Starting phenix.real_space_refine on Thu Sep 18 09:07:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j8a_6124/09_2025/3j8a_6124.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j8a_6124/09_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_6124/09_2025/3j8a_6124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j8a_6124/09_2025/3j8a_6124.map" model { file = "/net/cci-nas-00/data/ceres_data/3j8a_6124/09_2025/3j8a_6124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j8a_6124/09_2025/3j8a_6124.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.038 sd= 1.493 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9925 2.51 5 N 2700 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.96, per 1000 atoms: 0.25 Number of scatterers: 15800 At special positions: 0 Unit cell: (103.04, 97.44, 207.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 O 3060 8.00 N 2700 7.00 C 9925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 466.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 0 sheets defined 52.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'F' and resid 97 through 231 removed outlier: 3.829A pdb=" N UNK F 129 " --> pdb=" O UNK F 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK F 143 " --> pdb=" O UNK F 139 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK F 164 " --> pdb=" O UNK F 160 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N UNK F 170 " --> pdb=" O UNK F 166 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK F 177 " --> pdb=" O UNK F 173 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK F 178 " --> pdb=" O UNK F 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK F 205 " --> pdb=" O UNK F 201 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK F 209 " --> pdb=" O UNK F 205 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK F 220 " --> pdb=" O UNK F 216 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N UNK F 223 " --> pdb=" O UNK F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 231 removed outlier: 3.577A pdb=" N UNK G 123 " --> pdb=" O UNK G 119 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK G 129 " --> pdb=" O UNK G 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK G 143 " --> pdb=" O UNK G 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK G 164 " --> pdb=" O UNK G 160 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK G 198 " --> pdb=" O UNK G 194 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N UNK G 219 " --> pdb=" O UNK G 215 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK G 226 " --> pdb=" O UNK G 222 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK G 227 " --> pdb=" O UNK G 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.613A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.888A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 141' Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.753A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.557A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 4.209A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.922A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.507A pdb=" N LEU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.687A pdb=" N ILE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.577A pdb=" N ASP A 363 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.637A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.657A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 4.052A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.920A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.741A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.638A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.562A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.768A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 205 through 215 removed outlier: 3.711A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 4.444A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.994A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.509A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.542A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.756A pdb=" N ILE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.683A pdb=" N ASP C 363 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.622A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.697A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.959A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 removed outlier: 4.250A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 273 through 283 removed outlier: 3.909A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 310 through 321 removed outlier: 3.606A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.696A pdb=" N ILE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.691A pdb=" N ASP D 363 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.516A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 127 Processing helix chain 'E' and resid 137 through 141 removed outlier: 3.871A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 141' Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.764A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.728A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 removed outlier: 4.401A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.816A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.847A pdb=" N ILE E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 359 through 363 removed outlier: 3.705A pdb=" N ASP E 363 " --> pdb=" O GLN E 360 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5092 1.33 - 1.45: 2089 1.45 - 1.57: 8736 1.57 - 1.69: 16 1.69 - 1.81: 180 Bond restraints: 16113 Sorted by residual: bond pdb=" NE2 HIC A 73 " pdb=" CZ HIC A 73 " ideal model delta sigma weight residual 1.444 1.273 0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" NE2 HIC B 73 " pdb=" CZ HIC B 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" NE2 HIC D 73 " pdb=" CZ HIC D 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" NE2 HIC C 73 " pdb=" CZ HIC C 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" NE2 HIC E 73 " pdb=" CZ HIC E 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.20e+01 ... (remaining 16108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 20765 2.62 - 5.24: 1056 5.24 - 7.86: 101 7.86 - 10.48: 11 10.48 - 13.10: 1 Bond angle restraints: 21934 Sorted by residual: angle pdb=" C GLN E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta sigma weight residual 119.84 109.99 9.85 1.25e+00 6.40e-01 6.21e+01 angle pdb=" N VAL E 201 " pdb=" CA VAL E 201 " pdb=" C VAL E 201 " ideal model delta sigma weight residual 110.62 118.31 -7.69 1.02e+00 9.61e-01 5.69e+01 angle pdb=" N LEU A 236 " pdb=" CA LEU A 236 " pdb=" C LEU A 236 " ideal model delta sigma weight residual 112.72 104.27 8.45 1.14e+00 7.69e-01 5.49e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 110.62 117.99 -7.37 1.02e+00 9.61e-01 5.22e+01 angle pdb=" N LEU D 236 " pdb=" CA LEU D 236 " pdb=" C LEU D 236 " ideal model delta sigma weight residual 112.72 104.70 8.02 1.14e+00 7.69e-01 4.95e+01 ... (remaining 21929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 8963 21.37 - 42.74: 579 42.74 - 64.11: 125 64.11 - 85.48: 1 85.48 - 106.85: 10 Dihedral angle restraints: 9678 sinusoidal: 3570 harmonic: 6108 Sorted by residual: dihedral pdb=" CA HIS C 101 " pdb=" C HIS C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 -166.86 106.85 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 -163.67 103.66 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 9675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1645 0.038 - 0.075: 522 0.075 - 0.113: 232 0.113 - 0.150: 90 0.150 - 0.188: 16 Chirality restraints: 2505 Sorted by residual: chirality pdb=" CA VAL B 54 " pdb=" N VAL B 54 " pdb=" C VAL B 54 " pdb=" CB VAL B 54 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA GLN E 263 " pdb=" N GLN E 263 " pdb=" C GLN E 263 " pdb=" CB GLN E 263 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA VAL D 54 " pdb=" N VAL D 54 " pdb=" C VAL D 54 " pdb=" CB VAL D 54 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 2502 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 263 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" CD GLN A 263 " 0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN A 263 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN A 263 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 102 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 102 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.024 5.00e-02 4.00e+02 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 741 2.70 - 3.25: 16846 3.25 - 3.80: 24089 3.80 - 4.35: 32022 4.35 - 4.90: 49075 Nonbonded interactions: 122773 Sorted by model distance: nonbonded pdb=" OD2 ASP A 286 " pdb=" NH2 ARG C 39 " model vdw 2.145 3.120 nonbonded pdb=" OG SER B 52 " pdb=" NZ LYS B 84 " model vdw 2.153 3.120 nonbonded pdb=" OD2 ASP D 286 " pdb=" NH2 ARG E 39 " model vdw 2.169 3.120 nonbonded pdb=" O PRO C 332 " pdb=" NH1 ARG C 335 " model vdw 2.213 3.120 nonbonded pdb=" O LEU E 221 " pdb=" NZ LYS E 315 " model vdw 2.220 3.120 ... (remaining 122768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.160 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- 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 : 19.71 Ramachandran Plot: Outliers : 1.38 % Allowed : 11.22 % Favored : 87.40 % Rotamer: Outliers : 6.28 % Allowed : 15.08 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.31 (0.15), residues: 1810 helix: -4.21 (0.10), residues: 670 sheet: -2.64 (0.32), residues: 200 loop : -3.20 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 254 TYR 0.013 0.002 TYR A 169 PHE 0.016 0.002 PHE D 255 TRP 0.013 0.002 TRP D 340 HIS 0.016 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00602 (16113) covalent geometry : angle 1.27050 (21934) hydrogen bonds : bond 0.22471 ( 577) hydrogen bonds : angle 9.19302 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 535 time to evaluate : 0.674 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: 0.8658 (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: 0.1146 time to fit residues: 103.3179 Evaluate side-chains 467 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 422 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 60.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** B 280 ASN C 92 ASN C 263 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 115 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100686 restraints weight = 31723.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103236 restraints weight = 15037.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104980 restraints weight = 8635.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106176 restraints weight = 5606.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106919 restraints weight = 3919.487| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 16113 Z= 0.226 Angle : 0.817 7.722 21934 Z= 0.417 Chirality : 0.045 0.173 2505 Planarity : 0.005 0.052 2828 Dihedral : 10.096 94.364 2421 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.24 % Favored : 92.93 % Rotamer: Outliers : 7.38 % Allowed : 20.71 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.73 (0.17), residues: 1810 helix: -2.89 (0.16), residues: 650 sheet: -1.73 (0.34), residues: 200 loop : -2.32 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 335 TYR 0.017 0.001 TYR D 169 PHE 0.012 0.002 PHE D 255 TRP 0.035 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00521 (16113) covalent geometry : angle 0.81655 (21934) hydrogen bonds : bond 0.05504 ( 577) hydrogen bonds : angle 5.11611 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 435 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9166 (m) REVERT: A 10 CYS cc_start: 0.8872 (t) cc_final: 0.8375 (p) REVERT: A 328 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8233 (mttp) REVERT: B 18 LYS cc_start: 0.9190 (mmtm) cc_final: 0.8960 (mmtm) REVERT: B 121 GLN cc_start: 0.9170 (tt0) cc_final: 0.8849 (tm-30) REVERT: B 162 ASN cc_start: 0.8790 (t0) cc_final: 0.8301 (t0) REVERT: B 256 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8474 (ttm110) REVERT: B 313 MET cc_start: 0.8532 (tpp) cc_final: 0.8301 (tpp) REVERT: B 329 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9019 (mm) REVERT: B 369 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8836 (mm) REVERT: C 18 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9124 (mmtp) REVERT: C 115 ASN cc_start: 0.9291 (t0) cc_final: 0.8391 (t0) REVERT: C 121 GLN cc_start: 0.9385 (tm-30) cc_final: 0.9066 (tm-30) REVERT: C 157 ASP cc_start: 0.8882 (t0) cc_final: 0.8574 (t0) REVERT: C 161 HIS cc_start: 0.9000 (OUTLIER) cc_final: 0.8361 (m-70) REVERT: C 205 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7934 (tm-30) REVERT: C 246 GLN cc_start: 0.9223 (tp-100) cc_final: 0.8688 (tm-30) REVERT: C 248 ILE cc_start: 0.9554 (mt) cc_final: 0.9282 (tt) REVERT: C 300 SER cc_start: 0.9355 (m) cc_final: 0.8878 (p) REVERT: C 325 MET cc_start: 0.8788 (tpp) cc_final: 0.8499 (tpt) REVERT: D 44 MET cc_start: 0.8485 (ttt) cc_final: 0.8262 (ttp) REVERT: D 100 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: D 115 ASN cc_start: 0.8940 (t0) cc_final: 0.8473 (t0) REVERT: D 242 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8732 (mp) REVERT: D 282 ILE cc_start: 0.9403 (mt) cc_final: 0.9044 (mt) REVERT: D 334 GLU cc_start: 0.8172 (pt0) cc_final: 0.7933 (pt0) REVERT: D 340 TRP cc_start: 0.8748 (t60) cc_final: 0.8016 (t60) REVERT: E 39 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8197 (ptt180) REVERT: E 132 MET cc_start: 0.9067 (tpp) cc_final: 0.8764 (tpp) REVERT: E 263 GLN cc_start: 0.8752 (mt0) cc_final: 0.8543 (mt0) outliers start: 114 outliers final: 64 residues processed: 502 average time/residue: 0.1121 time to fit residues: 87.0421 Evaluate side-chains 453 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 380 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 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 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 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 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 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 56 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 14 optimal weight: 110.0000 chunk 67 optimal weight: 0.0770 chunk 148 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 overall best weight: 4.7544 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 115 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3420 r_free = 0.3420 target = 0.118325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.101462 restraints weight = 32099.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103965 restraints weight = 15093.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105777 restraints weight = 8709.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106979 restraints weight = 5550.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107750 restraints weight = 3881.396| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16113 Z= 0.186 Angle : 0.756 8.013 21934 Z= 0.375 Chirality : 0.045 0.182 2505 Planarity : 0.005 0.041 2828 Dihedral : 9.463 89.883 2390 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.41 % Favored : 92.76 % Rotamer: Outliers : 6.99 % Allowed : 22.65 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.18), residues: 1810 helix: -2.31 (0.17), residues: 645 sheet: -1.42 (0.42), residues: 150 loop : -2.03 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.026 0.001 TYR B 279 PHE 0.012 0.002 PHE E 255 TRP 0.047 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00423 (16113) covalent geometry : angle 0.75564 (21934) hydrogen bonds : bond 0.05003 ( 577) hydrogen bonds : angle 4.71049 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 404 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8843 (t) cc_final: 0.8413 (p) REVERT: A 39 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8585 (ptt180) REVERT: A 105 LEU cc_start: 0.9014 (mt) cc_final: 0.8793 (mt) REVERT: A 328 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8018 (mttp) REVERT: B 121 GLN cc_start: 0.9180 (tt0) cc_final: 0.8850 (tm-30) REVERT: B 124 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: B 132 MET cc_start: 0.8664 (tpp) cc_final: 0.8371 (tpt) REVERT: B 154 ASP cc_start: 0.8613 (t0) cc_final: 0.8395 (t0) REVERT: B 162 ASN cc_start: 0.8721 (t0) cc_final: 0.8264 (t0) REVERT: B 190 MET cc_start: 0.8973 (ttp) cc_final: 0.8720 (ttt) REVERT: B 256 ARG cc_start: 0.8819 (ttp80) cc_final: 0.8574 (ttm110) REVERT: B 313 MET cc_start: 0.8570 (tpp) cc_final: 0.8308 (tpp) REVERT: B 329 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9030 (mm) REVERT: B 340 TRP cc_start: 0.8686 (t60) cc_final: 0.8141 (t60) REVERT: C 121 GLN cc_start: 0.9370 (tm-30) cc_final: 0.9023 (tm-30) REVERT: C 246 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8582 (tm-30) REVERT: C 325 MET cc_start: 0.8761 (tpp) cc_final: 0.8491 (tpt) REVERT: C 354 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8897 (mt0) REVERT: D 115 ASN cc_start: 0.8942 (t0) cc_final: 0.8509 (t0) REVERT: D 242 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8713 (mp) REVERT: D 325 MET cc_start: 0.9041 (tpp) cc_final: 0.8284 (tpp) REVERT: D 334 GLU cc_start: 0.8248 (pt0) cc_final: 0.7954 (pt0) REVERT: D 340 TRP cc_start: 0.8714 (t60) cc_final: 0.7998 (t60) REVERT: E 121 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8441 (tm-30) REVERT: E 125 GLU cc_start: 0.8030 (pt0) cc_final: 0.7771 (pt0) REVERT: E 263 GLN cc_start: 0.8816 (mt0) cc_final: 0.8440 (mt0) REVERT: E 270 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8132 (mt-10) outliers start: 108 outliers final: 70 residues processed: 469 average time/residue: 0.1180 time to fit residues: 85.5814 Evaluate side-chains 458 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 382 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 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 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 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 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 32 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 21 optimal weight: 220.0000 chunk 108 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099888 restraints weight = 32122.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.102426 restraints weight = 15178.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104248 restraints weight = 8831.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105443 restraints weight = 5654.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106225 restraints weight = 3961.295| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 16113 Z= 0.233 Angle : 0.761 7.958 21934 Z= 0.376 Chirality : 0.046 0.192 2505 Planarity : 0.005 0.055 2828 Dihedral : 9.195 87.819 2383 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.02 % Favored : 92.15 % Rotamer: Outliers : 8.93 % Allowed : 22.52 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.18), residues: 1810 helix: -2.19 (0.17), residues: 675 sheet: -1.36 (0.42), residues: 150 loop : -1.92 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 183 TYR 0.016 0.001 TYR A 198 PHE 0.018 0.002 PHE D 200 TRP 0.054 0.002 TRP A 340 HIS 0.011 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00534 (16113) covalent geometry : angle 0.76074 (21934) hydrogen bonds : bond 0.04718 ( 577) hydrogen bonds : angle 4.58944 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 396 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8854 (t) cc_final: 0.8418 (p) REVERT: A 39 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8593 (ptt180) REVERT: A 153 LEU cc_start: 0.9171 (tp) cc_final: 0.8950 (tp) REVERT: A 328 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8272 (mttp) REVERT: B 44 MET cc_start: 0.8309 (ttp) cc_final: 0.8003 (ttm) REVERT: B 121 GLN cc_start: 0.9147 (tt0) cc_final: 0.8859 (tm-30) REVERT: B 124 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: B 154 ASP cc_start: 0.8546 (t0) cc_final: 0.8341 (t0) REVERT: B 162 ASN cc_start: 0.8758 (t0) cc_final: 0.8264 (t0) REVERT: B 256 ARG cc_start: 0.8848 (ttp80) cc_final: 0.8599 (ttm110) REVERT: B 313 MET cc_start: 0.8549 (tpp) cc_final: 0.8242 (tpp) REVERT: B 329 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9047 (mm) REVERT: B 334 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: B 336 LYS cc_start: 0.9286 (tttm) cc_final: 0.9077 (tttm) REVERT: C 161 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8425 (m-70) REVERT: C 246 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8529 (tm-30) REVERT: C 259 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8521 (tm-30) REVERT: C 263 GLN cc_start: 0.9300 (tt0) cc_final: 0.9031 (pt0) REVERT: C 283 MET cc_start: 0.8573 (mtp) cc_final: 0.8334 (tpp) REVERT: C 325 MET cc_start: 0.8703 (tpp) cc_final: 0.8403 (tpt) REVERT: D 115 ASN cc_start: 0.9017 (t0) cc_final: 0.8575 (t0) REVERT: D 124 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: D 132 MET cc_start: 0.8879 (mmm) cc_final: 0.8532 (mmm) REVERT: D 242 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8659 (mp) REVERT: D 334 GLU cc_start: 0.8163 (pt0) cc_final: 0.7823 (pt0) REVERT: D 340 TRP cc_start: 0.8746 (t60) cc_final: 0.8059 (t60) REVERT: E 263 GLN cc_start: 0.8856 (mt0) cc_final: 0.8508 (mt0) outliers start: 138 outliers final: 87 residues processed: 480 average time/residue: 0.1085 time to fit residues: 81.3456 Evaluate side-chains 467 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 372 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 257 CYS 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 346 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 250 ILE 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 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 209 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 17 optimal weight: 100.0000 chunk 200 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 110 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 A 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** 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 = 0.3449 r_free = 0.3449 target = 0.120127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103228 restraints weight = 31841.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.105787 restraints weight = 15014.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107681 restraints weight = 8693.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108872 restraints weight = 5545.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109601 restraints weight = 3862.398| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16113 Z= 0.159 Angle : 0.722 8.564 21934 Z= 0.352 Chirality : 0.044 0.185 2505 Planarity : 0.004 0.040 2828 Dihedral : 8.714 87.042 2377 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.19 % Favored : 93.98 % Rotamer: Outliers : 7.31 % Allowed : 24.27 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.19), residues: 1810 helix: -1.90 (0.18), residues: 670 sheet: -2.34 (0.34), residues: 205 loop : -1.47 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.016 0.001 TYR A 198 PHE 0.012 0.001 PHE C 255 TRP 0.069 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00364 (16113) covalent geometry : angle 0.72175 (21934) hydrogen bonds : bond 0.04339 ( 577) hydrogen bonds : angle 4.31459 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 408 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8788 (t) cc_final: 0.8270 (p) REVERT: A 39 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8490 (ptt180) REVERT: A 153 LEU cc_start: 0.9140 (tp) cc_final: 0.8938 (tp) REVERT: A 262 PHE cc_start: 0.9311 (m-80) cc_final: 0.9090 (m-80) REVERT: A 328 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8279 (mttp) REVERT: B 44 MET cc_start: 0.8270 (ttp) cc_final: 0.7919 (ttm) REVERT: B 121 GLN cc_start: 0.9115 (tt0) cc_final: 0.8824 (tm-30) REVERT: B 124 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: B 162 ASN cc_start: 0.8705 (t0) cc_final: 0.8271 (t0) REVERT: B 167 GLU cc_start: 0.8496 (tt0) cc_final: 0.8289 (tt0) REVERT: B 190 MET cc_start: 0.8966 (ttp) cc_final: 0.8722 (ttt) REVERT: B 299 MET cc_start: 0.8443 (mtm) cc_final: 0.8232 (mtm) REVERT: B 313 MET cc_start: 0.8521 (tpp) cc_final: 0.8277 (tpp) REVERT: B 329 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9044 (mm) REVERT: B 334 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: B 336 LYS cc_start: 0.9226 (tttm) cc_final: 0.8996 (tttm) REVERT: B 340 TRP cc_start: 0.8541 (t60) cc_final: 0.7931 (t60) REVERT: B 364 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: C 115 ASN cc_start: 0.9180 (t0) cc_final: 0.8791 (t0) REVERT: C 161 HIS cc_start: 0.8858 (OUTLIER) cc_final: 0.8407 (m-70) REVERT: C 283 MET cc_start: 0.8498 (mtp) cc_final: 0.8223 (tpp) REVERT: C 325 MET cc_start: 0.8659 (tpp) cc_final: 0.8368 (tpt) REVERT: C 354 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8799 (mt0) REVERT: D 124 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: D 242 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8642 (mp) REVERT: D 275 HIS cc_start: 0.9529 (OUTLIER) cc_final: 0.9136 (p-80) REVERT: D 325 MET cc_start: 0.8993 (tpp) cc_final: 0.8124 (tpp) REVERT: E 263 GLN cc_start: 0.8829 (mt0) cc_final: 0.8623 (mt0) REVERT: E 275 HIS cc_start: 0.9528 (OUTLIER) cc_final: 0.9059 (p-80) outliers start: 113 outliers final: 64 residues processed: 471 average time/residue: 0.1085 time to fit residues: 79.2882 Evaluate side-chains 463 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 387 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 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 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL 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 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 22 optimal weight: 90.0000 chunk 55 optimal weight: 20.0000 chunk 64 optimal weight: 0.0270 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 71 optimal weight: 30.0000 overall best weight: 4.4046 ------------------------------------------------------------------------------- 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** A 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103045 restraints weight = 31791.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105638 restraints weight = 14976.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107508 restraints weight = 8686.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108665 restraints weight = 5504.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109404 restraints weight = 3806.810| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3015 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= 0.172 Angle : 0.724 8.536 21934 Z= 0.354 Chirality : 0.045 0.189 2505 Planarity : 0.004 0.039 2828 Dihedral : 8.268 85.609 2368 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.80 % Favored : 93.37 % Rotamer: Outliers : 6.67 % Allowed : 24.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.19), residues: 1810 helix: -1.78 (0.18), residues: 670 sheet: -2.30 (0.34), residues: 205 loop : -1.42 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 183 TYR 0.015 0.001 TYR A 198 PHE 0.013 0.002 PHE C 255 TRP 0.076 0.002 TRP A 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00400 (16113) covalent geometry : angle 0.72394 (21934) hydrogen bonds : bond 0.04220 ( 577) hydrogen bonds : angle 4.26052 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 402 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8779 (t) cc_final: 0.8221 (p) REVERT: A 39 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8539 (ptt180) REVERT: A 153 LEU cc_start: 0.9161 (tp) cc_final: 0.8946 (tp) REVERT: A 328 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8288 (mttp) REVERT: B 44 MET cc_start: 0.8245 (ttp) cc_final: 0.7967 (ttm) REVERT: B 121 GLN cc_start: 0.9109 (tt0) cc_final: 0.8809 (tm-30) REVERT: B 124 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: B 162 ASN cc_start: 0.8681 (t0) cc_final: 0.8177 (t0) REVERT: B 190 MET cc_start: 0.8964 (ttp) cc_final: 0.8724 (ttt) REVERT: B 299 MET cc_start: 0.8462 (mtm) cc_final: 0.8195 (mtm) REVERT: B 313 MET cc_start: 0.8551 (tpp) cc_final: 0.8272 (tpp) REVERT: B 329 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9036 (mm) REVERT: B 334 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: B 336 LYS cc_start: 0.9214 (tttm) cc_final: 0.8979 (tttm) REVERT: B 340 TRP cc_start: 0.8583 (t60) cc_final: 0.7959 (t60) REVERT: B 364 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: C 115 ASN cc_start: 0.9204 (t0) cc_final: 0.8825 (t0) REVERT: C 161 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.8465 (m-70) REVERT: C 190 MET cc_start: 0.8444 (ttt) cc_final: 0.8049 (ttt) REVERT: C 325 MET cc_start: 0.8703 (tpp) cc_final: 0.8432 (tpt) REVERT: C 354 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8736 (mt0) REVERT: D 124 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: D 132 MET cc_start: 0.9045 (mmm) cc_final: 0.8774 (mmm) REVERT: D 242 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8627 (mp) REVERT: D 275 HIS cc_start: 0.9516 (OUTLIER) cc_final: 0.9266 (p-80) REVERT: D 325 MET cc_start: 0.8981 (tpp) cc_final: 0.8118 (tpp) REVERT: E 263 GLN cc_start: 0.8837 (mt0) cc_final: 0.8589 (mt0) REVERT: E 275 HIS cc_start: 0.9540 (OUTLIER) cc_final: 0.9150 (p-80) outliers start: 103 outliers final: 74 residues processed: 466 average time/residue: 0.1004 time to fit residues: 73.7984 Evaluate side-chains 473 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 387 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 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 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU 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 271 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 134 VAL 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 Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 79 optimal weight: 30.0000 chunk 23 optimal weight: 100.0000 chunk 87 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 1 optimal weight: 110.0000 chunk 167 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 92 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102549 restraints weight = 31890.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105255 restraints weight = 15182.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107030 restraints weight = 8540.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108168 restraints weight = 5562.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108932 restraints weight = 3882.183| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16113 Z= 0.189 Angle : 0.733 8.243 21934 Z= 0.358 Chirality : 0.045 0.182 2505 Planarity : 0.005 0.065 2828 Dihedral : 8.122 85.285 2365 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.97 % Favored : 93.20 % Rotamer: Outliers : 7.57 % Allowed : 24.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.19), residues: 1810 helix: -1.76 (0.18), residues: 670 sheet: -2.33 (0.34), residues: 205 loop : -1.40 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 183 TYR 0.038 0.001 TYR B 69 PHE 0.014 0.002 PHE C 255 TRP 0.081 0.002 TRP A 340 HIS 0.013 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00442 (16113) covalent geometry : angle 0.73321 (21934) hydrogen bonds : bond 0.04177 ( 577) hydrogen bonds : angle 4.26081 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 392 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8756 (t) cc_final: 0.8250 (p) REVERT: A 39 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8588 (ptt180) REVERT: A 328 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8283 (mttp) REVERT: B 69 TYR cc_start: 0.8869 (m-80) cc_final: 0.8510 (m-10) REVERT: B 121 GLN cc_start: 0.9087 (tt0) cc_final: 0.8793 (tm-30) REVERT: B 124 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: B 162 ASN cc_start: 0.8680 (t0) cc_final: 0.8138 (t0) REVERT: B 190 MET cc_start: 0.8955 (ttp) cc_final: 0.8707 (ttt) REVERT: B 283 MET cc_start: 0.9094 (mtm) cc_final: 0.8858 (mtm) REVERT: B 299 MET cc_start: 0.8444 (mtm) cc_final: 0.8194 (mtm) REVERT: B 329 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9030 (mm) REVERT: B 334 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: B 336 LYS cc_start: 0.9196 (tttm) cc_final: 0.8968 (tttm) REVERT: B 340 TRP cc_start: 0.8617 (t60) cc_final: 0.7956 (t60) REVERT: B 364 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: C 161 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8443 (m-70) REVERT: C 190 MET cc_start: 0.8430 (ttt) cc_final: 0.8148 (ttt) REVERT: C 325 MET cc_start: 0.8677 (tpp) cc_final: 0.8438 (tpt) REVERT: C 354 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8693 (mt0) REVERT: D 124 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: D 132 MET cc_start: 0.9011 (mmm) cc_final: 0.8757 (mmm) REVERT: D 242 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8601 (mp) REVERT: D 325 MET cc_start: 0.8977 (tpp) cc_final: 0.8103 (tpp) REVERT: E 263 GLN cc_start: 0.8854 (mt0) cc_final: 0.8606 (mt0) REVERT: E 275 HIS cc_start: 0.9554 (OUTLIER) cc_final: 0.9173 (p-80) outliers start: 117 outliers final: 87 residues processed: 463 average time/residue: 0.0995 time to fit residues: 72.6422 Evaluate side-chains 476 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 378 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 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 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 121 GLN 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 202 THR 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 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 5 THR 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 106 THR 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 186 THR 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 250 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 134 VAL 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 Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 178 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 25 optimal weight: 110.0000 chunk 186 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 167 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 275 HIS ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105079 restraints weight = 31688.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107676 restraints weight = 14964.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109614 restraints weight = 8557.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110794 restraints weight = 5392.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111548 restraints weight = 3747.528| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16113 Z= 0.140 Angle : 0.720 9.205 21934 Z= 0.349 Chirality : 0.045 0.195 2505 Planarity : 0.004 0.045 2828 Dihedral : 7.862 83.906 2363 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.14 % Favored : 94.03 % Rotamer: Outliers : 6.60 % Allowed : 25.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.19), residues: 1810 helix: -1.63 (0.19), residues: 670 sheet: -2.26 (0.34), residues: 205 loop : -1.32 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 183 TYR 0.024 0.001 TYR B 69 PHE 0.011 0.001 PHE C 255 TRP 0.077 0.002 TRP A 340 HIS 0.013 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00321 (16113) covalent geometry : angle 0.71973 (21934) hydrogen bonds : bond 0.03964 ( 577) hydrogen bonds : angle 4.13138 ( 1635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 404 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8430 (t) cc_final: 0.8178 (p) REVERT: A 39 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8501 (ptt180) REVERT: A 328 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8280 (mttp) REVERT: B 69 TYR cc_start: 0.8859 (m-80) cc_final: 0.8466 (m-10) REVERT: B 121 GLN cc_start: 0.9055 (tt0) cc_final: 0.8755 (tm-30) REVERT: B 124 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: B 162 ASN cc_start: 0.8615 (t0) cc_final: 0.8150 (t0) REVERT: B 190 MET cc_start: 0.8887 (ttp) cc_final: 0.8671 (ttt) REVERT: B 299 MET cc_start: 0.8440 (mtm) cc_final: 0.8197 (mtm) REVERT: B 329 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8998 (mm) REVERT: B 334 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: B 336 LYS cc_start: 0.9171 (tttm) cc_final: 0.8924 (tttm) REVERT: B 340 TRP cc_start: 0.8515 (t60) cc_final: 0.8063 (t60) REVERT: B 364 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: C 115 ASN cc_start: 0.9180 (t0) cc_final: 0.8178 (t0) REVERT: C 161 HIS cc_start: 0.8871 (OUTLIER) cc_final: 0.8430 (m-70) REVERT: C 325 MET cc_start: 0.8669 (tpp) cc_final: 0.8394 (tpt) REVERT: C 354 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8631 (mt0) REVERT: D 121 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8957 (tm-30) REVERT: D 124 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: D 132 MET cc_start: 0.9014 (mmm) cc_final: 0.8767 (mmm) REVERT: D 242 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8542 (mp) REVERT: D 325 MET cc_start: 0.8959 (tpp) cc_final: 0.8089 (tpp) REVERT: D 352 PHE cc_start: 0.9219 (p90) cc_final: 0.8991 (p90) REVERT: E 189 LEU cc_start: 0.9640 (tp) cc_final: 0.9433 (tp) REVERT: E 275 HIS cc_start: 0.9514 (OUTLIER) cc_final: 0.9186 (p-80) outliers start: 102 outliers final: 71 residues processed: 462 average time/residue: 0.1040 time to fit residues: 75.2604 Evaluate side-chains 463 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 381 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 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 178 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 121 GLN 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 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 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 224 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 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 143 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 110.0000 chunk 172 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 2 optimal weight: 120.0000 chunk 181 optimal weight: 9.9990 chunk 7 optimal weight: 100.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 252 ASN ** 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 C 252 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.101378 restraints weight = 32035.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103989 restraints weight = 15177.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105851 restraints weight = 8715.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107032 restraints weight = 5642.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107833 restraints weight = 3882.701| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 16113 Z= 0.211 Angle : 0.751 7.919 21934 Z= 0.366 Chirality : 0.046 0.187 2505 Planarity : 0.005 0.050 2828 Dihedral : 7.919 84.148 2363 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.91 % Favored : 92.43 % Rotamer: Outliers : 6.41 % Allowed : 27.06 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.19), residues: 1810 helix: -1.70 (0.18), residues: 675 sheet: -2.31 (0.34), residues: 205 loop : -1.36 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.022 0.001 TYR B 69 PHE 0.017 0.002 PHE C 255 TRP 0.088 0.002 TRP A 340 HIS 0.012 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00492 (16113) covalent geometry : angle 0.75073 (21934) hydrogen bonds : bond 0.04065 ( 577) hydrogen bonds : angle 4.25742 ( 1635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 388 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8602 (t) cc_final: 0.8254 (p) REVERT: A 39 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8550 (ptt180) REVERT: A 328 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (mttp) REVERT: B 69 TYR cc_start: 0.8946 (m-80) cc_final: 0.8550 (m-10) REVERT: B 121 GLN cc_start: 0.9150 (tt0) cc_final: 0.8842 (tm-30) REVERT: B 124 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: B 162 ASN cc_start: 0.8697 (t0) cc_final: 0.8103 (t0) REVERT: B 329 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9016 (mm) REVERT: B 334 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: B 336 LYS cc_start: 0.9199 (tttm) cc_final: 0.8973 (tttm) REVERT: B 340 TRP cc_start: 0.8635 (t60) cc_final: 0.7995 (t60) REVERT: C 161 HIS cc_start: 0.8971 (OUTLIER) cc_final: 0.8499 (m-70) REVERT: C 238 LYS cc_start: 0.9230 (mttm) cc_final: 0.8881 (mttm) REVERT: C 248 ILE cc_start: 0.9352 (mt) cc_final: 0.9079 (tt) REVERT: C 325 MET cc_start: 0.8639 (tpp) cc_final: 0.8426 (tpt) REVERT: C 354 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8664 (mt0) REVERT: D 115 ASN cc_start: 0.8944 (t0) cc_final: 0.8524 (t0) REVERT: D 124 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: D 132 MET cc_start: 0.8999 (mmm) cc_final: 0.8792 (mmm) REVERT: D 190 MET cc_start: 0.8900 (tpp) cc_final: 0.7710 (ttt) REVERT: D 242 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8531 (mp) REVERT: D 276 GLU cc_start: 0.9072 (tt0) cc_final: 0.8811 (tt0) REVERT: D 325 MET cc_start: 0.9003 (tpp) cc_final: 0.8171 (tpp) REVERT: D 352 PHE cc_start: 0.9228 (p90) cc_final: 0.9000 (p90) REVERT: E 39 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8532 (ptt180) REVERT: E 275 HIS cc_start: 0.9586 (OUTLIER) cc_final: 0.9254 (p-80) outliers start: 99 outliers final: 75 residues processed: 443 average time/residue: 0.1022 time to fit residues: 71.0794 Evaluate side-chains 471 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 385 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 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 178 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 64 ILE 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 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 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 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 186 THR 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 271 SER Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 134 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101708 restraints weight = 32089.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104290 restraints weight = 15071.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106179 restraints weight = 8681.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107380 restraints weight = 5635.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108135 restraints weight = 3872.206| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 16113 Z= 0.194 Angle : 0.904 59.200 21934 Z= 0.483 Chirality : 0.046 0.382 2505 Planarity : 0.005 0.051 2828 Dihedral : 7.922 84.288 2363 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.69 % Favored : 92.71 % Rotamer: Outliers : 5.95 % Allowed : 28.03 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.19), residues: 1810 helix: -1.69 (0.18), residues: 675 sheet: -2.31 (0.34), residues: 205 loop : -1.35 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.019 0.001 TYR B 279 PHE 0.016 0.002 PHE C 255 TRP 0.081 0.003 TRP A 340 HIS 0.011 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00451 (16113) covalent geometry : angle 0.90441 (21934) hydrogen bonds : bond 0.04069 ( 577) hydrogen bonds : angle 4.24914 ( 1635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 385 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8635 (t) cc_final: 0.8298 (p) REVERT: A 39 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8542 (ptt180) REVERT: A 328 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8289 (mttp) REVERT: B 69 TYR cc_start: 0.8947 (m-80) cc_final: 0.8547 (m-10) REVERT: B 121 GLN cc_start: 0.9144 (tt0) cc_final: 0.8831 (tm-30) REVERT: B 124 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 162 ASN cc_start: 0.8672 (t0) cc_final: 0.8096 (t0) REVERT: B 329 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9016 (mm) REVERT: B 334 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: B 336 LYS cc_start: 0.9194 (tttm) cc_final: 0.8971 (tttm) REVERT: B 340 TRP cc_start: 0.8639 (t60) cc_final: 0.7993 (t60) REVERT: C 161 HIS cc_start: 0.8966 (OUTLIER) cc_final: 0.8493 (m-70) REVERT: C 238 LYS cc_start: 0.9226 (mttm) cc_final: 0.8880 (mttm) REVERT: C 248 ILE cc_start: 0.9353 (mt) cc_final: 0.9096 (tt) REVERT: C 325 MET cc_start: 0.8634 (tpp) cc_final: 0.8421 (tpt) REVERT: C 354 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8660 (mt0) REVERT: D 115 ASN cc_start: 0.8936 (t0) cc_final: 0.8448 (t0) REVERT: D 124 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: D 132 MET cc_start: 0.8993 (mmm) cc_final: 0.8787 (mmm) REVERT: D 190 MET cc_start: 0.8897 (tpp) cc_final: 0.7713 (ttt) REVERT: D 242 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8562 (mp) REVERT: D 314 GLN cc_start: 0.9147 (tt0) cc_final: 0.8862 (mt0) REVERT: D 325 MET cc_start: 0.9001 (tpp) cc_final: 0.8172 (tpp) REVERT: D 352 PHE cc_start: 0.9226 (p90) cc_final: 0.8995 (p90) REVERT: E 39 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8524 (ptt180) REVERT: E 263 GLN cc_start: 0.8947 (mt0) cc_final: 0.8687 (mt0) REVERT: E 275 HIS cc_start: 0.9583 (OUTLIER) cc_final: 0.9245 (p-80) outliers start: 92 outliers final: 77 residues processed: 438 average time/residue: 0.1006 time to fit residues: 69.5083 Evaluate side-chains 476 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 388 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 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 267 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 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 178 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 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 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 271 SER Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 134 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 220.0000 chunk 139 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101764 restraints weight = 31928.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.104441 restraints weight = 15031.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106337 restraints weight = 8482.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107491 restraints weight = 5433.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108247 restraints weight = 3762.065| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 16113 Z= 0.194 Angle : 0.904 59.200 21934 Z= 0.483 Chirality : 0.046 0.382 2505 Planarity : 0.005 0.051 2828 Dihedral : 7.922 84.288 2363 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.69 % Favored : 92.71 % Rotamer: Outliers : 5.70 % Allowed : 28.16 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.19), residues: 1810 helix: -1.69 (0.18), residues: 675 sheet: -2.31 (0.34), residues: 205 loop : -1.35 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.019 0.001 TYR B 279 PHE 0.016 0.002 PHE C 255 TRP 0.081 0.003 TRP A 340 HIS 0.011 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00451 (16113) covalent geometry : angle 0.90440 (21934) hydrogen bonds : bond 0.04069 ( 577) hydrogen bonds : angle 4.24914 ( 1635) =============================================================================== Job complete usr+sys time: 2450.70 seconds wall clock time: 43 minutes 16.50 seconds (2596.50 seconds total)