Starting phenix.real_space_refine on Sat Mar 16 22:40:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8163/03_2024/5jlf_8163_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8163/03_2024/5jlf_8163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8163/03_2024/5jlf_8163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8163/03_2024/5jlf_8163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8163/03_2024/5jlf_8163_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8163/03_2024/5jlf_8163_updated.pdb" } resolution = 3.6 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= -0.000 sd= 0.011 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 Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 346} 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': 1, 'PTRANS': 19, 'TRANS': 346} 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': 1, 'PTRANS': 19, 'TRANS': 346} 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': 1, 'PTRANS': 19, 'TRANS': 346} 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': 1, 'PTRANS': 19, 'TRANS': 346} 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: "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: 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: 8.83, per 1000 atoms: 0.56 Number of scatterers: 15800 At special positions: 0 Unit cell: (99, 93.5, 207.9, 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 - 3.50 Amino acid : False - 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: 6.58 Conformation dependent library (CDL) restraints added in 2.6 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... running ksdssp... Secondary structure from input PDB file: 97 helices and 15 sheets defined 59.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.922A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.800A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.820A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.697A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.045A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.892A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 370 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.905A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.803A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.825A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.665A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.055A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.896A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.902A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.800A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.810A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 295 removed outlier: 3.673A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.050A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.892A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 370 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.905A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.808A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.821A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 287 through 295 removed outlier: 3.684A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.059A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.896A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 370 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.915A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.798A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.830A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.681A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.049A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.897A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 370 Processing helix chain 'F' and resid 98 through 230 removed outlier: 3.830A 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: 3.846A 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: 3.603A 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: 3.613A pdb=" N UNK F 223 " --> pdb=" O UNK F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 230 removed outlier: 3.577A pdb=" N UNK G 123 " --> pdb=" O UNK G 119 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.616A pdb=" N UNK G 164 " --> pdb=" O UNK G 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N UNK G 198 " --> pdb=" O UNK G 194 " (cutoff:3.500A) removed outlier: 3.713A 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 sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 7.699A pdb=" N CYS A 10 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 104 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR A 106 " --> pdb=" O ASN A 12 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 298 through 300 Processing sheet with id= C, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= D, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.705A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN B 12 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR B 106 " --> pdb=" O ASN B 12 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 298 through 300 Processing sheet with id= F, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= G, first strand: chain 'C' and resid 29 through 31 removed outlier: 7.704A pdb=" N CYS C 10 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 104 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN C 12 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR C 106 " --> pdb=" O ASN C 12 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 298 through 300 Processing sheet with id= I, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'D' and resid 29 through 31 removed outlier: 7.711A pdb=" N CYS D 10 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN D 12 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR D 106 " --> pdb=" O ASN D 12 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 298 through 300 Processing sheet with id= L, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'E' and resid 29 through 31 removed outlier: 7.703A pdb=" N CYS E 10 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU E 104 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN E 12 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR E 106 " --> pdb=" O ASN E 12 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 298 through 300 Processing sheet with id= O, first strand: chain 'E' and resid 238 through 241 820 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2705 1.31 - 1.44: 4170 1.44 - 1.57: 9014 1.57 - 1.70: 44 1.70 - 1.83: 180 Bond restraints: 16113 Sorted by residual: bond pdb=" C ILE D 165 " pdb=" O ILE D 165 " ideal model delta sigma weight residual 1.236 1.301 -0.066 1.00e-02 1.00e+04 4.35e+01 bond pdb=" C ILE A 165 " pdb=" O ILE A 165 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.04e-02 9.25e+03 3.69e+01 bond pdb=" C ILE B 165 " pdb=" O ILE B 165 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.04e-02 9.25e+03 3.39e+01 bond pdb=" C ILE C 165 " pdb=" O ILE C 165 " ideal model delta sigma weight residual 1.236 1.294 -0.058 1.04e-02 9.25e+03 3.09e+01 bond pdb=" C ILE E 165 " pdb=" O ILE E 165 " ideal model delta sigma weight residual 1.236 1.292 -0.056 1.04e-02 9.25e+03 2.90e+01 ... (remaining 16108 not shown) Histogram of bond angle deviations from ideal: 96.14 - 104.16: 331 104.16 - 112.18: 7186 112.18 - 120.20: 7702 120.20 - 128.22: 6615 128.22 - 136.25: 100 Bond angle restraints: 21934 Sorted by residual: angle pdb=" N PHE C 127 " pdb=" CA PHE C 127 " pdb=" C PHE C 127 " ideal model delta sigma weight residual 110.55 97.02 13.53 1.35e+00 5.49e-01 1.00e+02 angle pdb=" N PHE E 127 " pdb=" CA PHE E 127 " pdb=" C PHE E 127 " ideal model delta sigma weight residual 110.48 96.98 13.50 1.48e+00 4.57e-01 8.32e+01 angle pdb=" N PHE A 127 " pdb=" CA PHE A 127 " pdb=" C PHE A 127 " ideal model delta sigma weight residual 110.48 97.12 13.36 1.48e+00 4.57e-01 8.15e+01 angle pdb=" N PHE D 127 " pdb=" CA PHE D 127 " pdb=" C PHE D 127 " ideal model delta sigma weight residual 110.48 97.21 13.27 1.48e+00 4.57e-01 8.04e+01 angle pdb=" N PHE B 127 " pdb=" CA PHE B 127 " pdb=" C PHE B 127 " ideal model delta sigma weight residual 110.48 97.30 13.18 1.48e+00 4.57e-01 7.93e+01 ... (remaining 21929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.56: 9095 18.56 - 37.13: 485 37.13 - 55.69: 91 55.69 - 74.25: 2 74.25 - 92.81: 5 Dihedral angle restraints: 9678 sinusoidal: 3570 harmonic: 6108 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 32.82 -92.81 1 2.00e+01 2.50e-03 2.52e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 31.39 -91.39 1 2.00e+01 2.50e-03 2.46e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 30.05 -90.05 1 2.00e+01 2.50e-03 2.40e+01 ... (remaining 9675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1565 0.085 - 0.170: 648 0.170 - 0.254: 186 0.254 - 0.339: 78 0.339 - 0.424: 28 Chirality restraints: 2505 Sorted by residual: chirality pdb=" CA VAL B 17 " pdb=" N VAL B 17 " pdb=" C VAL B 17 " pdb=" CB VAL B 17 " both_signs ideal model delta sigma weight residual False 2.44 2.87 -0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CA VAL E 17 " pdb=" N VAL E 17 " pdb=" C VAL E 17 " pdb=" CB VAL E 17 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA VAL A 17 " pdb=" N VAL A 17 " pdb=" C VAL A 17 " pdb=" CB VAL A 17 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 2502 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 340 " -0.046 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP A 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 340 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 340 " 0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 340 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP A 340 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 340 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 340 " -0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 340 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP A 340 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 340 " -0.047 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP E 340 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP E 340 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP E 340 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP E 340 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP E 340 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP E 340 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 340 " -0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 340 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP E 340 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " -0.044 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " -0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " -0.012 2.00e-02 2.50e+03 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 927 2.73 - 3.27: 16982 3.27 - 3.81: 26178 3.81 - 4.36: 33320 4.36 - 4.90: 54100 Nonbonded interactions: 131507 Sorted by model distance: nonbonded pdb=" OD2 ASP D 286 " pdb=" O GLY E 63 " model vdw 2.184 3.040 nonbonded pdb=" O ALA A 295 " pdb=" O LYS A 328 " model vdw 2.322 3.040 nonbonded pdb=" O ALA C 295 " pdb=" O LYS C 328 " model vdw 2.324 3.040 nonbonded pdb=" O ALA D 295 " pdb=" O LYS D 328 " model vdw 2.326 3.040 nonbonded pdb=" O ALA B 295 " pdb=" O LYS B 328 " model vdw 2.332 3.040 ... (remaining 131502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.840 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: 4.380 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 44.000 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.013 0.066 16113 Z= 0.838 Angle : 1.579 13.532 21934 Z= 1.040 Chirality : 0.111 0.424 2505 Planarity : 0.010 0.055 2828 Dihedral : 12.258 92.812 5748 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.87 % Favored : 96.57 % Rotamer: Outliers : 1.29 % Allowed : 4.34 % Favored : 94.37 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.70 (0.19), residues: 1810 helix: -0.40 (0.18), residues: 710 sheet: -0.88 (0.25), residues: 350 loop : -0.04 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.011 TRP E 340 HIS 0.033 0.007 HIS D 275 PHE 0.060 0.008 PHE C 262 TYR 0.037 0.006 TYR E 166 ARG 0.030 0.003 ARG E 39 *********************** 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 537 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 517 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9202 (m-40) cc_final: 0.8679 (m-40) REVERT: A 78 ASN cc_start: 0.8865 (t0) cc_final: 0.8179 (t0) REVERT: A 81 ASP cc_start: 0.8846 (m-30) cc_final: 0.8426 (m-30) REVERT: A 121 GLN cc_start: 0.9204 (tt0) cc_final: 0.8797 (tm-30) REVERT: A 225 ASN cc_start: 0.8899 (m-40) cc_final: 0.8699 (m-40) REVERT: A 313 MET cc_start: 0.8545 (mmm) cc_final: 0.8152 (mmm) REVERT: A 351 THR cc_start: 0.8723 (p) cc_final: 0.8510 (p) REVERT: B 40 HIS cc_start: 0.7813 (m-70) cc_final: 0.7605 (m-70) REVERT: B 47 MET cc_start: 0.1557 (ptm) cc_final: 0.0882 (ttt) REVERT: B 69 TYR cc_start: 0.9114 (m-10) cc_final: 0.8896 (m-10) REVERT: B 115 ASN cc_start: 0.8348 (m-40) cc_final: 0.8089 (m110) REVERT: B 160 THR cc_start: 0.8978 (m) cc_final: 0.8759 (m) REVERT: B 242 LEU cc_start: 0.9076 (mp) cc_final: 0.8801 (mt) REVERT: B 279 TYR cc_start: 0.9151 (t80) cc_final: 0.8939 (t80) REVERT: C 123 MET cc_start: 0.8732 (mmt) cc_final: 0.8515 (tpp) REVERT: C 162 ASN cc_start: 0.8216 (m-40) cc_final: 0.7946 (m-40) REVERT: C 186 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9231 (t) REVERT: C 187 ASP cc_start: 0.8681 (m-30) cc_final: 0.8436 (t0) REVERT: C 191 LYS cc_start: 0.8824 (ptmt) cc_final: 0.8248 (mtpp) REVERT: D 10 CYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8859 (t) REVERT: D 12 ASN cc_start: 0.8786 (m-40) cc_final: 0.8572 (m110) REVERT: D 44 MET cc_start: 0.8117 (mmm) cc_final: 0.7083 (mtt) REVERT: D 78 ASN cc_start: 0.8796 (t0) cc_final: 0.8394 (t0) REVERT: D 81 ASP cc_start: 0.8984 (m-30) cc_final: 0.8668 (m-30) REVERT: D 110 LEU cc_start: 0.9215 (tp) cc_final: 0.8974 (tt) REVERT: D 160 THR cc_start: 0.9399 (m) cc_final: 0.9071 (p) REVERT: D 192 ILE cc_start: 0.9089 (tp) cc_final: 0.8636 (tp) REVERT: D 237 GLU cc_start: 0.8599 (pt0) cc_final: 0.8356 (pm20) REVERT: D 353 GLN cc_start: 0.8727 (mt0) cc_final: 0.8511 (tm-30) REVERT: D 355 MET cc_start: 0.8730 (mtt) cc_final: 0.8302 (tpt) REVERT: E 12 ASN cc_start: 0.9247 (m-40) cc_final: 0.8670 (p0) REVERT: E 78 ASN cc_start: 0.8864 (t0) cc_final: 0.8617 (t0) REVERT: E 157 ASP cc_start: 0.8753 (t0) cc_final: 0.8498 (t0) REVERT: E 162 ASN cc_start: 0.8491 (m-40) cc_final: 0.8134 (m-40) REVERT: E 283 MET cc_start: 0.9321 (mmp) cc_final: 0.9005 (mmt) REVERT: E 327 ILE cc_start: 0.8874 (mt) cc_final: 0.8654 (mp) outliers start: 20 outliers final: 2 residues processed: 532 average time/residue: 0.2925 time to fit residues: 223.3291 Evaluate side-chains 272 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 268 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 92 ASN A 162 ASN A 246 GLN A 280 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 280 ASN B 296 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 88 HIS D 92 ASN D 296 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN E 297 ASN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16113 Z= 0.239 Angle : 0.716 11.006 21934 Z= 0.362 Chirality : 0.045 0.246 2505 Planarity : 0.006 0.103 2828 Dihedral : 7.006 66.888 2327 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.88 % Favored : 97.85 % Rotamer: Outliers : 3.30 % Allowed : 15.15 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.23 (0.19), residues: 1810 helix: -0.22 (0.18), residues: 715 sheet: -0.31 (0.28), residues: 285 loop : 0.21 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 340 HIS 0.005 0.001 HIS D 101 PHE 0.019 0.002 PHE A 352 TYR 0.014 0.001 TYR C 166 ARG 0.006 0.001 ARG A 210 *********************** 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 358 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7934 (tpp) cc_final: 0.7711 (tpp) REVERT: A 78 ASN cc_start: 0.8947 (t0) cc_final: 0.8207 (t0) REVERT: A 325 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7937 (ptm) REVERT: B 44 MET cc_start: 0.8208 (mpp) cc_final: 0.7578 (mpp) REVERT: B 47 MET cc_start: 0.1846 (ptm) cc_final: 0.1101 (ttt) REVERT: B 80 ASP cc_start: 0.8109 (p0) cc_final: 0.7815 (p0) REVERT: B 82 MET cc_start: 0.8993 (tpp) cc_final: 0.8723 (tpp) REVERT: B 313 MET cc_start: 0.8884 (mmm) cc_final: 0.8588 (mmm) REVERT: B 325 MET cc_start: 0.7520 (ptm) cc_final: 0.7242 (ttp) REVERT: B 354 GLN cc_start: 0.9382 (mp10) cc_final: 0.9144 (pm20) REVERT: B 360 GLN cc_start: 0.8964 (pp30) cc_final: 0.8720 (pp30) REVERT: C 123 MET cc_start: 0.8941 (mmt) cc_final: 0.8718 (tpp) REVERT: C 137 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8630 (mm-40) REVERT: C 190 MET cc_start: 0.9009 (mmm) cc_final: 0.8744 (mtt) REVERT: C 263 GLN cc_start: 0.9012 (mm110) cc_final: 0.8500 (mt0) REVERT: C 270 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7034 (mp0) REVERT: C 276 GLU cc_start: 0.8834 (mp0) cc_final: 0.8585 (mp0) REVERT: D 44 MET cc_start: 0.7946 (mmm) cc_final: 0.7026 (mtt) REVERT: D 47 MET cc_start: 0.3171 (ppp) cc_final: 0.2964 (ppp) REVERT: D 77 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.8822 (t) REVERT: D 110 LEU cc_start: 0.9150 (tp) cc_final: 0.8832 (tt) REVERT: D 192 ILE cc_start: 0.9186 (tp) cc_final: 0.8725 (tp) REVERT: D 237 GLU cc_start: 0.8491 (pt0) cc_final: 0.8091 (pm20) REVERT: D 355 MET cc_start: 0.8820 (mtt) cc_final: 0.8317 (tpt) REVERT: E 82 MET cc_start: 0.8726 (tpp) cc_final: 0.8479 (tpp) REVERT: E 93 GLU cc_start: 0.8503 (mp0) cc_final: 0.8276 (mm-30) REVERT: E 157 ASP cc_start: 0.8503 (t0) cc_final: 0.8226 (t0) REVERT: E 190 MET cc_start: 0.8836 (tpp) cc_final: 0.8595 (mmm) REVERT: E 191 LYS cc_start: 0.9139 (ptmt) cc_final: 0.8937 (ptpt) REVERT: E 206 ARG cc_start: 0.8794 (mtp-110) cc_final: 0.8343 (ttp-170) outliers start: 51 outliers final: 26 residues processed: 340 average time/residue: 0.2482 time to fit residues: 127.4362 Evaluate side-chains 266 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 238 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 51 optimal weight: 9.9990 chunk 187 optimal weight: 30.0000 chunk 202 optimal weight: 30.0000 chunk 166 optimal weight: 9.9990 chunk 185 optimal weight: 50.0000 chunk 63 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS B 88 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 263 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 59 GLN E 78 ASN E 92 ASN E 115 ASN E 246 GLN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16113 Z= 0.489 Angle : 0.794 8.881 21934 Z= 0.397 Chirality : 0.049 0.209 2505 Planarity : 0.005 0.055 2828 Dihedral : 6.802 67.074 2324 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.71 % Favored : 97.02 % Rotamer: Outliers : 5.70 % Allowed : 17.22 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.45 (0.20), residues: 1810 helix: -0.20 (0.19), residues: 705 sheet: -0.65 (0.27), residues: 320 loop : 0.02 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 340 HIS 0.008 0.002 HIS E 88 PHE 0.021 0.002 PHE A 352 TYR 0.028 0.002 TYR C 166 ARG 0.007 0.001 ARG E 95 *********************** 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 319 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 231 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9019 (t0) cc_final: 0.8709 (t0) REVERT: A 132 MET cc_start: 0.9186 (ptm) cc_final: 0.8910 (ppp) REVERT: A 211 ASP cc_start: 0.8713 (t0) cc_final: 0.8512 (t0) REVERT: A 325 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8141 (ptp) REVERT: B 44 MET cc_start: 0.8242 (tpp) cc_final: 0.7613 (mpp) REVERT: B 47 MET cc_start: 0.1849 (ptm) cc_final: 0.1189 (ttt) REVERT: B 80 ASP cc_start: 0.8129 (p0) cc_final: 0.7902 (p0) REVERT: C 47 MET cc_start: 0.2977 (ppp) cc_final: 0.2759 (ppp) REVERT: C 270 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7339 (mp0) REVERT: C 271 SER cc_start: 0.9041 (m) cc_final: 0.8628 (p) REVERT: C 276 GLU cc_start: 0.8854 (mp0) cc_final: 0.8614 (mp0) REVERT: D 44 MET cc_start: 0.8094 (mmm) cc_final: 0.7272 (mtt) REVERT: D 47 MET cc_start: 0.3348 (ppp) cc_final: 0.2595 (tmm) REVERT: D 142 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9058 (mp) REVERT: D 192 ILE cc_start: 0.9320 (tp) cc_final: 0.8974 (tp) REVERT: D 237 GLU cc_start: 0.8561 (pt0) cc_final: 0.8230 (pm20) REVERT: D 292 ASP cc_start: 0.8780 (m-30) cc_final: 0.8546 (m-30) REVERT: D 355 MET cc_start: 0.8827 (mtt) cc_final: 0.8276 (tpt) REVERT: E 93 GLU cc_start: 0.8627 (mp0) cc_final: 0.8352 (mm-30) REVERT: E 190 MET cc_start: 0.8967 (tpp) cc_final: 0.8634 (mmm) REVERT: E 191 LYS cc_start: 0.9205 (ptmt) cc_final: 0.9003 (ptpt) outliers start: 88 outliers final: 55 residues processed: 296 average time/residue: 0.2309 time to fit residues: 107.4958 Evaluate side-chains 262 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 205 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 50.0000 chunk 140 optimal weight: 0.0770 chunk 97 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 188 optimal weight: 40.0000 chunk 199 optimal weight: 50.0000 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16113 Z= 0.233 Angle : 0.634 7.180 21934 Z= 0.312 Chirality : 0.044 0.188 2505 Planarity : 0.004 0.050 2828 Dihedral : 6.279 60.876 2324 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.82 % Favored : 96.91 % Rotamer: Outliers : 3.88 % Allowed : 19.29 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.30 (0.20), residues: 1810 helix: -0.03 (0.19), residues: 705 sheet: -0.66 (0.27), residues: 320 loop : 0.08 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 340 HIS 0.007 0.001 HIS B 88 PHE 0.025 0.002 PHE A 352 TYR 0.021 0.001 TYR C 166 ARG 0.004 0.000 ARG E 95 *********************** 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 288 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 228 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8979 (t0) cc_final: 0.8716 (t0) REVERT: A 95 ARG cc_start: 0.8920 (mtm-85) cc_final: 0.8158 (mtm-85) REVERT: A 132 MET cc_start: 0.9123 (ptm) cc_final: 0.8711 (ppp) REVERT: A 211 ASP cc_start: 0.8691 (t0) cc_final: 0.8460 (t0) REVERT: A 241 GLU cc_start: 0.8145 (pp20) cc_final: 0.7932 (pm20) REVERT: B 44 MET cc_start: 0.8235 (tpp) cc_final: 0.7411 (mpp) REVERT: B 47 MET cc_start: 0.1840 (ptm) cc_final: 0.1037 (ttt) REVERT: B 72 GLU cc_start: 0.8774 (mp0) cc_final: 0.8557 (mp0) REVERT: B 80 ASP cc_start: 0.8274 (p0) cc_final: 0.7978 (p0) REVERT: B 84 LYS cc_start: 0.9258 (tttm) cc_final: 0.9046 (tttt) REVERT: B 169 TYR cc_start: 0.8529 (m-80) cc_final: 0.8271 (m-80) REVERT: B 299 MET cc_start: 0.8811 (mmm) cc_final: 0.8375 (mtt) REVERT: C 137 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8639 (mm-40) REVERT: C 270 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7359 (mp0) REVERT: C 271 SER cc_start: 0.9036 (m) cc_final: 0.8713 (p) REVERT: C 340 TRP cc_start: 0.8764 (t60) cc_final: 0.8465 (t60) REVERT: D 44 MET cc_start: 0.8177 (mmm) cc_final: 0.7366 (mtt) REVERT: D 47 MET cc_start: 0.3269 (ppp) cc_final: 0.2842 (tmm) REVERT: D 142 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8794 (mp) REVERT: D 192 ILE cc_start: 0.9217 (tp) cc_final: 0.8762 (tp) REVERT: D 237 GLU cc_start: 0.8495 (pt0) cc_final: 0.8214 (pm20) REVERT: D 292 ASP cc_start: 0.8717 (m-30) cc_final: 0.8493 (m-30) REVERT: D 355 MET cc_start: 0.8796 (mtt) cc_final: 0.8287 (tpt) REVERT: E 93 GLU cc_start: 0.8546 (mp0) cc_final: 0.8270 (mm-30) REVERT: E 191 LYS cc_start: 0.9109 (ptmt) cc_final: 0.8860 (ttpt) REVERT: E 206 ARG cc_start: 0.8788 (mtp-110) cc_final: 0.8524 (ttp80) REVERT: E 236 LEU cc_start: 0.7844 (mt) cc_final: 0.7611 (mt) outliers start: 60 outliers final: 38 residues processed: 272 average time/residue: 0.2328 time to fit residues: 98.6070 Evaluate side-chains 244 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 205 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 0.0010 chunk 169 optimal weight: 0.9990 chunk 137 optimal weight: 0.0870 chunk 0 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 128 ASN D 162 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16113 Z= 0.170 Angle : 0.601 10.239 21934 Z= 0.292 Chirality : 0.043 0.205 2505 Planarity : 0.004 0.053 2828 Dihedral : 5.793 57.173 2323 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.93 % Favored : 96.80 % Rotamer: Outliers : 3.82 % Allowed : 20.26 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.01 (0.20), residues: 1810 helix: 0.21 (0.20), residues: 670 sheet: -0.52 (0.28), residues: 320 loop : 0.25 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 340 HIS 0.005 0.001 HIS E 88 PHE 0.035 0.001 PHE C 352 TYR 0.024 0.001 TYR C 166 ARG 0.003 0.000 ARG E 95 *********************** 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 318 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 259 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8360 (tpp) cc_final: 0.8149 (tpp) REVERT: A 78 ASN cc_start: 0.8973 (t0) cc_final: 0.8723 (t0) REVERT: A 95 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8155 (mtm-85) REVERT: A 107 GLU cc_start: 0.8623 (tt0) cc_final: 0.7834 (tt0) REVERT: A 121 GLN cc_start: 0.9185 (tt0) cc_final: 0.8835 (tm-30) REVERT: A 132 MET cc_start: 0.9111 (ptm) cc_final: 0.8785 (ppp) REVERT: A 211 ASP cc_start: 0.8652 (t0) cc_final: 0.8410 (t0) REVERT: B 44 MET cc_start: 0.8045 (tpp) cc_final: 0.7671 (tpp) REVERT: B 47 MET cc_start: 0.1790 (ptm) cc_final: 0.0818 (ttt) REVERT: B 72 GLU cc_start: 0.8799 (mp0) cc_final: 0.8479 (mp0) REVERT: B 80 ASP cc_start: 0.8192 (p0) cc_final: 0.7902 (p0) REVERT: B 132 MET cc_start: 0.8963 (ppp) cc_final: 0.8675 (ppp) REVERT: B 299 MET cc_start: 0.8736 (mmm) cc_final: 0.8431 (mtt) REVERT: C 104 LEU cc_start: 0.9049 (tt) cc_final: 0.8796 (tp) REVERT: C 191 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8631 (mmtp) REVERT: C 270 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7276 (mp0) REVERT: C 271 SER cc_start: 0.9012 (m) cc_final: 0.8786 (p) REVERT: C 340 TRP cc_start: 0.8696 (t60) cc_final: 0.8473 (t60) REVERT: C 353 GLN cc_start: 0.9376 (tp40) cc_final: 0.9033 (mm-40) REVERT: D 44 MET cc_start: 0.8087 (mmm) cc_final: 0.7276 (mtt) REVERT: D 47 MET cc_start: 0.3076 (ppp) cc_final: 0.1855 (tmm) REVERT: D 82 MET cc_start: 0.9280 (tpt) cc_final: 0.9044 (tpp) REVERT: D 142 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8757 (mp) REVERT: D 192 ILE cc_start: 0.9142 (tp) cc_final: 0.8640 (tp) REVERT: D 237 GLU cc_start: 0.8394 (pt0) cc_final: 0.8188 (pm20) REVERT: E 93 GLU cc_start: 0.8460 (mp0) cc_final: 0.8206 (mm-30) REVERT: E 206 ARG cc_start: 0.8803 (mtp-110) cc_final: 0.8397 (ttp-170) outliers start: 59 outliers final: 33 residues processed: 300 average time/residue: 0.2441 time to fit residues: 112.2847 Evaluate side-chains 256 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 176 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 199 optimal weight: 50.0000 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16113 Z= 0.294 Angle : 0.651 11.306 21934 Z= 0.316 Chirality : 0.044 0.181 2505 Planarity : 0.004 0.054 2828 Dihedral : 5.778 54.369 2323 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.26 % Favored : 96.46 % Rotamer: Outliers : 4.60 % Allowed : 20.65 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.06 (0.20), residues: 1810 helix: 0.07 (0.20), residues: 675 sheet: -0.60 (0.28), residues: 310 loop : 0.33 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.006 0.001 HIS E 88 PHE 0.018 0.002 PHE C 352 TYR 0.023 0.001 TYR C 166 ARG 0.007 0.000 ARG C 206 *********************** 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 298 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 227 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8966 (t0) cc_final: 0.8693 (t0) REVERT: A 107 GLU cc_start: 0.8682 (tt0) cc_final: 0.7950 (tt0) REVERT: A 121 GLN cc_start: 0.9199 (tt0) cc_final: 0.8855 (tm-30) REVERT: A 132 MET cc_start: 0.9180 (ptm) cc_final: 0.8772 (ppp) REVERT: A 211 ASP cc_start: 0.8704 (t0) cc_final: 0.8451 (t0) REVERT: A 241 GLU cc_start: 0.7794 (pm20) cc_final: 0.7568 (pm20) REVERT: B 44 MET cc_start: 0.8151 (tpp) cc_final: 0.7776 (tpp) REVERT: B 47 MET cc_start: 0.2065 (ptm) cc_final: 0.1229 (ttt) REVERT: B 72 GLU cc_start: 0.8794 (mp0) cc_final: 0.8490 (mp0) REVERT: B 80 ASP cc_start: 0.8178 (p0) cc_final: 0.7955 (p0) REVERT: B 132 MET cc_start: 0.9052 (ppp) cc_final: 0.8765 (ppp) REVERT: B 299 MET cc_start: 0.8810 (mmm) cc_final: 0.8454 (mtt) REVERT: C 191 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8609 (mmtp) REVERT: C 270 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7154 (mp0) REVERT: C 271 SER cc_start: 0.9092 (m) cc_final: 0.8835 (p) REVERT: D 44 MET cc_start: 0.8229 (mmm) cc_final: 0.7361 (mtt) REVERT: D 47 MET cc_start: 0.3215 (ppp) cc_final: 0.2981 (tmm) REVERT: D 82 MET cc_start: 0.9325 (tpt) cc_final: 0.9038 (tpp) REVERT: D 142 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8813 (mp) REVERT: D 192 ILE cc_start: 0.9194 (tp) cc_final: 0.8731 (tp) REVERT: D 237 GLU cc_start: 0.8429 (pt0) cc_final: 0.8169 (pm20) REVERT: E 93 GLU cc_start: 0.8533 (mp0) cc_final: 0.8251 (mm-30) REVERT: E 206 ARG cc_start: 0.8830 (mtp-110) cc_final: 0.8476 (ttp-170) outliers start: 71 outliers final: 57 residues processed: 277 average time/residue: 0.2182 time to fit residues: 96.1000 Evaluate side-chains 275 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 217 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 40.0000 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 198 optimal weight: 50.0000 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16113 Z= 0.290 Angle : 0.655 14.940 21934 Z= 0.315 Chirality : 0.044 0.175 2505 Planarity : 0.004 0.056 2828 Dihedral : 5.714 53.331 2323 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.09 % Favored : 95.64 % Rotamer: Outliers : 4.40 % Allowed : 21.29 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.01 (0.20), residues: 1810 helix: 0.10 (0.20), residues: 675 sheet: -0.69 (0.28), residues: 320 loop : 0.44 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 340 HIS 0.007 0.001 HIS E 88 PHE 0.024 0.002 PHE A 352 TYR 0.027 0.001 TYR C 166 ARG 0.006 0.000 ARG C 206 *********************** 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 304 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 236 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9030 (t0) cc_final: 0.8728 (t0) REVERT: A 107 GLU cc_start: 0.8628 (tt0) cc_final: 0.7748 (tt0) REVERT: A 121 GLN cc_start: 0.9175 (tt0) cc_final: 0.8862 (tm-30) REVERT: A 132 MET cc_start: 0.9182 (ptm) cc_final: 0.8756 (ppp) REVERT: A 211 ASP cc_start: 0.8722 (t0) cc_final: 0.8470 (t0) REVERT: A 227 MET cc_start: 0.9053 (mmm) cc_final: 0.8764 (mmt) REVERT: A 241 GLU cc_start: 0.7869 (pm20) cc_final: 0.7631 (pm20) REVERT: B 40 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7683 (m90) REVERT: B 44 MET cc_start: 0.8121 (tpp) cc_final: 0.7750 (tpp) REVERT: B 47 MET cc_start: 0.2125 (ptm) cc_final: 0.1312 (ttt) REVERT: B 72 GLU cc_start: 0.8753 (mp0) cc_final: 0.8449 (mp0) REVERT: B 80 ASP cc_start: 0.8199 (p0) cc_final: 0.7975 (p0) REVERT: B 132 MET cc_start: 0.8977 (ppp) cc_final: 0.8672 (ppp) REVERT: B 283 MET cc_start: 0.9134 (mmp) cc_final: 0.8905 (mmt) REVERT: B 299 MET cc_start: 0.8863 (mmm) cc_final: 0.8626 (mtt) REVERT: C 191 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8608 (mmtp) REVERT: C 270 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7020 (mp0) REVERT: C 271 SER cc_start: 0.9062 (m) cc_final: 0.8829 (p) REVERT: C 290 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8024 (mtt180) REVERT: C 313 MET cc_start: 0.9078 (mmm) cc_final: 0.8799 (tpp) REVERT: D 44 MET cc_start: 0.8250 (mmm) cc_final: 0.7365 (mtt) REVERT: D 47 MET cc_start: 0.3209 (ppp) cc_final: 0.2992 (tmm) REVERT: D 142 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8855 (mp) REVERT: D 192 ILE cc_start: 0.9196 (tp) cc_final: 0.8738 (tp) REVERT: E 107 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7907 (mm-30) REVERT: E 206 ARG cc_start: 0.8902 (mtp-110) cc_final: 0.8370 (ttt90) outliers start: 68 outliers final: 59 residues processed: 287 average time/residue: 0.2277 time to fit residues: 102.3568 Evaluate side-chains 274 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 212 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 78 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16113 Z= 0.187 Angle : 0.623 14.857 21934 Z= 0.298 Chirality : 0.043 0.179 2505 Planarity : 0.004 0.058 2828 Dihedral : 5.467 51.227 2323 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.70 % Favored : 96.02 % Rotamer: Outliers : 3.69 % Allowed : 22.65 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.14 (0.20), residues: 1810 helix: 0.21 (0.20), residues: 670 sheet: -0.62 (0.29), residues: 320 loop : 0.55 (0.24), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 86 HIS 0.005 0.001 HIS E 88 PHE 0.012 0.001 PHE B 352 TYR 0.026 0.001 TYR C 166 ARG 0.006 0.000 ARG C 206 *********************** 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 290 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 233 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8923 (t0) cc_final: 0.8696 (t0) REVERT: A 107 GLU cc_start: 0.8651 (tt0) cc_final: 0.7713 (tt0) REVERT: A 121 GLN cc_start: 0.9157 (tt0) cc_final: 0.8848 (tm-30) REVERT: A 132 MET cc_start: 0.9133 (ptm) cc_final: 0.8751 (ppp) REVERT: A 211 ASP cc_start: 0.8690 (t0) cc_final: 0.8467 (t0) REVERT: A 241 GLU cc_start: 0.7795 (pm20) cc_final: 0.7551 (pm20) REVERT: B 47 MET cc_start: 0.1975 (ptm) cc_final: 0.1183 (ttt) REVERT: B 72 GLU cc_start: 0.8745 (mp0) cc_final: 0.8450 (mp0) REVERT: B 80 ASP cc_start: 0.8158 (p0) cc_final: 0.7912 (p0) REVERT: C 82 MET cc_start: 0.8975 (mmm) cc_final: 0.8486 (tpp) REVERT: C 270 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7015 (mp0) REVERT: C 290 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7919 (mtt-85) REVERT: D 44 MET cc_start: 0.8267 (mmm) cc_final: 0.7346 (mtt) REVERT: D 47 MET cc_start: 0.3038 (ppp) cc_final: 0.1867 (tmm) REVERT: D 142 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8786 (mp) REVERT: D 192 ILE cc_start: 0.9144 (tp) cc_final: 0.8675 (tp) REVERT: E 107 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7785 (mm-30) REVERT: E 206 ARG cc_start: 0.8800 (mtp-110) cc_final: 0.8438 (ttp-170) outliers start: 57 outliers final: 45 residues processed: 278 average time/residue: 0.2273 time to fit residues: 99.9890 Evaluate side-chains 262 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 215 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 50.0000 chunk 190 optimal weight: 30.0000 chunk 173 optimal weight: 6.9990 chunk 185 optimal weight: 50.0000 chunk 111 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 184 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 137 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 16113 Z= 0.615 Angle : 0.859 13.996 21934 Z= 0.426 Chirality : 0.050 0.222 2505 Planarity : 0.005 0.055 2828 Dihedral : 6.140 59.861 2323 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.36 % Favored : 95.36 % Rotamer: Outliers : 4.34 % Allowed : 22.01 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.68 (0.20), residues: 1810 helix: -0.41 (0.19), residues: 715 sheet: -0.97 (0.28), residues: 320 loop : 0.01 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C 86 HIS 0.014 0.002 HIS A 161 PHE 0.017 0.003 PHE C 255 TYR 0.029 0.002 TYR C 166 ARG 0.007 0.001 ARG E 312 *********************** 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 262 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 195 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9056 (t0) cc_final: 0.8706 (t0) REVERT: A 107 GLU cc_start: 0.8750 (tt0) cc_final: 0.8032 (tt0) REVERT: A 121 GLN cc_start: 0.9179 (tt0) cc_final: 0.8829 (tm-30) REVERT: A 211 ASP cc_start: 0.8798 (t0) cc_final: 0.8597 (t0) REVERT: B 40 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7771 (m90) REVERT: B 44 MET cc_start: 0.8352 (tpp) cc_final: 0.7946 (tpp) REVERT: B 47 MET cc_start: 0.2536 (ptm) cc_final: 0.1757 (ttt) REVERT: B 72 GLU cc_start: 0.8737 (mp0) cc_final: 0.8427 (mp0) REVERT: B 227 MET cc_start: 0.9397 (mmm) cc_final: 0.9104 (mmm) REVERT: C 50 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8603 (mmmt) REVERT: C 263 GLN cc_start: 0.9145 (mm110) cc_final: 0.8915 (mt0) REVERT: C 340 TRP cc_start: 0.8883 (t60) cc_final: 0.8681 (t60) REVERT: D 44 MET cc_start: 0.8298 (mmm) cc_final: 0.7318 (mtt) REVERT: D 47 MET cc_start: 0.3653 (ppp) cc_final: 0.3399 (tmm) REVERT: D 82 MET cc_start: 0.9144 (tpp) cc_final: 0.8543 (tmm) REVERT: D 142 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9096 (mp) REVERT: D 192 ILE cc_start: 0.9252 (tp) cc_final: 0.8857 (tp) REVERT: D 269 MET cc_start: 0.8658 (mtm) cc_final: 0.8423 (mtm) REVERT: D 283 MET cc_start: 0.8888 (mmp) cc_final: 0.8572 (mmp) REVERT: E 107 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8043 (mm-30) outliers start: 67 outliers final: 55 residues processed: 245 average time/residue: 0.2243 time to fit residues: 87.8460 Evaluate side-chains 244 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 187 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 2.9990 chunk 195 optimal weight: 50.0000 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 205 optimal weight: 40.0000 chunk 188 optimal weight: 40.0000 chunk 163 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 314 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16113 Z= 0.204 Angle : 0.660 14.365 21934 Z= 0.319 Chirality : 0.043 0.177 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.641 52.752 2323 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.03 % Favored : 95.69 % Rotamer: Outliers : 2.39 % Allowed : 23.95 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -0.09 (0.20), residues: 1810 helix: 0.08 (0.21), residues: 670 sheet: -0.83 (0.28), residues: 320 loop : 0.40 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 86 HIS 0.005 0.001 HIS A 275 PHE 0.013 0.001 PHE C 352 TYR 0.026 0.001 TYR C 166 ARG 0.005 0.000 ARG C 206 ********************** 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 248 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8999 (t0) cc_final: 0.8702 (t0) REVERT: A 107 GLU cc_start: 0.8692 (tt0) cc_final: 0.7766 (tt0) REVERT: A 132 MET cc_start: 0.9130 (ptm) cc_final: 0.8729 (ppp) REVERT: A 211 ASP cc_start: 0.8710 (t0) cc_final: 0.8467 (t0) REVERT: A 241 GLU cc_start: 0.7937 (pm20) cc_final: 0.7691 (pm20) REVERT: A 352 PHE cc_start: 0.8404 (t80) cc_final: 0.8175 (t80) REVERT: B 47 MET cc_start: 0.2336 (ptm) cc_final: 0.1594 (ttt) REVERT: B 72 GLU cc_start: 0.8693 (mp0) cc_final: 0.8362 (mp0) REVERT: B 82 MET cc_start: 0.9245 (tpt) cc_final: 0.8745 (tpt) REVERT: B 227 MET cc_start: 0.9360 (mmm) cc_final: 0.9049 (mmm) REVERT: B 269 MET cc_start: 0.8181 (mtm) cc_final: 0.7828 (ptp) REVERT: C 50 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8672 (mmmt) REVERT: C 270 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7064 (mp0) REVERT: D 44 MET cc_start: 0.8282 (mmm) cc_final: 0.7323 (mtt) REVERT: D 47 MET cc_start: 0.3331 (ppp) cc_final: 0.3113 (tmm) REVERT: D 72 GLU cc_start: 0.8630 (pp20) cc_final: 0.8400 (pp20) REVERT: D 82 MET cc_start: 0.9041 (tpp) cc_final: 0.8360 (tmm) REVERT: D 132 MET cc_start: 0.9180 (ppp) cc_final: 0.8863 (ppp) REVERT: D 142 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8801 (mp) REVERT: D 192 ILE cc_start: 0.9176 (tp) cc_final: 0.8825 (tp) REVERT: E 107 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7970 (mm-30) REVERT: E 280 ASN cc_start: 0.9111 (m-40) cc_final: 0.8895 (m-40) outliers start: 37 outliers final: 32 residues processed: 240 average time/residue: 0.2267 time to fit residues: 86.1312 Evaluate side-chains 237 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.0040 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 168 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 128 ASN E 92 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.096876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077108 restraints weight = 40728.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079521 restraints weight = 19227.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081117 restraints weight = 11139.324| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16113 Z= 0.190 Angle : 0.638 13.709 21934 Z= 0.307 Chirality : 0.042 0.169 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.356 46.836 2323 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.76 % Favored : 95.97 % Rotamer: Outliers : 2.20 % Allowed : 24.60 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.00 (0.20), residues: 1810 helix: 0.15 (0.21), residues: 670 sheet: -0.72 (0.29), residues: 310 loop : 0.42 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 86 HIS 0.008 0.001 HIS E 88 PHE 0.009 0.001 PHE A 262 TYR 0.024 0.001 TYR C 166 ARG 0.006 0.000 ARG C 206 =============================================================================== Job complete usr+sys time: 2948.30 seconds wall clock time: 54 minutes 16.35 seconds (3256.35 seconds total)