Starting phenix.real_space_refine on Sat Jun 14 00:21:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j8a_6124/06_2025/3j8a_6124.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j8a_6124/06_2025/3j8a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3j8a_6124/06_2025/3j8a_6124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j8a_6124/06_2025/3j8a_6124.map" model { file = "/net/cci-nas-00/data/ceres_data/3j8a_6124/06_2025/3j8a_6124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j8a_6124/06_2025/3j8a_6124.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.08, per 1000 atoms: 0.57 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: 3.84 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.47 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: 4.60 Time building geometry restraints manager: 4.56 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: 0.04 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.930 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 19.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP D 340 HIS 0.016 0.002 HIS C 275 PHE 0.016 0.002 PHE D 255 TYR 0.013 0.002 TYR A 169 ARG 0.005 0.001 ARG D 254 Details of bonding type rmsd hydrogen bonds : bond 0.22471 ( 577) hydrogen bonds : angle 9.19302 ( 1635) covalent geometry : bond 0.00602 (16113) covalent geometry : angle 1.27050 (21934) *********************** 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 : 1.596 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: 0.8704 (p) REVERT: A 100 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7449 (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: 0.8874 (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: 0.9088 (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: 0.8658 (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: 0.8085 (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: 0.8558 (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: 0.2421 time to fit residues: 215.5263 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 : 1.586 ------------------------------------------------------------------------------- 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 173 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** 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** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101867 restraints weight = 31468.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104389 restraints weight = 14805.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106229 restraints weight = 8600.416| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16113 Z= 0.197 Angle : 0.803 7.807 21934 Z= 0.410 Chirality : 0.045 0.183 2505 Planarity : 0.005 0.053 2828 Dihedral : 10.032 95.870 2421 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.91 % Favored : 93.26 % Rotamer: Outliers : 7.18 % Allowed : 20.58 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.17), residues: 1810 helix: -2.87 (0.16), residues: 650 sheet: -1.57 (0.40), residues: 150 loop : -2.27 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 340 HIS 0.013 0.001 HIS C 275 PHE 0.011 0.002 PHE D 255 TYR 0.017 0.001 TYR D 169 ARG 0.005 0.001 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.05558 ( 577) hydrogen bonds : angle 5.11114 ( 1635) covalent geometry : bond 0.00447 (16113) covalent geometry : angle 0.80259 (21934) *********************** 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: 111 poor density : 436 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9193 (m) REVERT: A 10 CYS cc_start: 0.8896 (t) cc_final: 0.8425 (p) REVERT: A 195 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: A 328 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8024 (mttp) REVERT: B 18 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8940 (mmtm) REVERT: B 47 MET cc_start: 0.6896 (ptm) cc_final: 0.6685 (ptp) REVERT: B 121 GLN cc_start: 0.9168 (tt0) cc_final: 0.8841 (tm-30) REVERT: B 162 ASN cc_start: 0.8767 (t0) cc_final: 0.8342 (t0) REVERT: B 256 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8426 (ttm110) REVERT: B 329 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 340 TRP cc_start: 0.8694 (t60) cc_final: 0.8042 (t60) REVERT: B 369 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8867 (mm) REVERT: C 18 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9125 (mmtp) REVERT: C 39 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8471 (ptp-170) REVERT: C 115 ASN cc_start: 0.9253 (t0) cc_final: 0.8350 (t0) REVERT: C 121 GLN cc_start: 0.9392 (tm-30) cc_final: 0.9057 (tm-30) REVERT: C 157 ASP cc_start: 0.8814 (t0) cc_final: 0.8590 (t0) REVERT: C 205 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7967 (tm-30) REVERT: C 246 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8689 (tm-30) REVERT: C 248 ILE cc_start: 0.9551 (mt) cc_final: 0.9248 (tt) REVERT: C 300 SER cc_start: 0.9368 (m) cc_final: 0.8933 (p) REVERT: C 325 MET cc_start: 0.8795 (tpp) cc_final: 0.8470 (tpt) REVERT: D 44 MET cc_start: 0.8536 (ttt) cc_final: 0.8282 (ttp) REVERT: D 100 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: D 115 ASN cc_start: 0.8870 (t0) cc_final: 0.8440 (t0) REVERT: D 242 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8738 (mp) REVERT: D 325 MET cc_start: 0.9155 (mmm) cc_final: 0.8447 (tpp) REVERT: D 334 GLU cc_start: 0.8179 (pt0) cc_final: 0.7931 (pt0) REVERT: D 340 TRP cc_start: 0.8722 (t60) cc_final: 0.7973 (t60) REVERT: E 39 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8210 (ptt180) REVERT: E 132 MET cc_start: 0.9080 (tpp) cc_final: 0.8806 (tpp) REVERT: E 270 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8076 (mt-10) outliers start: 111 outliers final: 60 residues processed: 502 average time/residue: 0.2424 time to fit residues: 185.4408 Evaluate side-chains 455 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 385 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 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 75 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 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 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 75 ILE 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 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 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 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 172 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 196 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 189 optimal weight: 0.0970 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 275 HIS ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104956 restraints weight = 31127.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107517 restraints weight = 14728.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109278 restraints weight = 8440.746| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16113 Z= 0.146 Angle : 0.740 7.950 21934 Z= 0.366 Chirality : 0.044 0.182 2505 Planarity : 0.005 0.041 2828 Dihedral : 9.292 90.140 2390 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.14 % Favored : 94.03 % Rotamer: Outliers : 6.47 % Allowed : 22.72 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.18), residues: 1810 helix: -2.33 (0.17), residues: 675 sheet: -2.75 (0.28), residues: 255 loop : -1.67 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 340 HIS 0.013 0.001 HIS C 275 PHE 0.010 0.001 PHE D 255 TYR 0.029 0.001 TYR B 279 ARG 0.003 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 577) hydrogen bonds : angle 4.63408 ( 1635) covalent geometry : bond 0.00314 (16113) covalent geometry : angle 0.74035 (21934) *********************** 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 526 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 426 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8828 (t) cc_final: 0.8477 (p) REVERT: A 39 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8505 (ptt180) REVERT: A 195 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: A 328 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: B 121 GLN cc_start: 0.9189 (tt0) cc_final: 0.8830 (tm-30) REVERT: B 124 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: B 132 MET cc_start: 0.8673 (tpp) cc_final: 0.8316 (tpt) REVERT: B 162 ASN cc_start: 0.8608 (t0) cc_final: 0.8346 (t0) REVERT: B 190 MET cc_start: 0.9007 (ttp) cc_final: 0.8789 (ttt) REVERT: B 329 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9027 (mm) REVERT: B 340 TRP cc_start: 0.8616 (t60) cc_final: 0.7917 (t60) REVERT: B 364 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7931 (pp20) REVERT: C 39 ARG cc_start: 0.8646 (ptp-170) cc_final: 0.8181 (ptt180) REVERT: C 115 ASN cc_start: 0.9213 (t0) cc_final: 0.8164 (t0) REVERT: C 121 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8541 (tm-30) REVERT: C 183 ARG cc_start: 0.9240 (tpp80) cc_final: 0.8870 (tpp80) REVERT: C 246 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8581 (tm-30) REVERT: C 248 ILE cc_start: 0.9500 (mt) cc_final: 0.9299 (mt) REVERT: C 300 SER cc_start: 0.9346 (m) cc_final: 0.8906 (p) REVERT: C 325 MET cc_start: 0.8768 (tpp) cc_final: 0.8460 (tpt) REVERT: C 359 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9015 (mtpp) REVERT: D 242 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8688 (mp) REVERT: D 325 MET cc_start: 0.9089 (mmm) cc_final: 0.8385 (tpp) REVERT: D 334 GLU cc_start: 0.8207 (pt0) cc_final: 0.7897 (pt0) REVERT: E 39 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8367 (ptt180) REVERT: E 121 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: E 125 GLU cc_start: 0.8049 (pt0) cc_final: 0.7791 (pt0) REVERT: E 263 GLN cc_start: 0.8737 (mt0) cc_final: 0.8303 (mt0) REVERT: E 270 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8130 (mt-10) outliers start: 100 outliers final: 57 residues processed: 487 average time/residue: 0.2416 time to fit residues: 179.8062 Evaluate side-chains 455 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 388 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 75 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 193 LEU Chi-restraints excluded: chain A residue 195 GLU 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 330 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 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 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 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR 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 269 MET Chi-restraints excluded: chain C residue 275 HIS 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 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE 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 236 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 329 ILE 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 100 GLU Chi-restraints excluded: chain E residue 121 GLN 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 275 HIS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 78 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 14 optimal weight: 110.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103362 restraints weight = 31645.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.105895 restraints weight = 14948.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107714 restraints weight = 8602.042| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16113 Z= 0.179 Angle : 0.736 8.331 21934 Z= 0.361 Chirality : 0.045 0.188 2505 Planarity : 0.004 0.039 2828 Dihedral : 8.907 86.875 2382 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.86 % Favored : 93.31 % Rotamer: Outliers : 7.06 % Allowed : 24.27 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.19), residues: 1810 helix: -2.05 (0.17), residues: 675 sheet: -2.33 (0.34), residues: 205 loop : -1.54 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 340 HIS 0.014 0.001 HIS C 275 PHE 0.013 0.002 PHE C 255 TYR 0.017 0.001 TYR D 169 ARG 0.004 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 577) hydrogen bonds : angle 4.45815 ( 1635) covalent geometry : bond 0.00411 (16113) covalent geometry : angle 0.73574 (21934) *********************** 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 517 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 408 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8811 (t) cc_final: 0.8488 (p) REVERT: A 39 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8563 (ptt180) REVERT: A 195 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: A 328 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8286 (mttp) REVERT: B 121 GLN cc_start: 0.9183 (tt0) cc_final: 0.8827 (tm-30) REVERT: B 124 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: B 162 ASN cc_start: 0.8622 (t0) cc_final: 0.8339 (t0) REVERT: B 190 MET cc_start: 0.8985 (ttp) cc_final: 0.8763 (ttt) REVERT: B 329 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9054 (mm) REVERT: B 334 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: B 336 LYS cc_start: 0.9263 (tttm) cc_final: 0.9044 (tttm) REVERT: B 340 TRP cc_start: 0.8628 (t60) cc_final: 0.7983 (t60) REVERT: C 39 ARG cc_start: 0.8703 (ptp-170) cc_final: 0.8266 (ptp-170) REVERT: C 121 GLN cc_start: 0.9328 (tm-30) cc_final: 0.9088 (tm-30) REVERT: C 202 THR cc_start: 0.8843 (t) cc_final: 0.8307 (t) REVERT: C 246 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8697 (tm-30) REVERT: C 259 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8614 (tm-30) REVERT: C 300 SER cc_start: 0.9379 (m) cc_final: 0.8958 (p) REVERT: C 325 MET cc_start: 0.8717 (tpp) cc_final: 0.8393 (tpt) REVERT: C 359 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9027 (mtpp) REVERT: D 115 ASN cc_start: 0.8744 (t0) cc_final: 0.8301 (t0) REVERT: D 242 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8690 (mp) REVERT: D 325 MET cc_start: 0.9089 (mmm) cc_final: 0.8386 (tpp) REVERT: E 121 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8661 (tm-30) REVERT: E 125 GLU cc_start: 0.7908 (pt0) cc_final: 0.7601 (pt0) REVERT: E 270 GLU cc_start: 0.8887 (mt-10) cc_final: 0.7939 (mt-10) outliers start: 109 outliers final: 71 residues processed: 471 average time/residue: 0.2330 time to fit residues: 169.0205 Evaluate side-chains 475 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 396 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 71 ILE Chi-restraints excluded: chain A residue 75 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 193 LEU Chi-restraints excluded: chain A residue 195 GLU 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 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 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 236 LEU Chi-restraints excluded: chain B residue 242 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 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR 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 267 ILE Chi-restraints excluded: chain C residue 275 HIS 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 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 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 237 GLU 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 237 GLU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 145 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 114 optimal weight: 0.2980 chunk 173 optimal weight: 50.0000 chunk 122 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 198 optimal weight: 0.2980 chunk 11 optimal weight: 110.0000 chunk 105 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106302 restraints weight = 31676.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108943 restraints weight = 14966.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110820 restraints weight = 8509.113| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16113 Z= 0.137 Angle : 0.713 9.376 21934 Z= 0.345 Chirality : 0.044 0.199 2505 Planarity : 0.004 0.037 2828 Dihedral : 8.610 84.275 2382 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.83 % Allowed : 4.64 % Favored : 94.53 % Rotamer: Outliers : 7.25 % Allowed : 24.98 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.19), residues: 1810 helix: -1.77 (0.18), residues: 675 sheet: -2.20 (0.34), residues: 205 loop : -1.42 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 PHE 0.012 0.001 PHE C 255 TYR 0.014 0.001 TYR A 198 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 577) hydrogen bonds : angle 4.23233 ( 1635) covalent geometry : bond 0.00302 (16113) covalent geometry : angle 0.71272 (21934) *********************** 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 534 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 422 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8620 (t) cc_final: 0.8181 (p) REVERT: A 39 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8557 (ptt180) REVERT: A 153 LEU cc_start: 0.9121 (tp) cc_final: 0.8894 (tp) REVERT: A 328 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: B 44 MET cc_start: 0.8344 (ttp) cc_final: 0.7958 (ttm) REVERT: B 121 GLN cc_start: 0.9142 (tt0) cc_final: 0.8784 (tm-30) REVERT: B 124 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: B 162 ASN cc_start: 0.8539 (t0) cc_final: 0.8270 (t0) REVERT: B 190 MET cc_start: 0.8979 (ttp) cc_final: 0.8748 (ttt) REVERT: B 329 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9051 (mm) REVERT: B 334 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: B 336 LYS cc_start: 0.9225 (tttm) cc_final: 0.8986 (tttm) REVERT: B 340 TRP cc_start: 0.8507 (t60) cc_final: 0.8054 (t60) REVERT: C 115 ASN cc_start: 0.9070 (t0) cc_final: 0.7957 (t0) REVERT: C 246 GLN cc_start: 0.9089 (tp-100) cc_final: 0.8756 (tm-30) REVERT: C 325 MET cc_start: 0.8674 (tpp) cc_final: 0.8379 (tpt) REVERT: D 121 GLN cc_start: 0.9310 (tm-30) cc_final: 0.8797 (tm-30) REVERT: D 124 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: D 242 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8631 (mp) REVERT: D 325 MET cc_start: 0.9043 (mmm) cc_final: 0.8348 (tpp) REVERT: E 100 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: E 121 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: E 125 GLU cc_start: 0.7720 (pt0) cc_final: 0.7355 (pt0) REVERT: E 275 HIS cc_start: 0.9513 (OUTLIER) cc_final: 0.9040 (p-80) outliers start: 112 outliers final: 63 residues processed: 485 average time/residue: 0.2514 time to fit residues: 187.2137 Evaluate side-chains 449 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 376 time to evaluate : 2.210 ------------------------------------------------------------------------------- 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 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 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 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 5 THR 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 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 267 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 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 124 PHE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU 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 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 80 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 22 optimal weight: 90.0000 chunk 137 optimal weight: 20.0000 chunk 119 optimal weight: 0.0870 chunk 166 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 275 HIS ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103066 restraints weight = 31865.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105557 restraints weight = 15097.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107448 restraints weight = 8694.608| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 16113 Z= 0.198 Angle : 0.729 7.929 21934 Z= 0.356 Chirality : 0.046 0.202 2505 Planarity : 0.004 0.039 2828 Dihedral : 8.175 84.309 2370 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.19 % Favored : 92.98 % Rotamer: Outliers : 7.25 % Allowed : 24.27 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.19), residues: 1810 helix: -1.70 (0.18), residues: 670 sheet: -2.19 (0.34), residues: 205 loop : -1.35 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.015 0.002 PHE E 255 TYR 0.024 0.001 TYR B 69 ARG 0.006 0.000 ARG B 183 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 577) hydrogen bonds : angle 4.23185 ( 1635) covalent geometry : bond 0.00459 (16113) covalent geometry : angle 0.72917 (21934) *********************** 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 511 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 399 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8597 (t) cc_final: 0.8291 (p) REVERT: A 39 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8552 (ptt180) REVERT: A 153 LEU cc_start: 0.9127 (tp) cc_final: 0.8906 (tp) REVERT: A 328 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8316 (mttp) REVERT: B 44 MET cc_start: 0.8346 (ttp) cc_final: 0.7989 (ttm) REVERT: B 121 GLN cc_start: 0.9161 (tt0) cc_final: 0.8819 (tm-30) REVERT: B 124 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: B 162 ASN cc_start: 0.8648 (t0) cc_final: 0.8161 (t0) REVERT: B 190 MET cc_start: 0.9012 (ttp) cc_final: 0.8773 (ttt) REVERT: B 329 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9043 (mm) REVERT: B 334 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: B 336 LYS cc_start: 0.9213 (tttm) cc_final: 0.8971 (tttm) REVERT: B 340 TRP cc_start: 0.8636 (t60) cc_final: 0.7942 (t60) REVERT: C 115 ASN cc_start: 0.9189 (t0) cc_final: 0.8198 (t0) REVERT: C 161 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.8544 (m-70) REVERT: C 190 MET cc_start: 0.8397 (ttt) cc_final: 0.8061 (ttt) REVERT: C 225 ASN cc_start: 0.8717 (t0) cc_final: 0.8379 (t0) REVERT: C 259 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8802 (tm-30) REVERT: C 325 MET cc_start: 0.8670 (tpp) cc_final: 0.8398 (tpt) REVERT: D 100 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: D 115 ASN cc_start: 0.8821 (t0) cc_final: 0.8355 (t0) REVERT: D 124 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: D 242 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8669 (mp) REVERT: D 275 HIS cc_start: 0.9500 (OUTLIER) cc_final: 0.9087 (p-80) REVERT: D 325 MET cc_start: 0.9036 (mmm) cc_final: 0.8466 (tpp) REVERT: E 100 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: E 121 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8881 (tt0) REVERT: E 275 HIS cc_start: 0.9546 (OUTLIER) cc_final: 0.9120 (p-80) outliers start: 112 outliers final: 76 residues processed: 460 average time/residue: 0.2687 time to fit residues: 193.4527 Evaluate side-chains 479 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 390 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 106 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 282 ILE 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 364 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 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 309 ILE 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 5 THR 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 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL 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 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 237 GLU 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 75 ILE Chi-restraints excluded: chain E residue 76 ILE 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 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 120 optimal weight: 10.0000 chunk 1 optimal weight: 100.0000 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 220.0000 chunk 98 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105318 restraints weight = 31951.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107808 restraints weight = 15090.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109733 restraints weight = 8762.151| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16113 Z= 0.151 Angle : 0.716 8.487 21934 Z= 0.346 Chirality : 0.045 0.179 2505 Planarity : 0.004 0.038 2828 Dihedral : 8.031 83.972 2370 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.83 % Allowed : 4.86 % Favored : 94.31 % Rotamer: Outliers : 6.28 % Allowed : 25.37 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.19), residues: 1810 helix: -1.61 (0.19), residues: 670 sheet: -2.18 (0.34), residues: 205 loop : -1.25 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP A 340 HIS 0.013 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.015 0.001 TYR B 279 ARG 0.003 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 577) hydrogen bonds : angle 4.17162 ( 1635) covalent geometry : bond 0.00347 (16113) covalent geometry : angle 0.71571 (21934) *********************** 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 500 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 403 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8515 (t) cc_final: 0.8188 (p) REVERT: A 39 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8476 (ptt180) REVERT: A 153 LEU cc_start: 0.9127 (tp) cc_final: 0.8905 (tp) REVERT: A 328 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8307 (mttp) REVERT: B 121 GLN cc_start: 0.9135 (tt0) cc_final: 0.8772 (tm-30) REVERT: B 124 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: B 162 ASN cc_start: 0.8617 (t0) cc_final: 0.8142 (t0) REVERT: B 190 MET cc_start: 0.8984 (ttp) cc_final: 0.8738 (ttt) REVERT: B 283 MET cc_start: 0.9035 (mtm) cc_final: 0.8796 (mtm) REVERT: B 329 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9053 (mm) REVERT: B 334 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.6742 (pm20) REVERT: B 336 LYS cc_start: 0.9184 (tttm) cc_final: 0.8925 (tttm) REVERT: B 340 TRP cc_start: 0.8582 (t60) cc_final: 0.8052 (t60) REVERT: C 115 ASN cc_start: 0.9157 (t0) cc_final: 0.8803 (t0) REVERT: C 161 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8506 (m-70) REVERT: C 190 MET cc_start: 0.8399 (ttt) cc_final: 0.8140 (ttt) REVERT: C 259 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8804 (tm-30) REVERT: C 325 MET cc_start: 0.8656 (tpp) cc_final: 0.8379 (tpt) REVERT: D 100 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: D 124 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: D 242 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8610 (mp) REVERT: D 275 HIS cc_start: 0.9489 (OUTLIER) cc_final: 0.9157 (p-80) REVERT: D 314 GLN cc_start: 0.9092 (tt0) cc_final: 0.8829 (mt0) REVERT: D 325 MET cc_start: 0.9021 (mmm) cc_final: 0.8386 (tpp) REVERT: E 189 LEU cc_start: 0.9667 (tp) cc_final: 0.9460 (tp) REVERT: E 263 GLN cc_start: 0.8886 (mt0) cc_final: 0.8649 (mt0) REVERT: E 275 HIS cc_start: 0.9518 (OUTLIER) cc_final: 0.9194 (p-80) outliers start: 97 outliers final: 70 residues processed: 460 average time/residue: 0.2493 time to fit residues: 178.0499 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 : 1.799 ------------------------------------------------------------------------------- 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 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 275 HIS Chi-restraints excluded: chain A residue 282 ILE 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 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 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 LEU 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 C residue 5 THR Chi-restraints excluded: chain C residue 71 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 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 275 HIS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL 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 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 237 GLU Chi-restraints excluded: chain D residue 242 LEU 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 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 25 optimal weight: 120.0000 chunk 184 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 10 optimal weight: 110.0000 chunk 19 optimal weight: 220.0000 chunk 193 optimal weight: 20.0000 chunk 175 optimal weight: 0.0170 chunk 95 optimal weight: 20.0000 chunk 202 optimal weight: 30.0000 overall best weight: 5.0028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.103643 restraints weight = 31703.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106165 restraints weight = 15057.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108097 restraints weight = 8789.273| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16113 Z= 0.184 Angle : 0.732 9.444 21934 Z= 0.355 Chirality : 0.045 0.184 2505 Planarity : 0.004 0.038 2828 Dihedral : 7.879 83.568 2364 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.13 % Favored : 93.09 % Rotamer: Outliers : 6.67 % Allowed : 25.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.19), residues: 1810 helix: -1.62 (0.19), residues: 670 sheet: -2.23 (0.34), residues: 205 loop : -1.29 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.003 TRP A 340 HIS 0.012 0.001 HIS C 275 PHE 0.021 0.002 PHE D 352 TYR 0.034 0.001 TYR B 69 ARG 0.006 0.000 ARG B 183 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 577) hydrogen bonds : angle 4.15163 ( 1635) covalent geometry : bond 0.00428 (16113) covalent geometry : angle 0.73235 (21934) *********************** 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 496 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 393 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8567 (t) cc_final: 0.8260 (p) REVERT: A 39 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8526 (ptt180) REVERT: A 153 LEU cc_start: 0.9148 (tp) cc_final: 0.8932 (tp) REVERT: A 328 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8320 (mttp) REVERT: B 121 GLN cc_start: 0.9096 (tt0) cc_final: 0.8773 (tm-30) REVERT: B 124 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: B 162 ASN cc_start: 0.8656 (t0) cc_final: 0.8239 (t0) REVERT: B 190 MET cc_start: 0.9007 (ttp) cc_final: 0.8772 (ttt) REVERT: B 299 MET cc_start: 0.8456 (mtm) cc_final: 0.8222 (mtm) REVERT: B 329 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9064 (mm) REVERT: B 334 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: B 336 LYS cc_start: 0.9205 (tttm) cc_final: 0.8940 (tttm) REVERT: B 340 TRP cc_start: 0.8620 (t60) cc_final: 0.7896 (t60) REVERT: C 115 ASN cc_start: 0.9222 (t0) cc_final: 0.8241 (t0) REVERT: C 124 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: C 161 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8535 (m-70) REVERT: C 248 ILE cc_start: 0.9317 (mt) cc_final: 0.9051 (tt) REVERT: C 259 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8770 (tm-30) REVERT: C 325 MET cc_start: 0.8709 (tpp) cc_final: 0.8470 (tpt) REVERT: D 47 MET cc_start: 0.7017 (ttp) cc_final: 0.6812 (mtp) REVERT: D 115 ASN cc_start: 0.8890 (t0) cc_final: 0.8403 (t0) REVERT: D 124 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: D 242 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8594 (mp) REVERT: D 275 HIS cc_start: 0.9500 (OUTLIER) cc_final: 0.9286 (p-80) REVERT: D 325 MET cc_start: 0.9055 (mmm) cc_final: 0.8471 (tpp) REVERT: E 39 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8518 (ptt180) REVERT: E 121 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8725 (tm-30) REVERT: E 189 LEU cc_start: 0.9621 (tp) cc_final: 0.9417 (tp) REVERT: E 275 HIS cc_start: 0.9547 (OUTLIER) cc_final: 0.9224 (p-80) outliers start: 103 outliers final: 74 residues processed: 451 average time/residue: 0.2390 time to fit residues: 168.1159 Evaluate side-chains 469 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 383 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 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 275 HIS Chi-restraints excluded: chain A residue 282 ILE 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 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 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 LEU 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 C residue 5 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 124 PHE 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 193 LEU Chi-restraints excluded: chain C residue 202 THR 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 275 HIS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL 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 237 GLU 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 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 51 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 25 optimal weight: 120.0000 chunk 122 optimal weight: 7.9990 chunk 2 optimal weight: 120.0000 chunk 132 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106733 restraints weight = 31677.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109242 restraints weight = 15009.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111149 restraints weight = 8752.583| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16113 Z= 0.144 Angle : 0.726 8.903 21934 Z= 0.350 Chirality : 0.045 0.187 2505 Planarity : 0.004 0.039 2828 Dihedral : 7.651 82.210 2361 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.66 % Allowed : 4.86 % Favored : 94.48 % Rotamer: Outliers : 5.70 % Allowed : 26.73 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.19), residues: 1810 helix: -1.40 (0.19), residues: 640 sheet: -2.17 (0.34), residues: 205 loop : -1.22 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.002 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.018 0.001 PHE D 352 TYR 0.023 0.001 TYR B 69 ARG 0.004 0.000 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 577) hydrogen bonds : angle 4.08026 ( 1635) covalent geometry : bond 0.00328 (16113) covalent geometry : angle 0.72578 (21934) *********************** 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 486 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 398 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8522 (t) cc_final: 0.8168 (p) REVERT: A 39 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8494 (ptt180) REVERT: A 328 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8304 (mttp) REVERT: B 121 GLN cc_start: 0.9076 (tt0) cc_final: 0.8736 (tm-30) REVERT: B 124 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: B 162 ASN cc_start: 0.8639 (t0) cc_final: 0.8248 (t0) REVERT: B 167 GLU cc_start: 0.8400 (tt0) cc_final: 0.8167 (tt0) REVERT: B 184 ASP cc_start: 0.9086 (m-30) cc_final: 0.8844 (m-30) REVERT: B 190 MET cc_start: 0.8967 (ttp) cc_final: 0.8718 (ttt) REVERT: B 329 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9007 (mm) REVERT: B 336 LYS cc_start: 0.9169 (tttm) cc_final: 0.8900 (tttm) REVERT: B 340 TRP cc_start: 0.8536 (t60) cc_final: 0.8152 (t60) REVERT: C 115 ASN cc_start: 0.9198 (t0) cc_final: 0.8269 (t0) REVERT: C 124 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: C 161 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8482 (m-70) REVERT: C 248 ILE cc_start: 0.9282 (mt) cc_final: 0.8955 (tt) REVERT: C 259 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8757 (tm-30) REVERT: C 325 MET cc_start: 0.8680 (tpp) cc_final: 0.8445 (tpt) REVERT: D 47 MET cc_start: 0.6983 (ttp) cc_final: 0.6774 (mtp) REVERT: D 100 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: D 121 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8506 (tm-30) REVERT: D 124 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: D 125 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8080 (mt-10) REVERT: D 190 MET cc_start: 0.8874 (tpp) cc_final: 0.7475 (ttt) REVERT: D 242 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8546 (mp) REVERT: D 314 GLN cc_start: 0.9060 (tt0) cc_final: 0.8841 (tt0) REVERT: E 121 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8381 (tm-30) REVERT: E 275 HIS cc_start: 0.9509 (OUTLIER) cc_final: 0.9177 (p-80) outliers start: 88 outliers final: 66 residues processed: 448 average time/residue: 0.2274 time to fit residues: 158.1544 Evaluate side-chains 462 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 386 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 282 ILE 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 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 LEU 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 C residue 5 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 124 PHE 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 269 MET Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL 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 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 188 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 11 optimal weight: 120.0000 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS E 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104171 restraints weight = 31886.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106724 restraints weight = 14942.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108616 restraints weight = 8668.093| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3507 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= 0.167 Angle : 0.739 9.169 21934 Z= 0.357 Chirality : 0.045 0.194 2505 Planarity : 0.004 0.053 2828 Dihedral : 7.523 81.029 2359 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.91 % Favored : 93.48 % Rotamer: Outliers : 5.37 % Allowed : 27.18 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.19), residues: 1810 helix: -1.42 (0.19), residues: 640 sheet: -2.16 (0.34), residues: 205 loop : -1.22 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.003 TRP A 340 HIS 0.011 0.002 HIS C 275 PHE 0.017 0.002 PHE D 352 TYR 0.032 0.001 TYR B 279 ARG 0.009 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 577) hydrogen bonds : angle 4.10515 ( 1635) covalent geometry : bond 0.00387 (16113) covalent geometry : angle 0.73877 (21934) ********************** 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 475 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 392 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8551 (t) cc_final: 0.8268 (p) REVERT: A 39 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8454 (ptt180) REVERT: A 328 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8321 (mttp) REVERT: B 121 GLN cc_start: 0.9181 (tt0) cc_final: 0.8797 (tm-30) REVERT: B 124 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: B 162 ASN cc_start: 0.8680 (t0) cc_final: 0.8225 (t0) REVERT: B 184 ASP cc_start: 0.9070 (m-30) cc_final: 0.8822 (m-30) REVERT: B 190 MET cc_start: 0.8984 (ttp) cc_final: 0.8727 (ttt) REVERT: B 329 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8971 (mm) REVERT: B 336 LYS cc_start: 0.9162 (tttm) cc_final: 0.8893 (tttm) REVERT: B 340 TRP cc_start: 0.8599 (t60) cc_final: 0.8144 (t60) REVERT: C 115 ASN cc_start: 0.9237 (t0) cc_final: 0.8306 (t0) REVERT: C 124 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: C 161 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8537 (m-70) REVERT: C 248 ILE cc_start: 0.9327 (mt) cc_final: 0.8985 (tt) REVERT: C 325 MET cc_start: 0.8685 (tpp) cc_final: 0.8471 (tpt) REVERT: D 44 MET cc_start: 0.8689 (ttp) cc_final: 0.8444 (ttm) REVERT: D 47 MET cc_start: 0.7023 (ttp) cc_final: 0.6819 (mtp) REVERT: D 115 ASN cc_start: 0.8904 (t0) cc_final: 0.8351 (t0) REVERT: D 121 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8728 (tm-30) REVERT: D 124 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: D 125 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8211 (mt-10) REVERT: D 128 ASN cc_start: 0.8812 (m-40) cc_final: 0.8595 (m110) REVERT: D 314 GLN cc_start: 0.9104 (tt0) cc_final: 0.8835 (tt0) REVERT: E 275 HIS cc_start: 0.9543 (OUTLIER) cc_final: 0.9243 (p-80) REVERT: E 325 MET cc_start: 0.8686 (tpt) cc_final: 0.8463 (tpt) outliers start: 83 outliers final: 70 residues processed: 439 average time/residue: 0.2314 time to fit residues: 157.5194 Evaluate side-chains 459 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 381 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 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 275 HIS Chi-restraints excluded: chain A residue 282 ILE 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 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 LEU 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 C residue 5 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 124 PHE 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 269 MET Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL 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 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 237 GLU 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 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 55 optimal weight: 0.0980 chunk 173 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 135 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 13 optimal weight: 110.0000 chunk 34 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105626 restraints weight = 31607.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108226 restraints weight = 14857.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110126 restraints weight = 8564.426| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16113 Z= 0.144 Angle : 0.735 9.693 21934 Z= 0.354 Chirality : 0.045 0.196 2505 Planarity : 0.004 0.039 2828 Dihedral : 7.451 80.265 2359 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.41 % Favored : 94.03 % Rotamer: Outliers : 5.24 % Allowed : 27.51 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.19), residues: 1810 helix: -1.34 (0.19), residues: 640 sheet: -2.08 (0.34), residues: 205 loop : -1.16 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.016 0.001 PHE D 352 TYR 0.031 0.001 TYR B 279 ARG 0.006 0.000 ARG B 183 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 577) hydrogen bonds : angle 4.10137 ( 1635) covalent geometry : bond 0.00328 (16113) covalent geometry : angle 0.73533 (21934) =============================================================================== Job complete usr+sys time: 5183.70 seconds wall clock time: 92 minutes 15.66 seconds (5535.66 seconds total)