Starting phenix.real_space_refine on Sat Mar 16 22:40:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/03_2024/5jlf_8162_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/03_2024/5jlf_8162.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_8162/03_2024/5jlf_8162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/03_2024/5jlf_8162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/03_2024/5jlf_8162_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/03_2024/5jlf_8162_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= 0.001 sd= 0.010 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: 8.55, per 1000 atoms: 0.54 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: 6.94 Conformation dependent library (CDL) restraints added in 2.7 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: 3.15 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: 4.94 Time building geometry restraints manager: 7.38 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: 0.870 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: 4.270 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 45.450 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 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 507 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 487 time to evaluate : 1.709 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 121 GLN cc_start: 0.9234 (tt0) cc_final: 0.8962 (tm-30) REVERT: B 40 HIS cc_start: 0.7884 (m-70) cc_final: 0.7647 (m-70) REVERT: B 47 MET cc_start: 0.1902 (ptm) cc_final: 0.0929 (ttt) REVERT: B 86 TRP cc_start: 0.9389 (m-10) cc_final: 0.9176 (m-10) REVERT: B 115 ASN cc_start: 0.8510 (m-40) cc_final: 0.8260 (m110) REVERT: B 250 ILE cc_start: 0.9266 (pt) cc_final: 0.9025 (mm) REVERT: C 162 ASN cc_start: 0.8330 (m-40) cc_final: 0.8081 (m-40) REVERT: C 186 THR cc_start: 0.9580 (OUTLIER) cc_final: 0.9360 (t) REVERT: C 191 LYS cc_start: 0.8957 (ptmt) cc_final: 0.8472 (mtpp) REVERT: C 327 ILE cc_start: 0.9163 (mt) cc_final: 0.8927 (mp) REVERT: D 12 ASN cc_start: 0.8865 (m-40) cc_final: 0.8645 (m110) REVERT: D 44 MET cc_start: 0.8291 (mmm) cc_final: 0.7464 (mtt) REVERT: D 78 ASN cc_start: 0.8862 (t0) cc_final: 0.8520 (t0) REVERT: D 80 ASP cc_start: 0.8576 (p0) cc_final: 0.8324 (p0) REVERT: D 81 ASP cc_start: 0.9090 (m-30) cc_final: 0.8688 (m-30) REVERT: D 110 LEU cc_start: 0.9224 (tp) cc_final: 0.9019 (tt) REVERT: D 160 THR cc_start: 0.9438 (m) cc_final: 0.9195 (p) REVERT: D 353 GLN cc_start: 0.8783 (mt0) cc_final: 0.8522 (tm-30) REVERT: D 355 MET cc_start: 0.8740 (mtt) cc_final: 0.8347 (tpt) REVERT: E 12 ASN cc_start: 0.9209 (m-40) cc_final: 0.8785 (p0) REVERT: E 75 ILE cc_start: 0.9298 (mt) cc_final: 0.9073 (pt) REVERT: E 106 THR cc_start: 0.8429 (m) cc_final: 0.8125 (t) REVERT: E 157 ASP cc_start: 0.8577 (t0) cc_final: 0.8252 (t0) REVERT: E 162 ASN cc_start: 0.8471 (m-40) cc_final: 0.8173 (m-40) outliers start: 20 outliers final: 2 residues processed: 502 average time/residue: 0.2847 time to fit residues: 205.4443 Evaluate side-chains 285 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 282 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 186 THR 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: 0.8980 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 88 HIS A 92 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** 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 ** 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 162 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN E 280 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16113 Z= 0.248 Angle : 0.733 12.182 21934 Z= 0.370 Chirality : 0.046 0.258 2505 Planarity : 0.006 0.112 2828 Dihedral : 7.079 68.357 2326 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.04 % Favored : 97.68 % Rotamer: Outliers : 2.85 % Allowed : 15.40 % Favored : 81.75 % 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 (0.19), residues: 1810 helix: -0.08 (0.19), residues: 690 sheet: -0.29 (0.27), residues: 285 loop : 0.19 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 340 HIS 0.004 0.001 HIS D 101 PHE 0.018 0.002 PHE B 255 TYR 0.015 0.002 TYR C 166 ARG 0.006 0.001 ARG C 256 *********************** 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 355 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 311 time to evaluate : 1.741 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: symmetry clash REVERT: A 325 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7771 (ptm) REVERT: B 44 MET cc_start: 0.8242 (mpp) cc_final: 0.7608 (mpp) REVERT: B 47 MET cc_start: 0.2186 (ptm) cc_final: 0.1558 (ttm) REVERT: B 72 GLU cc_start: 0.8971 (mp0) cc_final: 0.8756 (mp0) REVERT: B 80 ASP cc_start: 0.8305 (p0) cc_final: 0.8071 (p0) REVERT: B 107 GLU cc_start: 0.7982 (pm20) cc_final: 0.7076 (pm20) REVERT: B 137 GLN cc_start: 0.9040 (mt0) cc_final: 0.8243 (mp10) REVERT: B 313 MET cc_start: 0.8813 (mmm) cc_final: 0.8496 (mmm) REVERT: B 354 GLN cc_start: 0.9453 (mp10) cc_final: 0.9241 (pm20) REVERT: C 123 MET cc_start: 0.8956 (mmp) cc_final: 0.8694 (tpp) REVERT: C 137 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8878 (mm-40) REVERT: C 190 MET cc_start: 0.9259 (mmm) cc_final: 0.8899 (mtp) REVERT: D 44 MET cc_start: 0.8105 (mmm) cc_final: 0.7421 (mtt) REVERT: D 47 MET cc_start: 0.3565 (ppp) cc_final: 0.3324 (tmm) REVERT: D 77 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8865 (t) REVERT: D 110 LEU cc_start: 0.9115 (tp) cc_final: 0.8797 (tt) REVERT: D 142 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9229 (mt) REVERT: D 355 MET cc_start: 0.8825 (mtt) cc_final: 0.8358 (tpt) REVERT: E 157 ASP cc_start: 0.8197 (t0) cc_final: 0.7950 (t0) REVERT: E 276 GLU cc_start: 0.8549 (mp0) cc_final: 0.8326 (mp0) outliers start: 44 outliers final: 20 residues processed: 343 average time/residue: 0.2546 time to fit residues: 131.5894 Evaluate side-chains 267 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 244 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS 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 B residue 88 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 85 ILE 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 C residue 219 VAL Chi-restraints excluded: chain D residue 77 THR 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 324 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 202 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 185 optimal weight: 30.0000 chunk 63 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN E 92 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 16113 Z= 0.482 Angle : 0.788 9.233 21934 Z= 0.394 Chirality : 0.048 0.204 2505 Planarity : 0.005 0.060 2828 Dihedral : 6.768 65.341 2324 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.76 % Favored : 96.96 % Rotamer: Outliers : 5.05 % Allowed : 15.99 % Favored : 78.96 % 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: -0.43 (0.20), residues: 1810 helix: -0.30 (0.19), residues: 705 sheet: -0.66 (0.27), residues: 325 loop : 0.17 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 340 HIS 0.008 0.002 HIS D 101 PHE 0.028 0.003 PHE E 223 TYR 0.027 0.002 TYR C 166 ARG 0.006 0.001 ARG E 312 *********************** 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 307 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 229 time to evaluate : 1.844 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: A 132 MET cc_start: 0.9106 (ptm) cc_final: 0.8870 (ppp) REVERT: A 242 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8601 (mt) REVERT: B 44 MET cc_start: 0.8318 (tpp) cc_final: 0.7680 (mpp) REVERT: B 47 MET cc_start: 0.2183 (ptm) cc_final: 0.1555 (ttt) REVERT: B 107 GLU cc_start: 0.7816 (pm20) cc_final: 0.6775 (tt0) REVERT: B 137 GLN cc_start: 0.9200 (mt0) cc_final: 0.8335 (mp10) REVERT: B 325 MET cc_start: 0.8105 (ppp) cc_final: 0.7860 (ttp) REVERT: B 360 GLN cc_start: 0.9111 (pp30) cc_final: 0.8817 (pp30) REVERT: C 123 MET cc_start: 0.8957 (mmp) cc_final: 0.8716 (tpp) REVERT: C 137 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8901 (mm-40) REVERT: C 192 ILE cc_start: 0.8979 (tp) cc_final: 0.8683 (tp) REVERT: C 270 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7327 (mp0) REVERT: C 271 SER cc_start: 0.9134 (m) cc_final: 0.8747 (p) REVERT: C 283 MET cc_start: 0.9061 (mmp) cc_final: 0.8818 (mmt) REVERT: C 340 TRP cc_start: 0.9031 (t60) cc_final: 0.8785 (t60) REVERT: D 44 MET cc_start: 0.8281 (mmm) cc_final: 0.7453 (mtt) REVERT: D 47 MET cc_start: 0.3841 (ppp) cc_final: 0.3505 (tmm) REVERT: D 142 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9272 (mp) REVERT: E 82 MET cc_start: 0.8972 (tpp) cc_final: 0.8726 (tpp) REVERT: E 276 GLU cc_start: 0.8533 (mp0) cc_final: 0.8202 (mp0) REVERT: E 280 ASN cc_start: 0.9174 (m-40) cc_final: 0.8937 (m-40) outliers start: 78 outliers final: 47 residues processed: 293 average time/residue: 0.2194 time to fit residues: 102.0435 Evaluate side-chains 244 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 195 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 242 LEU 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 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 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 194 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 52 SER 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 286 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL 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 186 THR 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: 30.0000 chunk 140 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 188 optimal weight: 30.0000 chunk 199 optimal weight: 50.0000 chunk 98 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 263 GLN B 353 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16113 Z= 0.254 Angle : 0.651 9.367 21934 Z= 0.320 Chirality : 0.044 0.175 2505 Planarity : 0.004 0.052 2828 Dihedral : 6.245 59.505 2324 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.04 % Favored : 96.69 % Rotamer: Outliers : 4.01 % Allowed : 18.38 % Favored : 77.61 % 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: -0.20 (0.20), residues: 1810 helix: -0.11 (0.19), residues: 705 sheet: -0.52 (0.27), residues: 320 loop : 0.28 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.005 0.001 HIS E 88 PHE 0.026 0.002 PHE C 352 TYR 0.022 0.001 TYR C 166 ARG 0.006 0.000 ARG E 206 *********************** 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 289 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 227 time to evaluate : 1.696 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 75 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9104 (pt) REVERT: A 86 TRP cc_start: 0.9124 (m-10) cc_final: 0.8918 (m-10) REVERT: A 132 MET cc_start: 0.9110 (ptm) cc_final: 0.8858 (ppp) REVERT: B 44 MET cc_start: 0.8324 (tpp) cc_final: 0.7537 (mpp) REVERT: B 47 MET cc_start: 0.2182 (ptm) cc_final: 0.1215 (ttt) REVERT: B 72 GLU cc_start: 0.8893 (mp0) cc_final: 0.8634 (mp0) REVERT: B 107 GLU cc_start: 0.7636 (pm20) cc_final: 0.7385 (tt0) REVERT: B 137 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8653 (mp10) REVERT: B 227 MET cc_start: 0.9363 (mmm) cc_final: 0.9160 (mmm) REVERT: B 360 GLN cc_start: 0.9135 (pp30) cc_final: 0.8843 (pp30) REVERT: C 192 ILE cc_start: 0.8915 (tp) cc_final: 0.8622 (tp) REVERT: C 270 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7286 (mp0) REVERT: C 271 SER cc_start: 0.9214 (m) cc_final: 0.8875 (p) REVERT: C 340 TRP cc_start: 0.8987 (t60) cc_final: 0.8736 (t60) REVERT: D 44 MET cc_start: 0.8354 (mmm) cc_final: 0.7529 (mtt) REVERT: D 142 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9204 (mp) REVERT: E 82 MET cc_start: 0.8870 (tpp) cc_final: 0.8619 (tpp) REVERT: E 206 ARG cc_start: 0.8908 (mtp-110) cc_final: 0.8557 (ttp-170) REVERT: E 280 ASN cc_start: 0.9155 (m-40) cc_final: 0.8948 (m-40) REVERT: E 314 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8842 (tt0) outliers start: 62 outliers final: 37 residues processed: 274 average time/residue: 0.2234 time to fit residues: 96.7688 Evaluate side-chains 241 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 161 HIS 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 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 355 MET 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 195 GLU Chi-restraints excluded: chain C residue 261 LEU 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 233 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 88 HIS 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 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 92 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16113 Z= 0.241 Angle : 0.641 9.270 21934 Z= 0.314 Chirality : 0.043 0.218 2505 Planarity : 0.004 0.055 2828 Dihedral : 5.986 56.287 2323 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.09 % Favored : 96.63 % Rotamer: Outliers : 4.79 % Allowed : 17.48 % Favored : 77.73 % 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: 0.05 (0.20), residues: 1810 helix: 0.15 (0.20), residues: 675 sheet: -0.44 (0.27), residues: 320 loop : 0.37 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 356 HIS 0.018 0.002 HIS B 88 PHE 0.017 0.001 PHE E 223 TYR 0.042 0.001 TYR E 279 ARG 0.005 0.000 ARG C 62 *********************** 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 294 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 220 time to evaluate : 1.901 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 75 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9128 (pt) REVERT: A 132 MET cc_start: 0.9101 (ptm) cc_final: 0.8870 (ppp) REVERT: B 44 MET cc_start: 0.8286 (tpp) cc_final: 0.7509 (mpp) REVERT: B 47 MET cc_start: 0.2166 (ptm) cc_final: 0.1061 (ttt) REVERT: B 72 GLU cc_start: 0.8895 (mp0) cc_final: 0.8591 (mp0) REVERT: B 107 GLU cc_start: 0.7439 (pm20) cc_final: 0.6752 (pm20) REVERT: B 137 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8708 (mp10) REVERT: C 192 ILE cc_start: 0.8927 (tp) cc_final: 0.8616 (tp) REVERT: C 270 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7209 (mp0) REVERT: C 271 SER cc_start: 0.9209 (m) cc_final: 0.8934 (p) REVERT: C 340 TRP cc_start: 0.8993 (t60) cc_final: 0.8731 (t60) REVERT: C 353 GLN cc_start: 0.9365 (tp40) cc_final: 0.9067 (tp-100) REVERT: C 354 GLN cc_start: 0.9402 (pt0) cc_final: 0.8953 (mp10) REVERT: D 44 MET cc_start: 0.8411 (mmm) cc_final: 0.7514 (mtt) REVERT: D 142 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9181 (mp) REVERT: E 82 MET cc_start: 0.8816 (tpp) cc_final: 0.8595 (tpp) REVERT: E 107 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8026 (mm-30) REVERT: E 206 ARG cc_start: 0.8897 (mtp-110) cc_final: 0.8672 (ttm-80) REVERT: E 227 MET cc_start: 0.8763 (tpp) cc_final: 0.8524 (mpp) REVERT: E 283 MET cc_start: 0.8896 (mpp) cc_final: 0.8691 (mpp) outliers start: 74 outliers final: 55 residues processed: 277 average time/residue: 0.2257 time to fit residues: 98.8537 Evaluate side-chains 260 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 202 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 304 THR 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 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 137 GLN 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 311 ASP Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE 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 195 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 289 ILE 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 233 SER 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 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 132 MET 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 351 THR 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: 0.9980 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 199 optimal weight: 50.0000 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16113 Z= 0.250 Angle : 0.642 10.776 21934 Z= 0.311 Chirality : 0.043 0.171 2505 Planarity : 0.004 0.055 2828 Dihedral : 5.787 57.337 2323 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.43 % Favored : 96.30 % Rotamer: Outliers : 4.98 % Allowed : 18.58 % Favored : 76.44 % 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: 0.12 (0.20), residues: 1810 helix: 0.10 (0.20), residues: 675 sheet: -0.41 (0.28), residues: 320 loop : 0.53 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 356 HIS 0.006 0.001 HIS E 88 PHE 0.030 0.002 PHE C 352 TYR 0.024 0.001 TYR C 166 ARG 0.003 0.000 ARG E 254 *********************** 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 294 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 217 time to evaluate : 1.861 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: symmetry clash REVERT: A 75 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9101 (pt) REVERT: A 121 GLN cc_start: 0.9272 (tt0) cc_final: 0.8940 (tm-30) REVERT: B 47 MET cc_start: 0.2362 (ptm) cc_final: 0.1338 (ttt) REVERT: B 72 GLU cc_start: 0.8852 (mp0) cc_final: 0.8532 (mp0) REVERT: B 82 MET cc_start: 0.9187 (tpt) cc_final: 0.8962 (tpt) REVERT: B 107 GLU cc_start: 0.7315 (pm20) cc_final: 0.6563 (pm20) REVERT: B 137 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8801 (mp10) REVERT: C 270 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6740 (mp0) REVERT: C 271 SER cc_start: 0.9235 (m) cc_final: 0.9017 (p) REVERT: D 44 MET cc_start: 0.8378 (mmm) cc_final: 0.7630 (mtt) REVERT: D 47 MET cc_start: 0.4693 (tmm) cc_final: 0.3303 (tmm) REVERT: D 82 MET cc_start: 0.9058 (tpp) cc_final: 0.8621 (tmm) REVERT: D 142 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9158 (mp) REVERT: E 82 MET cc_start: 0.8832 (tpp) cc_final: 0.8491 (tpp) REVERT: E 106 THR cc_start: 0.8312 (m) cc_final: 0.7947 (p) REVERT: E 107 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8223 (mm-30) REVERT: E 206 ARG cc_start: 0.8908 (mtp-110) cc_final: 0.8636 (ttm-80) REVERT: E 305 MET cc_start: 0.8836 (mmm) cc_final: 0.8578 (mmt) outliers start: 77 outliers final: 56 residues processed: 275 average time/residue: 0.2242 time to fit residues: 97.5182 Evaluate side-chains 269 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 210 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 51 ASP Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 304 THR 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 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 137 GLN 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 159 VAL 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 304 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE 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 289 ILE Chi-restraints excluded: chain D residue 33 SER 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 233 SER Chi-restraints excluded: chain D residue 244 ASP 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 34 ILE Chi-restraints excluded: chain E residue 54 VAL 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 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 50.0000 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 198 optimal weight: 50.0000 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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: 0.7155 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16113 Z= 0.359 Angle : 0.695 11.895 21934 Z= 0.338 Chirality : 0.045 0.168 2505 Planarity : 0.004 0.054 2828 Dihedral : 5.838 55.962 2323 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.76 % Favored : 95.97 % Rotamer: Outliers : 4.92 % Allowed : 19.48 % Favored : 75.60 % 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: 0.04 (0.20), residues: 675 sheet: -0.45 (0.28), residues: 320 loop : 0.41 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 356 HIS 0.007 0.002 HIS E 88 PHE 0.024 0.002 PHE C 352 TYR 0.033 0.002 TYR E 279 ARG 0.004 0.000 ARG E 312 *********************** 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 282 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 206 time to evaluate : 1.701 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: A 75 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9113 (pt) REVERT: A 132 MET cc_start: 0.9157 (ppp) cc_final: 0.8950 (ppp) REVERT: B 40 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7767 (m90) REVERT: B 47 MET cc_start: 0.2387 (ptm) cc_final: 0.1413 (ttt) REVERT: B 72 GLU cc_start: 0.8875 (mp0) cc_final: 0.8591 (mp0) REVERT: B 107 GLU cc_start: 0.7421 (pm20) cc_final: 0.6504 (tt0) REVERT: B 137 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8344 (mp10) REVERT: C 270 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6814 (mp0) REVERT: C 271 SER cc_start: 0.9222 (m) cc_final: 0.8959 (p) REVERT: D 44 MET cc_start: 0.8429 (mmm) cc_final: 0.7383 (mtt) REVERT: D 47 MET cc_start: 0.4467 (tmm) cc_final: 0.3387 (tmm) REVERT: D 142 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9184 (mp) REVERT: D 269 MET cc_start: 0.8516 (mtm) cc_final: 0.8309 (mtm) REVERT: E 82 MET cc_start: 0.8896 (tpp) cc_final: 0.8669 (tpp) REVERT: E 180 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8905 (tt) REVERT: E 206 ARG cc_start: 0.8952 (mtp-110) cc_final: 0.8721 (ttm-80) outliers start: 76 outliers final: 58 residues processed: 262 average time/residue: 0.2306 time to fit residues: 94.8043 Evaluate side-chains 257 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 194 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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 51 ASP Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 304 THR 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 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 137 GLN 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 304 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 105 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 195 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 345 ILE 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 233 SER Chi-restraints excluded: chain D residue 244 ASP 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 34 ILE Chi-restraints excluded: chain E residue 54 VAL 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 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16113 Z= 0.201 Angle : 0.649 12.628 21934 Z= 0.311 Chirality : 0.043 0.181 2505 Planarity : 0.004 0.056 2828 Dihedral : 5.585 56.396 2323 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.76 % Favored : 95.97 % Rotamer: Outliers : 3.82 % Allowed : 21.04 % Favored : 75.15 % 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: 0.18 (0.21), residues: 1810 helix: 0.15 (0.20), residues: 675 sheet: -0.40 (0.28), residues: 320 loop : 0.57 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.005 0.001 HIS E 88 PHE 0.011 0.001 PHE C 352 TYR 0.025 0.001 TYR B 279 ARG 0.002 0.000 ARG D 210 *********************** 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 285 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 226 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9088 (pt) REVERT: A 121 GLN cc_start: 0.9234 (tt0) cc_final: 0.8927 (tm-30) REVERT: B 47 MET cc_start: 0.2279 (ptm) cc_final: 0.1420 (ttt) REVERT: B 72 GLU cc_start: 0.8855 (mp0) cc_final: 0.8555 (mp0) REVERT: B 83 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8793 (pp20) REVERT: B 95 ARG cc_start: 0.9316 (mmm-85) cc_final: 0.9036 (mmm-85) REVERT: C 137 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8987 (mm110) REVERT: C 270 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6803 (mp0) REVERT: C 271 SER cc_start: 0.9249 (m) cc_final: 0.9021 (p) REVERT: D 44 MET cc_start: 0.8476 (mmm) cc_final: 0.7424 (mtt) REVERT: D 47 MET cc_start: 0.3772 (tmm) cc_final: 0.2907 (tmm) REVERT: D 82 MET cc_start: 0.9133 (tpp) cc_final: 0.8650 (tmm) REVERT: D 142 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9158 (mp) REVERT: E 82 MET cc_start: 0.8781 (tpp) cc_final: 0.8510 (tpp) REVERT: E 106 THR cc_start: 0.8283 (m) cc_final: 0.8043 (p) REVERT: E 206 ARG cc_start: 0.8882 (mtp-110) cc_final: 0.8640 (ttm-80) outliers start: 59 outliers final: 47 residues processed: 272 average time/residue: 0.2348 time to fit residues: 99.9243 Evaluate side-chains 257 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 208 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 304 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 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 136 ILE 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 304 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 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 289 ILE Chi-restraints excluded: chain C residue 345 ILE 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 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 88 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 30.0000 chunk 190 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 185 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 50.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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: 0.7130 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16113 Z= 0.254 Angle : 0.666 12.732 21934 Z= 0.318 Chirality : 0.043 0.188 2505 Planarity : 0.004 0.055 2828 Dihedral : 5.548 55.927 2323 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.70 % Favored : 96.02 % Rotamer: Outliers : 4.01 % Allowed : 21.29 % Favored : 74.69 % 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: 0.17 (0.21), residues: 1810 helix: 0.11 (0.20), residues: 675 sheet: -0.36 (0.28), residues: 320 loop : 0.57 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 356 HIS 0.006 0.001 HIS E 88 PHE 0.010 0.001 PHE C 255 TYR 0.028 0.001 TYR C 166 ARG 0.004 0.000 ARG C 206 *********************** 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 269 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 1.933 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: A 75 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9119 (pt) REVERT: A 121 GLN cc_start: 0.9203 (tt0) cc_final: 0.8912 (tm-30) REVERT: B 47 MET cc_start: 0.2162 (ptm) cc_final: 0.1366 (ttt) REVERT: B 72 GLU cc_start: 0.8849 (mp0) cc_final: 0.8558 (mp0) REVERT: B 83 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8824 (pp20) REVERT: B 137 GLN cc_start: 0.9055 (mp10) cc_final: 0.8336 (mp10) REVERT: B 283 MET cc_start: 0.9078 (mmp) cc_final: 0.8795 (mmm) REVERT: C 270 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6818 (mp0) REVERT: C 271 SER cc_start: 0.9253 (m) cc_final: 0.9043 (p) REVERT: D 44 MET cc_start: 0.8461 (mmm) cc_final: 0.7331 (mtt) REVERT: D 47 MET cc_start: 0.3882 (tmm) cc_final: 0.3037 (tmm) REVERT: D 82 MET cc_start: 0.9117 (tpp) cc_final: 0.8606 (tmm) REVERT: D 142 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9146 (mp) REVERT: E 82 MET cc_start: 0.8888 (tpp) cc_final: 0.8575 (tpp) REVERT: E 106 THR cc_start: 0.8313 (m) cc_final: 0.8080 (p) REVERT: E 206 ARG cc_start: 0.8908 (mtp-110) cc_final: 0.8655 (ttm-80) outliers start: 62 outliers final: 54 residues processed: 257 average time/residue: 0.2304 time to fit residues: 93.3697 Evaluate side-chains 262 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 304 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 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 136 ILE 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 304 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 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 289 ILE 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 151 ILE 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 233 SER Chi-restraints excluded: chain D residue 244 ASP 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 34 ILE Chi-restraints excluded: chain E residue 54 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 205 optimal weight: 30.0000 chunk 188 optimal weight: 30.0000 chunk 163 optimal weight: 0.0050 chunk 16 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 overall best weight: 1.2754 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16113 Z= 0.203 Angle : 0.651 13.109 21934 Z= 0.310 Chirality : 0.043 0.170 2505 Planarity : 0.004 0.057 2828 Dihedral : 5.374 55.392 2323 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.92 % Favored : 95.80 % Rotamer: Outliers : 3.37 % Allowed : 22.33 % 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: -0.07 (0.20), residues: 1810 helix: -0.10 (0.20), residues: 705 sheet: -0.32 (0.28), residues: 320 loop : 0.39 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.005 0.001 HIS E 88 PHE 0.011 0.001 PHE C 262 TYR 0.025 0.001 TYR C 166 ARG 0.004 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 275 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 223 time to evaluate : 1.516 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 75 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9070 (pt) REVERT: A 121 GLN cc_start: 0.9194 (tt0) cc_final: 0.8908 (tm-30) REVERT: B 47 MET cc_start: 0.2015 (ptm) cc_final: 0.1210 (ttt) REVERT: B 72 GLU cc_start: 0.8842 (mp0) cc_final: 0.8604 (mp0) REVERT: B 83 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8798 (pp20) REVERT: B 137 GLN cc_start: 0.9015 (mp10) cc_final: 0.8275 (mp10) REVERT: B 176 MET cc_start: 0.8551 (ptp) cc_final: 0.8321 (mtt) REVERT: B 283 MET cc_start: 0.9067 (mmp) cc_final: 0.8828 (mmm) REVERT: C 270 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6886 (mp0) REVERT: C 314 GLN cc_start: 0.9017 (tt0) cc_final: 0.8779 (tp40) REVERT: D 44 MET cc_start: 0.8486 (mmm) cc_final: 0.7287 (mtt) REVERT: D 47 MET cc_start: 0.3755 (tmm) cc_final: 0.3018 (tmm) REVERT: D 82 MET cc_start: 0.9092 (tpp) cc_final: 0.8615 (tmm) REVERT: D 132 MET cc_start: 0.9204 (ppp) cc_final: 0.8929 (ppp) REVERT: D 142 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9137 (mp) REVERT: E 82 MET cc_start: 0.8870 (tpp) cc_final: 0.8528 (tpp) REVERT: E 206 ARG cc_start: 0.8855 (mtp-110) cc_final: 0.8620 (ttm-80) outliers start: 52 outliers final: 46 residues processed: 263 average time/residue: 0.2307 time to fit residues: 95.0029 Evaluate side-chains 259 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 304 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 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU 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 304 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 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 261 LEU Chi-restraints excluded: chain C residue 289 ILE 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 225 ASN Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 88 HIS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 168 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN B 92 ASN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089866 restraints weight = 54351.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091531 restraints weight = 29177.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.092652 restraints weight = 18239.520| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16113 Z= 0.312 Angle : 0.692 13.418 21934 Z= 0.333 Chirality : 0.044 0.183 2505 Planarity : 0.004 0.056 2828 Dihedral : 5.486 55.167 2323 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.86 % Rotamer: Outliers : 3.69 % Allowed : 21.75 % Favored : 74.56 % 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: -0.19 (0.20), residues: 1810 helix: -0.19 (0.20), residues: 705 sheet: -0.51 (0.28), residues: 325 loop : 0.38 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 86 HIS 0.006 0.001 HIS B 173 PHE 0.012 0.002 PHE B 223 TYR 0.027 0.001 TYR C 166 ARG 0.005 0.000 ARG C 206 =============================================================================== Job complete usr+sys time: 2843.76 seconds wall clock time: 52 minutes 27.16 seconds (3147.16 seconds total)