9526 (OUTLIER) cc_final: 0.9183 (p-80) outliers start: 107 outliers final: 70 residues processed: 465 average time/residue: 0.0985 time to fit residues: 72.5994 Evaluate side-chains 466 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 382 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 79 optimal weight: 0.0270 chunk 23 optimal weight: 100.0000 chunk 87 optimal weight: 0.4980 chunk 106 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 1 optimal weight: 110.0000 chunk 167 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 overall best weight: 4.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 92 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103878 restraints weight = 31531.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.106596 restraints weight = 14993.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108425 restraints weight = 8446.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109558 restraints weight = 5513.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110363 restraints weight = 3866.204| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16113 Z= 0.170 Angle : 0.724 8.364 21934 Z= 0.352 Chirality : 0.045 0.211 2505 Planarity : 0.004 0.047 2828 Dihedral : 8.170 83.472 2369 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.58 % Favored : 93.59 % Rotamer: Outliers : 7.12 % Allowed : 24.79 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.48 (0.19), residues: 1810 helix: -1.69 (0.18), residues: 670 sheet: -2.25 (0.34), residues: 205 loop : -1.36 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 256 TYR 0.018 0.001 TYR A 198 PHE 0.013 0.001 PHE C 255 TRP 0.075 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (16113) covalent geometry : angle 0.72394 / 0.35 (21934) hydrogen bonds : bond 0.04147 / 2.29 ( 577) hydrogen bonds : angle 4.20701 / 2.12 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 399 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8568 (t) cc_final: 0.8221 (p) REVERT: A 39 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8557 (ptt180) REVERT: A 153 LEU cc_start: 0.9138 (tp) cc_final: 0.8921 (tp) REVERT: A 328 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8287 (mttp) REVERT: B 121 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8879 (tm-30) REVERT: B 124 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: B 162 ASN cc_start: 0.8638 (t0) cc_final: 0.8152 (t0) REVERT: B 299 MET cc_start: 0.8512 (mtm) cc_final: 0.8244 (mtm) REVERT: B 313 MET cc_start: 0.8550 (tpp) cc_final: 0.8253 (tpp) REVERT: B 329 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9054 (mm) REVERT: B 334 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: B 340 TRP cc_start: 0.8566 (t60) cc_final: 0.7922 (t60) REVERT: B 364 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: C 161 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8454 (m-70) REVERT: C 190 MET cc_start: 0.8369 (ttt) cc_final: 0.7965 (ttt) REVERT: C 325 MET cc_start: 0.8677 (tpp) cc_final: 0.8422 (tpt) REVERT: C 354 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8649 (mt0) REVERT: C 359 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9044 (mtpp) REVERT: D 100 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: D 124 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: D 242 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8579 (mp) REVERT: D 325 MET cc_start: 0.8945 (tpp) cc_final: 0.8092 (tpp) REVERT: E 39 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8548 (ptt180) REVERT: E 121 GLN cc_start: 0.9216 (tt0) cc_final: 0.8897 (tm-30) REVERT: E 263 GLN cc_start: 0.8838 (mt0) cc_final: 0.8596 (mt0) REVERT: E 275 HIS cc_start: 0.9539 (OUTLIER) cc_final: 0.9193 (p-80) outliers start: 110 outliers final: 75 residues processed: 460 average time/residue: 0.0966 time to fit residues: 70.8405 Evaluate side-chains 471 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 382 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 178 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 25 optimal weight: 120.0000 chunk 186 optimal weight: 6.9990 chunk 26 optimal weight: 0.0870 chunk 114 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 0.0370 chunk 167 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** 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 = 0.3476 r_free = 0.3476 target = 0.121794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104837 restraints weight = 31773.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107533 restraints weight = 15080.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109429 restraints weight = 8627.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110615 restraints weight = 5489.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111394 restraints weight = 3802.776| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16113 Z= 0.153 Angle : 0.723 9.173 21934 Z= 0.350 Chirality : 0.045 0.186 2505 Planarity : 0.004 0.053 2828 Dihedral : 7.992 82.703 2367 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.52 % Favored : 93.65 % Rotamer: Outliers : 6.34 % Allowed : 26.02 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.42 (0.19), residues: 1810 helix: -1.64 (0.19), residues: 670 sheet: -2.21 (0.34), residues: 205 loop : -1.33 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 183 TYR 0.039 0.001 TYR B 69 PHE 0.012 0.001 PHE C 31 TRP 0.076 0.002 TRP A 340 HIS 0.012 0.002 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (16113) covalent geometry : angle 0.72304 / 0.35 (21934) hydrogen bonds : bond 0.03998 / 2.21 ( 577) hydrogen bonds : angle 4.17726 / 2.12 ( 1635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 397 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8529 (t) cc_final: 0.8185 (p) REVERT: A 39 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8526 (ptt180) REVERT: A 328 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8294 (mttp) REVERT: B 69 TYR cc_start: 0.8830 (m-80) cc_final: 0.8539 (m-10) REVERT: B 121 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8858 (tm-30) REVERT: B 124 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: B 162 ASN cc_start: 0.8624 (t0) cc_final: 0.8186 (t0) REVERT: B 190 MET cc_start: 0.8341 (ttt) cc_final: 0.7837 (ttt) REVERT: B 299 MET cc_start: 0.8476 (mtm) cc_final: 0.8235 (mtm) REVERT: B 313 MET cc_start: 0.8559 (tpp) cc_final: 0.8285 (tpp) REVERT: B 329 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9026 (mm) REVERT: B 334 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.6789 (pm20) REVERT: B 340 TRP cc_start: 0.8538 (t60) cc_final: 0.7997 (t60) REVERT: B 364 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: C 115 ASN cc_start: 0.9191 (t0) cc_final: 0.8865 (t0) REVERT: C 161 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8459 (m-70) REVERT: C 190 MET cc_start: 0.8394 (ttt) cc_final: 0.8082 (ttt) REVERT: C 325 MET cc_start: 0.8676 (tpp) cc_final: 0.8425 (tpt) REVERT: C 359 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9051 (mtpp) REVERT: D 124 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: D 242 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8540 (mp) REVERT: D 325 MET cc_start: 0.8942 (tpp) cc_final: 0.8078 (tpp) REVERT: D 334 GLU cc_start: 0.8217 (pt0) cc_final: 0.7992 (pp20) REVERT: D 352 PHE cc_start: 0.9232 (p90) cc_final: 0.8999 (p90) REVERT: E 39 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8523 (ptt180) REVERT: E 44 MET cc_start: 0.7803 (ttt) cc_final: 0.7142 (ttp) REVERT: E 263 GLN cc_start: 0.8837 (mt0) cc_final: 0.8586 (mt0) REVERT: E 275 HIS cc_start: 0.9533 (OUTLIER) cc_final: 0.9220 (p-80) outliers start: 98 outliers final: 71 residues processed: 451 average time/residue: 0.0973 time to fit residues: 69.3878 Evaluate side-chains 465 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 382 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 143 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 120.0000 chunk 172 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 chunk 2 optimal weight: 120.0000 chunk 181 optimal weight: 7.9990 chunk 7 optimal weight: 100.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS C 252 ASN ** D 88 HIS ** 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 = 0.3456 r_free = 0.3456 target = 0.120868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104104 restraints weight = 31688.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106694 restraints weight = 14965.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108438 restraints weight = 8575.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109760 restraints weight = 5725.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110608 restraints weight = 3920.496| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16113 Z= 0.159 Angle : 0.727 8.865 21934 Z= 0.352 Chirality : 0.045 0.193 2505 Planarity : 0.004 0.051 2828 Dihedral : 7.811 81.699 2364 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.75 % Favored : 93.59 % Rotamer: Outliers : 5.83 % Allowed : 27.06 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.27 (0.19), residues: 1810 helix: -1.44 (0.19), residues: 640 sheet: -2.20 (0.34), residues: 205 loop : -1.31 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 183 TYR 0.027 0.001 TYR B 69 PHE 0.012 0.001 PHE A 255 TRP 0.081 0.003 TRP A 340 HIS 0.012 0.002 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16113) covalent geometry : angle 0.72711 / 0.35 (21934) hydrogen bonds : bond 0.03962 / 2.19 ( 577) hydrogen bonds : angle 4.19130 / 2.12 ( 1635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 392 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8526 (t) cc_final: 0.8221 (p) REVERT: A 39 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8506 (ptt180) REVERT: A 328 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8287 (mttp) REVERT: B 69 TYR cc_start: 0.8934 (m-80) cc_final: 0.8609 (m-10) REVERT: B 121 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8879 (tm-30) REVERT: B 132 MET cc_start: 0.8983 (tpp) cc_final: 0.8569 (tpt) REVERT: B 162 ASN cc_start: 0.8623 (t0) cc_final: 0.8124 (t0) REVERT: B 167 GLU cc_start: 0.8409 (tt0) cc_final: 0.8139 (tt0) REVERT: B 190 MET cc_start: 0.8330 (ttt) cc_final: 0.7958 (ttt) REVERT: B 313 MET cc_start: 0.8619 (tpp) cc_final: 0.8342 (tpp) REVERT: B 329 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9020 (mm) REVERT: B 334 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: B 340 TRP cc_start: 0.8533 (t60) cc_final: 0.8028 (t60) REVERT: B 364 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: C 115 ASN cc_start: 0.9187 (t0) cc_final: 0.8881 (t0) REVERT: C 161 HIS cc_start: 0.8918 (OUTLIER) cc_final: 0.8448 (m-70) REVERT: C 190 MET cc_start: 0.8432 (ttt) cc_final: 0.8205 (ttt) REVERT: C 248 ILE cc_start: 0.9328 (mt) cc_final: 0.9087 (tt) REVERT: C 325 MET cc_start: 0.8685 (tpp) cc_final: 0.8451 (tpt) REVERT: C 359 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9048 (mtpp) REVERT: D 121 GLN cc_start: 0.9416 (tm-30) cc_final: 0.8848 (tm-30) REVERT: D 124 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: D 242 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 325 MET cc_start: 0.8921 (tpp) cc_final: 0.8061 (tpp) REVERT: D 334 GLU cc_start: 0.8196 (pt0) cc_final: 0.7958 (pp20) REVERT: D 352 PHE cc_start: 0.9194 (p90) cc_final: 0.8958 (p90) REVERT: E 39 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8534 (ptt180) REVERT: E 44 MET cc_start: 0.7779 (ttt) cc_final: 0.7054 (ttp) REVERT: E 275 HIS cc_start: 0.9539 (OUTLIER) cc_final: 0.9225 (p-80) outliers start: 90 outliers final: 70 residues processed: 445 average time/residue: 0.0944 time to fit residues: 66.7295 Evaluate side-chains 467 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 386 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 169 TYR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105405 restraints weight = 31816.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108013 restraints weight = 15074.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109783 restraints weight = 8611.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111061 restraints weight = 5692.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111841 restraints weight = 3912.993| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16113 Z= 0.146 Angle : 0.735 8.777 21934 Z= 0.357 Chirality : 0.045 0.193 2505 Planarity : 0.004 0.038 2828 Dihedral : 7.670 80.162 2363 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.36 % Favored : 94.03 % Rotamer: Outliers : 5.44 % Allowed : 27.25 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.20 (0.19), residues: 1810 helix: -1.38 (0.20), residues: 640 sheet: -2.16 (0.34), residues: 205 loop : -1.27 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 256 TYR 0.027 0.001 TYR B 279 PHE 0.014 0.001 PHE D 200 TRP 0.088 0.003 TRP E 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16113) covalent geometry : angle 0.73525 / 0.36 (21934) hydrogen bonds : bond 0.03929 / 2.17 ( 577) hydrogen bonds : angle 4.17650 / 2.12 ( 1635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 400 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8430 (ptt180) REVERT: A 328 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8289 (mttp) REVERT: A 352 PHE cc_start: 0.9181 (p90) cc_final: 0.8856 (p90) REVERT: B 69 TYR cc_start: 0.8956 (m-80) cc_final: 0.8695 (m-10) REVERT: B 121 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8877 (tm-30) REVERT: B 162 ASN cc_start: 0.8612 (t0) cc_final: 0.8116 (t0) REVERT: B 167 GLU cc_start: 0.8465 (tt0) cc_final: 0.8202 (tt0) REVERT: B 190 MET cc_start: 0.8263 (ttt) cc_final: 0.8024 (ttt) REVERT: B 313 MET cc_start: 0.8604 (tpp) cc_final: 0.8341 (tpp) REVERT: B 329 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8971 (mm) REVERT: B 340 TRP cc_start: 0.8504 (t60) cc_final: 0.8164 (t60) REVERT: B 364 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: C 115 ASN cc_start: 0.9170 (t0) cc_final: 0.8874 (t0) REVERT: C 161 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8446 (m-70) REVERT: C 190 MET cc_start: 0.8546 (ttt) cc_final: 0.8324 (ttt) REVERT: C 248 ILE cc_start: 0.9316 (mt) cc_final: 0.8982 (tt) REVERT: C 325 MET cc_start: 0.8670 (tpp) cc_final: 0.8433 (tpt) REVERT: C 359 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9042 (mtpp) REVERT: D 44 MET cc_start: 0.8665 (ttp) cc_final: 0.8418 (ttm) REVERT: D 121 GLN cc_start: 0.9400 (tm-30) cc_final: 0.8853 (tm-30) REVERT: D 124 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: D 242 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8495 (mp) REVERT: D 314 GLN cc_start: 0.9082 (tt0) cc_final: 0.8816 (tt0) REVERT: D 325 MET cc_start: 0.8924 (tpp) cc_final: 0.8063 (tpp) REVERT: D 352 PHE cc_start: 0.9143 (p90) cc_final: 0.8917 (p90) REVERT: E 39 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8609 (ptt180) REVERT: E 44 MET cc_start: 0.7771 (ttt) cc_final: 0.7259 (ttp) REVERT: E 132 MET cc_start: 0.9017 (tpp) cc_final: 0.8596 (mmm) REVERT: E 275 HIS cc_start: 0.9525 (OUTLIER) cc_final: 0.9248 (p-80) outliers start: 84 outliers final: 65 residues processed: 445 average time/residue: 0.0962 time to fit residues: 67.9947 Evaluate side-chains 464 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 389 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 169 TYR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 220.0000 chunk 139 optimal weight: 20.0000 chunk 133 optimal weight: 0.0470 chunk 113 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** 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 = 0.3510 r_free = 0.3510 target = 0.124392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107525 restraints weight = 31431.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110196 restraints weight = 14924.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112168 restraints weight = 8561.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113399 restraints weight = 5439.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114192 restraints weight = 3773.887| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16113 Z= 0.134 Angle : 0.731 9.166 21934 Z= 0.352 Chirality : 0.045 0.193 2505 Planarity : 0.004 0.037 2828 Dihedral : 7.425 75.684 2363 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.41 % Favored : 94.03 % Rotamer: Outliers : 4.47 % Allowed : 28.67 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.08 (0.20), residues: 1810 helix: -1.23 (0.20), residues: 640 sheet: -2.07 (0.35), residues: 205 loop : -1.25 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 183 TYR 0.031 0.001 TYR B 279 PHE 0.013 0.001 PHE C 255 TRP 0.095 0.003 TRP E 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16113) covalent geometry : angle 0.73070 / 0.35 (21934) hydrogen bonds : bond 0.03866 / 2.14 ( 577) hydrogen bonds : angle 4.14638 / 2.10 ( 1635) =============================================================================== Job complete usr+sys time: 2390.66 seconds wall clock time: 42 minutes 15.61 seconds (2535.61 seconds total)