Starting phenix.real_space_refine on Sun Dec 10 23:19:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/12_2023/5jlf_8162_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/12_2023/5jlf_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_8162/12_2023/5jlf_8162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/12_2023/5jlf_8162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/12_2023/5jlf_8162_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jlf_8162/12_2023/5jlf_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-1.21rc1-5172/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: 8.78, per 1000 atoms: 0.56 Number of scatterers: 15800 At special positions: 0 Unit cell: (99, 93.5, 207.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 O 3060 8.00 N 2700 7.00 C 9925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.34 Conformation dependent library (CDL) restraints added in 2.4 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: 2.94 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: 4.38 Time building geometry restraints manager: 6.80 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.210 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 41.470 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.200 ------------------------------------------------------------------------------- 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 : 1.841 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 outliers start: 20 outliers final: 2 residues processed: 502 average time/residue: 0.2911 time to fit residues: 211.4681 Evaluate side-chains 272 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1392 time to fit residues: 2.5861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 92 ASN D 162 ASN D 296 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 246 GLN E 280 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16113 Z= 0.242 Angle : 0.739 12.689 21934 Z= 0.370 Chirality : 0.046 0.264 2505 Planarity : 0.006 0.102 2828 Dihedral : 6.945 67.076 2323 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.04 % Favored : 97.68 % Rotamer: Outliers : 2.98 % Allowed : 14.95 % Favored : 82.07 % 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: -0.16 (0.19), residues: 1810 helix: -0.11 (0.19), residues: 690 sheet: -0.36 (0.27), residues: 285 loop : 0.22 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 340 HIS 0.006 0.001 HIS D 161 PHE 0.019 0.002 PHE B 255 TYR 0.014 0.001 TYR C 166 ARG 0.005 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 316 time to evaluate : 1.882 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 outliers start: 46 outliers final: 17 residues processed: 348 average time/residue: 0.2740 time to fit residues: 145.3955 Evaluate side-chains 244 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 227 time to evaluate : 1.630 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1600 time to fit residues: 6.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 185 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN C 12 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 263 GLN C 296 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16113 Z= 0.481 Angle : 0.795 9.423 21934 Z= 0.397 Chirality : 0.048 0.216 2505 Planarity : 0.005 0.060 2828 Dihedral : 6.703 64.632 2323 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.82 % Favored : 96.91 % Rotamer: Outliers : 4.14 % Allowed : 17.15 % Favored : 78.71 % 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: -0.28 (0.19), residues: 705 sheet: -0.66 (0.27), residues: 325 loop : 0.14 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 79 HIS 0.009 0.002 HIS D 161 PHE 0.018 0.002 PHE C 262 TYR 0.026 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 288 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 224 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 37 residues processed: 274 average time/residue: 0.2277 time to fit residues: 99.1290 Evaluate side-chains 235 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1502 time to fit residues: 12.5939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 188 optimal weight: 30.0000 chunk 199 optimal weight: 50.0000 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16113 Z= 0.236 Angle : 0.659 8.954 21934 Z= 0.323 Chirality : 0.044 0.178 2505 Planarity : 0.004 0.055 2828 Dihedral : 6.213 59.757 2323 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.87 % Favored : 96.85 % Rotamer: Outliers : 2.01 % Allowed : 18.83 % Favored : 79.16 % 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: -0.21 (0.20), residues: 1810 helix: -0.08 (0.19), residues: 705 sheet: -0.55 (0.27), residues: 320 loop : 0.25 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.008 0.001 HIS E 88 PHE 0.025 0.002 PHE C 352 TYR 0.022 0.001 TYR C 166 ARG 0.005 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 251 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 10 residues processed: 239 average time/residue: 0.2225 time to fit residues: 84.8418 Evaluate side-chains 204 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1511 time to fit residues: 5.0808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16113 Z= 0.225 Angle : 0.640 9.901 21934 Z= 0.312 Chirality : 0.043 0.212 2505 Planarity : 0.004 0.055 2828 Dihedral : 5.937 55.363 2323 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.09 % Favored : 96.63 % Rotamer: Outliers : 2.01 % Allowed : 19.09 % Favored : 78.90 % 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: 0.03 (0.20), residues: 1810 helix: 0.18 (0.20), residues: 675 sheet: -0.51 (0.27), residues: 320 loop : 0.34 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 340 HIS 0.006 0.001 HIS E 88 PHE 0.015 0.001 PHE C 352 TYR 0.023 0.001 TYR C 166 ARG 0.004 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 246 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 239 average time/residue: 0.2357 time to fit residues: 89.6361 Evaluate side-chains 213 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 1.700 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1452 time to fit residues: 6.3065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 199 optimal weight: 50.0000 chunk 165 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 314 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** 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: 0.7057 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16113 Z= 0.181 Angle : 0.642 14.149 21934 Z= 0.305 Chirality : 0.043 0.171 2505 Planarity : 0.004 0.056 2828 Dihedral : 5.641 58.101 2323 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.09 % Favored : 96.63 % Rotamer: Outliers : 1.88 % Allowed : 19.87 % Favored : 78.25 % 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: 0.21 (0.20), residues: 675 sheet: -0.46 (0.27), residues: 320 loop : 0.36 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 340 HIS 0.004 0.001 HIS D 87 PHE 0.024 0.001 PHE E 223 TYR 0.024 0.001 TYR C 166 ARG 0.004 0.000 ARG C 62 *********************** 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 271 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 242 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 7 residues processed: 262 average time/residue: 0.2347 time to fit residues: 96.6949 Evaluate side-chains 224 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 217 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1442 time to fit residues: 4.1236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 145 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 198 optimal weight: 50.0000 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN B 12 ASN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** 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: 0.7151 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16113 Z= 0.408 Angle : 0.743 11.969 21934 Z= 0.364 Chirality : 0.046 0.199 2505 Planarity : 0.004 0.055 2828 Dihedral : 5.876 57.656 2323 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.54 % Favored : 96.19 % Rotamer: Outliers : 1.29 % Allowed : 22.07 % Favored : 76.63 % 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: -0.15 (0.20), residues: 1810 helix: -0.07 (0.20), residues: 675 sheet: -0.63 (0.27), residues: 325 loop : 0.36 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP C 340 HIS 0.007 0.002 HIS E 161 PHE 0.015 0.002 PHE C 352 TYR 0.027 0.002 TYR C 166 ARG 0.006 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 221 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 214 average time/residue: 0.2388 time to fit residues: 80.5499 Evaluate side-chains 205 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1530 time to fit residues: 6.0138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** 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 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16113 Z= 0.222 Angle : 0.661 12.295 21934 Z= 0.319 Chirality : 0.044 0.216 2505 Planarity : 0.004 0.058 2828 Dihedral : 5.635 57.853 2323 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.43 % Favored : 96.30 % Rotamer: Outliers : 0.52 % Allowed : 22.33 % Favored : 77.15 % 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: -0.00 (0.20), residues: 1810 helix: 0.00 (0.20), residues: 675 sheet: -0.51 (0.27), residues: 320 loop : 0.47 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 340 HIS 0.004 0.001 HIS E 88 PHE 0.010 0.001 PHE A 255 TYR 0.025 0.001 TYR B 279 ARG 0.003 0.000 ARG A 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 223 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 215 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 220 average time/residue: 0.2402 time to fit residues: 83.1496 Evaluate side-chains 197 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1588 time to fit residues: 3.2485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 185 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 184 optimal weight: 50.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 16113 Z= 0.525 Angle : 0.826 13.216 21934 Z= 0.407 Chirality : 0.048 0.238 2505 Planarity : 0.005 0.054 2828 Dihedral : 6.099 56.895 2323 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.20 % Favored : 95.52 % Rotamer: Outliers : 0.71 % Allowed : 23.24 % Favored : 76.05 % 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: -0.65 (0.20), residues: 1810 helix: -0.54 (0.19), residues: 705 sheet: -0.81 (0.27), residues: 325 loop : 0.12 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP C 340 HIS 0.010 0.002 HIS E 161 PHE 0.018 0.002 PHE E 223 TYR 0.031 0.002 TYR C 166 ARG 0.006 0.001 ARG E 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 191 average time/residue: 0.2797 time to fit residues: 84.5861 Evaluate side-chains 186 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1605 time to fit residues: 4.4323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 1.9990 chunk 195 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 136 optimal weight: 0.0670 chunk 205 optimal weight: 30.0000 chunk 188 optimal weight: 30.0000 chunk 163 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16113 Z= 0.203 Angle : 0.685 13.270 21934 Z= 0.329 Chirality : 0.044 0.185 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.660 58.145 2323 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.81 % Favored : 95.91 % Rotamer: Outliers : 0.26 % Allowed : 23.69 % Favored : 76.05 % 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: -0.32 (0.20), residues: 1810 helix: -0.24 (0.20), residues: 705 sheet: -0.60 (0.27), residues: 320 loop : 0.25 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.003 TRP C 340 HIS 0.005 0.001 HIS D 87 PHE 0.011 0.001 PHE C 262 TYR 0.027 0.001 TYR B 279 ARG 0.003 0.000 ARG E 254 ********************** 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 218 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 216 average time/residue: 0.2393 time to fit residues: 81.9619 Evaluate side-chains 198 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1425 time to fit residues: 2.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 68 optimal weight: 0.0010 chunk 168 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN C 263 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.102644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095216 restraints weight = 57764.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096753 restraints weight = 31354.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.097738 restraints weight = 20574.640| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5344 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= 0.259 Angle : 0.700 13.326 21934 Z= 0.337 Chirality : 0.044 0.180 2505 Planarity : 0.004 0.058 2828 Dihedral : 5.617 58.028 2323 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.70 % Favored : 96.02 % Rotamer: Outliers : 0.45 % Allowed : 24.27 % Favored : 75.28 % 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: -0.38 (0.20), residues: 1810 helix: -0.29 (0.20), residues: 705 sheet: -0.65 (0.27), residues: 325 loop : 0.24 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.003 TRP C 340 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE C 262 TYR 0.026 0.001 TYR C 166 ARG 0.004 0.000 ARG E 206 =============================================================================== Job complete usr+sys time: 2800.90 seconds wall clock time: 52 minutes 24.22 seconds (3144.22 seconds total)