Starting phenix.real_space_refine on Fri Sep 27 09:26:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/09_2024/3j8a_6124.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/09_2024/3j8a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/09_2024/3j8a_6124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/09_2024/3j8a_6124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/09_2024/3j8a_6124.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/09_2024/3j8a_6124.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.038 sd= 1.493 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9925 2.51 5 N 2700 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.10, per 1000 atoms: 0.58 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: 4.45 Conformation dependent library (CDL) restraints added in 2.2 seconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 0 sheets defined 52.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 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: 3.66 Time building geometry restraints manager: 5.12 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.580 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- 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= 0.411 Angle : 1.270 13.096 21934 Z= 0.851 Chirality : 0.049 0.188 2505 Planarity : 0.005 0.047 2828 Dihedral : 14.877 106.855 5748 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.38 % Allowed : 11.22 % Favored : 87.40 % Rotamer: Outliers : 6.28 % Allowed : 15.08 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.15), residues: 1810 helix: -4.21 (0.10), residues: 670 sheet: -2.64 (0.32), residues: 200 loop : -3.20 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.016 0.002 HIS C 275 PHE 0.016 0.002 PHE D 255 TYR 0.013 0.002 TYR A 169 ARG 0.005 0.001 ARG D 254 *********************** 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 fitting. rotamer outliers: 97 poor density : 535 time to evaluate : 1.665 Fit side-chains revert: symmetry clash 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: 0.8757 (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: 0.8929 (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: 0.8848 (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: 0.9128 (tt) REVERT: C 277 THR cc_start: 0.9439 (p) cc_final: 0.8960 (t) REVERT: C 325 MET cc_start: 0.9064 (tpp) cc_final: 0.8660 (tpt) REVERT: C 328 LYS cc_start: 0.8830 (mttt) cc_final: 0.8574 (mptt) REVERT: C 334 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: D 16 LEU cc_start: 0.9610 (mm) cc_final: 0.9406 (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: 0.8511 (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 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: 0.8998 (t0) REVERT: E 289 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9349 (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: 0.8674 (pt0) outliers start: 97 outliers final: 33 residues processed: 590 average time/residue: 0.2515 time to fit residues: 224.1514 Evaluate side-chains 467 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 422 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 263 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 115 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1858 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= 0.283 Angle : 0.803 7.814 21934 Z= 0.412 Chirality : 0.045 0.177 2505 Planarity : 0.005 0.051 2828 Dihedral : 10.008 95.559 2421 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.35 % Favored : 92.82 % Rotamer: Outliers : 7.18 % Allowed : 20.78 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.17), residues: 1810 helix: -2.89 (0.16), residues: 650 sheet: -1.59 (0.40), residues: 150 loop : -2.30 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 340 HIS 0.013 0.001 HIS C 275 PHE 0.012 0.002 PHE D 255 TYR 0.017 0.001 TYR D 169 ARG 0.005 0.001 ARG B 335 *********************** 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 548 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 437 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: A 10 CYS cc_start: 0.9166 (t) cc_final: 0.8658 (p) REVERT: A 195 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8539 (pt0) REVERT: A 242 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9010 (mp) REVERT: A 328 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8230 (mttp) REVERT: B 47 MET cc_start: 0.7209 (ptm) cc_final: 0.6989 (ptp) REVERT: B 121 GLN cc_start: 0.9102 (tt0) cc_final: 0.8869 (tm-30) REVERT: B 133 TYR cc_start: 0.8936 (t80) cc_final: 0.8724 (t80) REVERT: B 162 ASN cc_start: 0.9063 (t0) cc_final: 0.8740 (t0) REVERT: B 329 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9107 (mm) REVERT: B 340 TRP cc_start: 0.8916 (t60) cc_final: 0.8396 (t60) REVERT: C 39 ARG cc_start: 0.8694 (ptp-170) cc_final: 0.8482 (ptp-170) REVERT: C 115 ASN cc_start: 0.9302 (t0) cc_final: 0.8430 (t0) REVERT: C 157 ASP cc_start: 0.8850 (t0) cc_final: 0.8642 (t0) REVERT: C 248 ILE cc_start: 0.9396 (mt) cc_final: 0.9154 (tt) REVERT: C 259 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9013 (tm-30) REVERT: C 300 SER cc_start: 0.9392 (m) cc_final: 0.9046 (p) REVERT: C 325 MET cc_start: 0.8904 (tpp) cc_final: 0.8533 (tpt) REVERT: C 328 LYS cc_start: 0.8617 (mttt) cc_final: 0.8220 (mptt) REVERT: D 100 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: D 115 ASN cc_start: 0.8999 (t0) cc_final: 0.8563 (t0) REVERT: D 183 ARG cc_start: 0.9202 (mtt-85) cc_final: 0.8950 (tpp80) REVERT: D 242 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8989 (mp) REVERT: D 325 MET cc_start: 0.9196 (mmm) cc_final: 0.8553 (tpp) REVERT: D 334 GLU cc_start: 0.8645 (pt0) cc_final: 0.8363 (pt0) REVERT: D 340 TRP cc_start: 0.8984 (t60) cc_final: 0.8343 (t60) REVERT: E 39 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8318 (ptt180) REVERT: E 167 GLU cc_start: 0.9028 (tt0) cc_final: 0.8742 (tm-30) REVERT: E 270 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8582 (mt-10) REVERT: E 289 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9220 (mm) outliers start: 111 outliers final: 65 residues processed: 504 average time/residue: 0.2403 time to fit residues: 184.0024 Evaluate side-chains 455 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 381 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 16 LEU 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 242 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain 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 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 259 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 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 289 ILE 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 103 optimal weight: 0.0980 chunk 58 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 127 optimal weight: 0.2980 chunk 51 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 202 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 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 ** 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 115 ASN E 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16113 Z= 0.240 Angle : 0.752 8.245 21934 Z= 0.373 Chirality : 0.044 0.184 2505 Planarity : 0.005 0.042 2828 Dihedral : 9.413 90.240 2391 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.91 % Favored : 93.26 % Rotamer: Outliers : 6.47 % Allowed : 22.65 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.18), residues: 1810 helix: -2.39 (0.17), residues: 675 sheet: -2.48 (0.33), residues: 205 loop : -1.77 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.011 0.002 PHE E 255 TYR 0.026 0.001 TYR B 279 ARG 0.003 0.000 ARG B 335 *********************** 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 510 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 410 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.9072 (t) cc_final: 0.8674 (p) REVERT: A 39 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8646 (ptt180) REVERT: A 105 LEU cc_start: 0.8617 (mt) cc_final: 0.8371 (mt) REVERT: A 195 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8544 (pt0) REVERT: A 237 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8720 (pt0) REVERT: A 328 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8263 (mttp) REVERT: B 121 GLN cc_start: 0.9091 (tt0) cc_final: 0.8852 (tm-30) REVERT: B 124 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: B 154 ASP cc_start: 0.8420 (t0) cc_final: 0.8047 (t0) REVERT: B 162 ASN cc_start: 0.8970 (t0) cc_final: 0.8721 (t0) REVERT: B 190 MET cc_start: 0.9229 (ttp) cc_final: 0.9023 (ttt) REVERT: B 329 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9115 (mm) REVERT: B 340 TRP cc_start: 0.8880 (t60) cc_final: 0.8375 (t60) REVERT: C 39 ARG cc_start: 0.8701 (ptp-170) cc_final: 0.8419 (ptp-170) REVERT: C 121 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8898 (tm-30) REVERT: C 259 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.9079 (tm-30) REVERT: C 300 SER cc_start: 0.9389 (m) cc_final: 0.9055 (p) REVERT: C 325 MET cc_start: 0.8873 (tpp) cc_final: 0.8495 (tpt) REVERT: C 359 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.9016 (mtpp) REVERT: D 115 ASN cc_start: 0.8957 (t0) cc_final: 0.8560 (t0) REVERT: D 242 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8981 (mp) REVERT: D 325 MET cc_start: 0.9155 (mmm) cc_final: 0.8521 (tpp) REVERT: D 334 GLU cc_start: 0.8686 (pt0) cc_final: 0.8359 (pt0) REVERT: E 121 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8643 (tm-30) REVERT: E 125 GLU cc_start: 0.8316 (pt0) cc_final: 0.8108 (pt0) REVERT: E 167 GLU cc_start: 0.9014 (tt0) cc_final: 0.8721 (tm-30) REVERT: E 263 GLN cc_start: 0.8718 (mt0) cc_final: 0.8423 (mt0) REVERT: E 270 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8478 (mt-10) REVERT: E 289 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9157 (mm) outliers start: 100 outliers final: 60 residues processed: 472 average time/residue: 0.2363 time to fit residues: 169.5150 Evaluate side-chains 457 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 386 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 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 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 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 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 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 259 GLU 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 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 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 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU 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 364 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.0370 chunk 140 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 20 optimal weight: 100.0000 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16113 Z= 0.203 Angle : 0.722 9.219 21934 Z= 0.353 Chirality : 0.044 0.184 2505 Planarity : 0.004 0.056 2828 Dihedral : 8.889 86.927 2383 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.19 % Favored : 93.98 % Rotamer: Outliers : 7.57 % Allowed : 23.43 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1810 helix: -1.99 (0.18), residues: 675 sheet: -2.34 (0.33), residues: 205 loop : -1.50 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.015 0.001 TYR A 198 ARG 0.003 0.000 ARG D 290 *********************** 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 526 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 409 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8926 (t) cc_final: 0.8470 (p) REVERT: A 39 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8590 (ptt180) REVERT: A 195 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8441 (pt0) REVERT: A 237 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: A 328 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8306 (mttp) REVERT: A 340 TRP cc_start: 0.8028 (t60) cc_final: 0.7582 (t60) REVERT: B 44 MET cc_start: 0.8481 (ttp) cc_final: 0.8174 (ttm) REVERT: B 121 GLN cc_start: 0.9072 (tt0) cc_final: 0.8824 (tm-30) REVERT: B 123 MET cc_start: 0.8200 (ttm) cc_final: 0.7997 (ttp) REVERT: B 124 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 154 ASP cc_start: 0.8336 (t0) cc_final: 0.8005 (t0) REVERT: B 190 MET cc_start: 0.9215 (ttp) cc_final: 0.9010 (ttt) REVERT: B 329 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9109 (mm) REVERT: B 334 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: B 340 TRP cc_start: 0.8773 (t60) cc_final: 0.8252 (t60) REVERT: C 39 ARG cc_start: 0.8622 (ptp-170) cc_final: 0.8238 (ptt180) REVERT: C 115 ASN cc_start: 0.9146 (t0) cc_final: 0.8162 (t0) REVERT: C 121 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8855 (tm-30) REVERT: C 202 THR cc_start: 0.8740 (t) cc_final: 0.8311 (t) REVERT: C 259 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8896 (tm-30) REVERT: C 300 SER cc_start: 0.9387 (m) cc_final: 0.9033 (p) REVERT: C 325 MET cc_start: 0.8820 (tpp) cc_final: 0.8453 (tpt) REVERT: C 359 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8985 (mtpp) REVERT: D 76 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9098 (pt) REVERT: D 242 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8860 (mp) REVERT: D 325 MET cc_start: 0.9077 (mmm) cc_final: 0.8484 (tpp) REVERT: E 121 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8689 (tm-30) REVERT: E 167 GLU cc_start: 0.8960 (tt0) cc_final: 0.8699 (tm-30) REVERT: E 270 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8299 (mt-10) REVERT: E 289 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9054 (mm) outliers start: 117 outliers final: 69 residues processed: 476 average time/residue: 0.2300 time to fit residues: 168.0208 Evaluate side-chains 471 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 391 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 195 GLU 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 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 17 VAL 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 248 ILE 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 339 VAL Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 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 189 LEU 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 289 ILE Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 2 optimal weight: 110.0000 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 101 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16113 Z= 0.231 Angle : 0.717 8.847 21934 Z= 0.348 Chirality : 0.045 0.198 2505 Planarity : 0.004 0.038 2828 Dihedral : 8.347 84.683 2374 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.25 % Favored : 93.92 % Rotamer: Outliers : 7.25 % Allowed : 24.14 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.19), residues: 1810 helix: -1.80 (0.18), residues: 675 sheet: -2.23 (0.34), residues: 205 loop : -1.43 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.015 0.002 PHE D 200 TYR 0.015 0.001 TYR A 198 ARG 0.003 0.000 ARG D 290 *********************** 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 fitting. rotamer outliers: 112 poor density : 409 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8868 (t) cc_final: 0.8529 (p) REVERT: A 39 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8673 (ptt180) REVERT: A 153 LEU cc_start: 0.9262 (tp) cc_final: 0.9020 (tp) REVERT: A 237 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8646 (pt0) REVERT: A 328 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8319 (mttp) REVERT: B 121 GLN cc_start: 0.9079 (tt0) cc_final: 0.8828 (tm-30) REVERT: B 124 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: B 154 ASP cc_start: 0.8278 (t0) cc_final: 0.7969 (t0) REVERT: B 190 MET cc_start: 0.9206 (ttp) cc_final: 0.8995 (ttt) REVERT: B 329 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9109 (mm) REVERT: B 334 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: B 340 TRP cc_start: 0.8775 (t60) cc_final: 0.8266 (t60) REVERT: C 115 ASN cc_start: 0.9171 (t0) cc_final: 0.8823 (t0) REVERT: C 121 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8858 (tm-30) REVERT: C 259 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8867 (tm-30) REVERT: C 283 MET cc_start: 0.8871 (mtp) cc_final: 0.8638 (mpp) REVERT: C 325 MET cc_start: 0.8778 (tpp) cc_final: 0.8410 (tpt) REVERT: D 124 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: D 242 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8854 (mp) REVERT: D 325 MET cc_start: 0.9127 (mmm) cc_final: 0.8545 (tpp) REVERT: E 167 GLU cc_start: 0.8979 (tt0) cc_final: 0.8692 (tm-30) REVERT: E 275 HIS cc_start: 0.9499 (OUTLIER) cc_final: 0.8883 (p-80) REVERT: E 289 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9042 (mm) outliers start: 112 outliers final: 71 residues processed: 469 average time/residue: 0.2289 time to fit residues: 164.9219 Evaluate side-chains 469 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 388 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 328 LYS Chi-restraints excluded: chain A residue 329 ILE 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 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 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 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 248 ILE 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 D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 8.9990 chunk 179 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 70.0000 chunk 65 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16113 Z= 0.212 Angle : 0.715 9.395 21934 Z= 0.345 Chirality : 0.045 0.188 2505 Planarity : 0.004 0.038 2828 Dihedral : 7.942 83.139 2365 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.83 % Allowed : 4.92 % Favored : 94.25 % Rotamer: Outliers : 6.54 % Allowed : 24.92 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.19), residues: 1810 helix: -1.65 (0.18), residues: 670 sheet: -2.18 (0.34), residues: 205 loop : -1.27 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 340 HIS 0.010 0.001 HIS C 275 PHE 0.012 0.001 PHE C 255 TYR 0.015 0.001 TYR B 279 ARG 0.004 0.000 ARG A 28 *********************** 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 525 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 424 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8827 (t) cc_final: 0.8296 (p) REVERT: A 39 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8633 (ptt180) REVERT: A 153 LEU cc_start: 0.9234 (tp) cc_final: 0.9015 (tp) REVERT: A 237 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8614 (pt0) REVERT: A 328 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8286 (mttp) REVERT: A 340 TRP cc_start: 0.7922 (t60) cc_final: 0.7433 (t60) REVERT: B 121 GLN cc_start: 0.9069 (tt0) cc_final: 0.8802 (tm-30) REVERT: B 124 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: B 154 ASP cc_start: 0.8198 (t0) cc_final: 0.7883 (t0) REVERT: B 190 MET cc_start: 0.9186 (ttp) cc_final: 0.8982 (ttt) REVERT: B 329 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9095 (mm) REVERT: B 334 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: B 340 TRP cc_start: 0.8750 (t60) cc_final: 0.8376 (t60) REVERT: C 115 ASN cc_start: 0.9152 (t0) cc_final: 0.8834 (t0) REVERT: C 259 GLU cc_start: 0.9330 (tm-30) cc_final: 0.8732 (tm-30) REVERT: C 325 MET cc_start: 0.8748 (tpp) cc_final: 0.8390 (tpt) REVERT: D 100 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: D 121 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8766 (tm-30) REVERT: D 124 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: D 242 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8846 (mp) REVERT: D 275 HIS cc_start: 0.9484 (OUTLIER) cc_final: 0.9015 (p-80) REVERT: D 325 MET cc_start: 0.9069 (mmm) cc_final: 0.8499 (tpp) REVERT: E 167 GLU cc_start: 0.8984 (tt0) cc_final: 0.8686 (tm-30) REVERT: E 193 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8673 (mt) REVERT: E 275 HIS cc_start: 0.9446 (OUTLIER) cc_final: 0.8995 (p-80) REVERT: E 289 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9117 (mm) outliers start: 101 outliers final: 69 residues processed: 479 average time/residue: 0.2267 time to fit residues: 168.0792 Evaluate side-chains 477 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 395 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 THR 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 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 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 248 ILE 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 D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 LEU 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 289 ILE Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 7.9990 chunk 22 optimal weight: 90.0000 chunk 113 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 92 ASN ** C 162 ASN ** 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 16113 Z= 0.358 Angle : 0.755 8.977 21934 Z= 0.368 Chirality : 0.047 0.206 2505 Planarity : 0.005 0.089 2828 Dihedral : 7.987 85.057 2361 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.96 % Favored : 92.21 % Rotamer: Outliers : 7.44 % Allowed : 24.92 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.19), residues: 1810 helix: -1.72 (0.18), residues: 670 sheet: -2.15 (0.30), residues: 255 loop : -1.31 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 340 HIS 0.007 0.001 HIS C 275 PHE 0.016 0.002 PHE E 255 TYR 0.046 0.002 TYR B 69 ARG 0.015 0.001 ARG B 183 *********************** 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 518 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 403 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8725 (ptt180) REVERT: A 153 LEU cc_start: 0.9288 (tp) cc_final: 0.9052 (tp) REVERT: A 328 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8337 (mttp) REVERT: A 340 TRP cc_start: 0.8247 (t60) cc_final: 0.7718 (t60) REVERT: B 121 GLN cc_start: 0.9119 (tt0) cc_final: 0.8862 (tm-30) REVERT: B 124 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: B 154 ASP cc_start: 0.8289 (t0) cc_final: 0.8013 (t0) REVERT: B 190 MET cc_start: 0.9224 (ttp) cc_final: 0.9022 (ttt) REVERT: B 329 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9114 (mm) REVERT: B 334 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: B 340 TRP cc_start: 0.8838 (t60) cc_final: 0.8081 (t60) REVERT: C 115 ASN cc_start: 0.9293 (t0) cc_final: 0.8956 (t0) REVERT: C 190 MET cc_start: 0.8770 (ttt) cc_final: 0.8555 (ttt) REVERT: C 225 ASN cc_start: 0.8651 (t0) cc_final: 0.8338 (t0) REVERT: C 259 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9001 (tm-30) REVERT: C 283 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8608 (mtt) REVERT: C 325 MET cc_start: 0.8731 (tpp) cc_final: 0.8447 (tpt) REVERT: D 115 ASN cc_start: 0.9008 (t0) cc_final: 0.8563 (t0) REVERT: D 124 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: D 190 MET cc_start: 0.9074 (tpp) cc_final: 0.8043 (ttt) REVERT: D 242 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8898 (mp) REVERT: D 275 HIS cc_start: 0.9533 (OUTLIER) cc_final: 0.9220 (p-80) REVERT: D 325 MET cc_start: 0.9089 (mmm) cc_final: 0.8616 (tpp) REVERT: E 167 GLU cc_start: 0.9026 (tt0) cc_final: 0.8692 (tm-30) REVERT: E 193 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8552 (mt) REVERT: E 275 HIS cc_start: 0.9533 (OUTLIER) cc_final: 0.9066 (p-80) REVERT: E 289 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9179 (mm) outliers start: 115 outliers final: 80 residues processed: 470 average time/residue: 0.2285 time to fit residues: 165.7212 Evaluate side-chains 486 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 394 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 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 261 LEU 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 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 248 ILE 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 283 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 D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 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 178 LEU 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 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 106 THR 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 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 120.0000 chunk 156 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16113 Z= 0.210 Angle : 0.729 9.937 21934 Z= 0.351 Chirality : 0.045 0.216 2505 Planarity : 0.005 0.094 2828 Dihedral : 7.669 84.108 2358 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.25 % Favored : 93.92 % Rotamer: Outliers : 6.41 % Allowed : 26.41 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.19), residues: 1810 helix: -1.59 (0.19), residues: 670 sheet: -2.22 (0.34), residues: 205 loop : -1.28 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 340 HIS 0.010 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.035 0.001 TYR B 69 ARG 0.009 0.000 ARG E 39 *********************** 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 504 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 405 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8724 (t) cc_final: 0.8466 (p) REVERT: A 39 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8647 (ptt180) REVERT: A 237 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8584 (pt0) REVERT: A 328 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: B 121 GLN cc_start: 0.9024 (tt0) cc_final: 0.8789 (tm-30) REVERT: B 124 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: B 154 ASP cc_start: 0.8209 (t0) cc_final: 0.7906 (t0) REVERT: B 329 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9085 (mm) REVERT: B 334 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7101 (pm20) REVERT: B 340 TRP cc_start: 0.8741 (t60) cc_final: 0.8403 (t60) REVERT: C 115 ASN cc_start: 0.9236 (t0) cc_final: 0.8945 (t0) REVERT: C 225 ASN cc_start: 0.8682 (t0) cc_final: 0.8268 (t0) REVERT: C 259 GLU cc_start: 0.9389 (tm-30) cc_final: 0.8977 (tm-30) REVERT: C 325 MET cc_start: 0.8758 (tpp) cc_final: 0.8439 (tpt) REVERT: D 121 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8786 (tm-30) REVERT: D 124 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: D 190 MET cc_start: 0.9078 (tpp) cc_final: 0.8115 (ttt) REVERT: D 242 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8834 (mp) REVERT: D 275 HIS cc_start: 0.9467 (OUTLIER) cc_final: 0.9231 (p-80) REVERT: D 352 PHE cc_start: 0.9101 (p90) cc_final: 0.8889 (p90) REVERT: E 44 MET cc_start: 0.8368 (ttm) cc_final: 0.7503 (ttp) REVERT: E 121 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8647 (tm-30) REVERT: E 167 GLU cc_start: 0.8967 (tt0) cc_final: 0.8671 (tm-30) REVERT: E 193 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8610 (mt) REVERT: E 275 HIS cc_start: 0.9465 (OUTLIER) cc_final: 0.9055 (p-80) REVERT: E 289 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9126 (mm) outliers start: 99 outliers final: 75 residues processed: 459 average time/residue: 0.2383 time to fit residues: 168.6191 Evaluate side-chains 467 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 380 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 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 261 LEU 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 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 248 ILE 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 D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 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 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE 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 180 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 185 optimal weight: 0.0970 chunk 111 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 0.1980 chunk 167 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 overall best weight: 3.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 161 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16113 Z= 0.228 Angle : 0.736 9.704 21934 Z= 0.356 Chirality : 0.045 0.184 2505 Planarity : 0.005 0.091 2828 Dihedral : 7.579 82.418 2358 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.08 % Favored : 93.26 % Rotamer: Outliers : 6.54 % Allowed : 26.67 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.19), residues: 1810 helix: -1.33 (0.20), residues: 635 sheet: -2.18 (0.34), residues: 205 loop : -1.27 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP A 340 HIS 0.010 0.001 HIS C 275 PHE 0.013 0.001 PHE D 200 TYR 0.030 0.001 TYR B 69 ARG 0.016 0.000 ARG B 183 *********************** 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 492 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 391 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8717 (t) cc_final: 0.8437 (p) REVERT: A 39 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8627 (ptt180) REVERT: A 237 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8587 (pt0) REVERT: A 328 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8306 (mttp) REVERT: B 121 GLN cc_start: 0.9023 (tt0) cc_final: 0.8773 (tm-30) REVERT: B 124 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: B 154 ASP cc_start: 0.8184 (t0) cc_final: 0.7964 (t0) REVERT: B 329 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9083 (mm) REVERT: B 334 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: B 340 TRP cc_start: 0.8757 (t60) cc_final: 0.8448 (t60) REVERT: C 115 ASN cc_start: 0.9249 (t0) cc_final: 0.8960 (t0) REVERT: C 259 GLU cc_start: 0.9384 (tm-30) cc_final: 0.8959 (tm-30) REVERT: C 325 MET cc_start: 0.8759 (tpp) cc_final: 0.8451 (tpt) REVERT: D 115 ASN cc_start: 0.8956 (t0) cc_final: 0.8494 (t0) REVERT: D 124 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: D 190 MET cc_start: 0.9052 (tpp) cc_final: 0.8128 (ttt) REVERT: D 242 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8841 (mp) REVERT: D 275 HIS cc_start: 0.9448 (OUTLIER) cc_final: 0.9243 (p-80) REVERT: E 44 MET cc_start: 0.8301 (ttm) cc_final: 0.7381 (ttp) REVERT: E 121 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8664 (tm-30) REVERT: E 167 GLU cc_start: 0.8972 (tt0) cc_final: 0.8677 (tm-30) REVERT: E 275 HIS cc_start: 0.9464 (OUTLIER) cc_final: 0.9041 (p-80) REVERT: E 289 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9006 (mm) outliers start: 101 outliers final: 79 residues processed: 445 average time/residue: 0.2399 time to fit residues: 167.3364 Evaluate side-chains 472 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 382 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE 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 261 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 248 ILE 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 D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 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 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE 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 121 optimal weight: 40.0000 chunk 195 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 16 optimal weight: 80.0000 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 246 GLN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 161 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** E 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16113 Z= 0.249 Angle : 0.741 8.946 21934 Z= 0.359 Chirality : 0.046 0.192 2505 Planarity : 0.005 0.080 2828 Dihedral : 7.474 82.017 2356 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.80 % Favored : 93.59 % Rotamer: Outliers : 6.28 % Allowed : 27.12 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.20), residues: 1810 helix: -1.31 (0.20), residues: 635 sheet: -2.20 (0.34), residues: 205 loop : -1.25 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP A 340 HIS 0.010 0.001 HIS C 275 PHE 0.023 0.002 PHE D 352 TYR 0.023 0.001 TYR C 133 ARG 0.014 0.000 ARG B 183 ********************** 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 481 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 384 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8674 (ptt180) REVERT: A 237 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: A 328 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8320 (mttp) REVERT: A 340 TRP cc_start: 0.7947 (t60) cc_final: 0.7605 (t60) REVERT: B 121 GLN cc_start: 0.9051 (tt0) cc_final: 0.8784 (tm-30) REVERT: B 124 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 154 ASP cc_start: 0.8198 (t0) cc_final: 0.7958 (t0) REVERT: B 190 MET cc_start: 0.8655 (ttt) cc_final: 0.8222 (ttt) REVERT: B 329 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9033 (mm) REVERT: B 334 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.7332 (pm20) REVERT: B 340 TRP cc_start: 0.8768 (t60) cc_final: 0.8418 (t60) REVERT: C 115 ASN cc_start: 0.9275 (t0) cc_final: 0.8990 (t0) REVERT: C 259 GLU cc_start: 0.9378 (tm-30) cc_final: 0.8965 (tm-30) REVERT: C 283 MET cc_start: 0.9071 (tpp) cc_final: 0.8682 (mtp) REVERT: C 325 MET cc_start: 0.8748 (tpp) cc_final: 0.8466 (tpt) REVERT: D 47 MET cc_start: 0.7520 (ttp) cc_final: 0.7252 (mtp) REVERT: D 121 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8949 (tm-30) REVERT: D 124 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: D 190 MET cc_start: 0.9064 (tpp) cc_final: 0.8203 (ttt) REVERT: D 242 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8839 (mp) REVERT: D 275 HIS cc_start: 0.9443 (OUTLIER) cc_final: 0.9234 (p-80) REVERT: E 44 MET cc_start: 0.8307 (ttm) cc_final: 0.7591 (ttp) REVERT: E 121 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8749 (tm-30) REVERT: E 167 GLU cc_start: 0.8974 (tt0) cc_final: 0.8677 (tm-30) REVERT: E 275 HIS cc_start: 0.9474 (OUTLIER) cc_final: 0.9072 (p-80) REVERT: E 289 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9104 (mm) outliers start: 97 outliers final: 79 residues processed: 440 average time/residue: 0.2276 time to fit residues: 155.7783 Evaluate side-chains 466 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 376 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 5 THR 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 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 261 LEU 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 71 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 249 THR 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 D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE 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 129 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 24 optimal weight: 110.0000 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 110.0000 chunk 30 optimal weight: 0.4980 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 161 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104835 restraints weight = 31768.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107378 restraints weight = 14941.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109158 restraints weight = 8623.097| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16113 Z= 0.226 Angle : 0.736 9.950 21934 Z= 0.356 Chirality : 0.045 0.190 2505 Planarity : 0.004 0.056 2828 Dihedral : 7.397 81.325 2356 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.13 % Favored : 93.31 % Rotamer: Outliers : 5.89 % Allowed : 27.90 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1810 helix: -1.27 (0.20), residues: 635 sheet: -2.18 (0.34), residues: 205 loop : -1.21 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP A 340 HIS 0.010 0.001 HIS C 275 PHE 0.017 0.001 PHE D 352 TYR 0.030 0.001 TYR B 279 ARG 0.009 0.000 ARG B 183 =============================================================================== Job complete usr+sys time: 3607.40 seconds wall clock time: 64 minutes 53.16 seconds (3893.16 seconds total)