Starting phenix.real_space_refine on Sat Mar 16 12:37:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/03_2024/5onv_3835_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/03_2024/5onv_3835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/03_2024/5onv_3835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/03_2024/5onv_3835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/03_2024/5onv_3835_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/03_2024/5onv_3835_updated.pdb" } resolution = 4.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2815 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 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.59, per 1000 atoms: 0.59 Number of scatterers: 14640 At special positions: 0 Unit cell: (98.04, 85.5, 192.66, 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 105 16.00 P 10 15.00 Mg 5 11.99 O 2815 8.00 N 2470 7.00 C 9235 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: 5.55 Conformation dependent library (CDL) restraints added in 2.6 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 20 sheets defined 44.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 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 114 through 123 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 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 261 removed outlier: 4.992A 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 283 Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.685A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP A 292 " --> 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: 5.363A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 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 114 through 123 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 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 4.992A 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 283 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.686A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP B 292 " --> 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: 5.363A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 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 114 through 123 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 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.991A 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 283 Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.686A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP C 292 " --> 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: 5.363A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 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 114 through 123 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 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 4.991A 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 283 Processing helix chain 'D' and resid 287 through 296 removed outlier: 4.684A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP D 292 " --> 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: 5.363A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 373 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 114 through 123 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 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 261 removed outlier: 4.992A 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 283 Processing helix chain 'E' and resid 287 through 296 removed outlier: 4.685A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP E 292 " --> 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: 5.363A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 373 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.561A pdb=" N CYS A 10 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 104 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR A 106 " --> pdb=" O ASN A 12 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.990A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.561A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN B 12 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR B 106 " --> pdb=" O ASN B 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.990A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 29 through 32 removed outlier: 7.561A pdb=" N CYS C 10 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 104 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN C 12 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR C 106 " --> pdb=" O ASN C 12 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.990A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 29 through 32 removed outlier: 7.561A pdb=" N CYS D 10 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN D 12 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR D 106 " --> pdb=" O ASN D 12 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.990A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 29 through 32 removed outlier: 7.561A pdb=" N CYS E 10 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU E 104 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN E 12 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR E 106 " --> pdb=" O ASN E 12 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.990A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 595 hydrogen bonds defined for protein. 1440 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: 4.48 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3568 1.33 - 1.45: 3352 1.45 - 1.57: 7844 1.57 - 1.69: 11 1.69 - 1.81: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.14e+01 bond pdb=" CA ILE E 151 " pdb=" C ILE E 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.12e+01 bond pdb=" CA ILE C 151 " pdb=" C ILE C 151 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.21e-02 6.83e+03 1.11e+01 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 98.73 - 106.03: 501 106.03 - 113.33: 8133 113.33 - 120.64: 6751 120.64 - 127.94: 4792 127.94 - 135.24: 128 Bond angle restraints: 20305 Sorted by residual: angle pdb=" C VAL B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta sigma weight residual 119.24 127.99 -8.75 1.04e+00 9.25e-01 7.08e+01 angle pdb=" C VAL E 129 " pdb=" N PRO E 130 " pdb=" CA PRO E 130 " ideal model delta sigma weight residual 119.24 127.98 -8.74 1.04e+00 9.25e-01 7.06e+01 angle pdb=" C VAL D 129 " pdb=" N PRO D 130 " pdb=" CA PRO D 130 " ideal model delta sigma weight residual 119.24 127.95 -8.71 1.04e+00 9.25e-01 7.01e+01 angle pdb=" C VAL A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta sigma weight residual 119.24 127.95 -8.71 1.04e+00 9.25e-01 7.01e+01 angle pdb=" C VAL C 129 " pdb=" N PRO C 130 " pdb=" CA PRO C 130 " ideal model delta sigma weight residual 119.24 127.94 -8.70 1.04e+00 9.25e-01 7.00e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 8735 24.98 - 49.97: 195 49.97 - 74.95: 55 74.95 - 99.94: 5 99.94 - 124.92: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.92 -124.92 1 2.00e+01 2.50e-03 3.77e+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 64.92 -124.91 1 2.00e+01 2.50e-03 3.77e+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 64.91 -124.91 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1159 0.047 - 0.093: 794 0.093 - 0.139: 229 0.139 - 0.186: 68 0.186 - 0.232: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" C PRO E 32 " pdb=" CB PRO E 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" C PRO A 32 " pdb=" CB PRO A 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.97e+01 pdb=" C PHE A 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE A 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE A 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.96e+01 pdb=" C PHE C 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE C 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE C 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.96e+01 pdb=" C PHE D 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE D 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE D 375 " -0.039 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 73 2.58 - 3.16: 14047 3.16 - 3.74: 23282 3.74 - 4.32: 35644 4.32 - 4.90: 53359 Nonbonded interactions: 126405 Sorted by model distance: nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.996 2.170 ... (remaining 126400 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' } 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: 1.290 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: 4.530 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 41.780 Find NCS groups from input model: 0.990 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 0.059 14960 Z= 0.874 Angle : 1.559 13.788 20305 Z= 1.007 Chirality : 0.065 0.232 2255 Planarity : 0.018 0.148 2595 Dihedral : 11.903 124.921 5565 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 3.55 % Allowed : 6.28 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.18), residues: 1830 helix: -1.67 (0.14), residues: 840 sheet: -1.16 (0.29), residues: 325 loop : -1.83 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.008 TRP C 340 HIS 0.007 0.002 HIS B 88 PHE 0.024 0.004 PHE D 375 TYR 0.048 0.006 TYR C 306 ARG 0.004 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 729 time to evaluate : 1.794 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: 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: symmetry clash REVERT: A 24 ASP cc_start: 0.6781 (m-30) cc_final: 0.6243 (t0) REVERT: A 34 ILE cc_start: 0.9600 (mt) cc_final: 0.9174 (tp) REVERT: A 78 ASN cc_start: 0.8024 (t0) cc_final: 0.6174 (t0) REVERT: A 81 ASP cc_start: 0.8614 (m-30) cc_final: 0.7840 (m-30) REVERT: A 86 TRP cc_start: 0.9000 (m-10) cc_final: 0.8461 (m-10) REVERT: A 101 HIS cc_start: 0.8657 (p-80) cc_final: 0.8381 (p-80) REVERT: A 103 THR cc_start: 0.9150 (m) cc_final: 0.8925 (t) REVERT: A 205 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7332 (mt-10) REVERT: A 212 ILE cc_start: 0.9101 (mt) cc_final: 0.8797 (mt) REVERT: A 217 CYS cc_start: 0.8849 (m) cc_final: 0.8635 (m) REVERT: A 287 ILE cc_start: 0.8526 (pt) cc_final: 0.8218 (tt) REVERT: A 291 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8397 (mptt) REVERT: B 39 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7328 (ttp-170) REVERT: B 153 LEU cc_start: 0.9277 (tp) cc_final: 0.8853 (mt) REVERT: B 192 ILE cc_start: 0.8894 (pt) cc_final: 0.8644 (mm) REVERT: B 280 ASN cc_start: 0.8454 (m-40) cc_final: 0.8099 (m-40) REVERT: B 305 MET cc_start: 0.9134 (mmm) cc_final: 0.8280 (mmt) REVERT: B 352 PHE cc_start: 0.8985 (t80) cc_final: 0.8538 (t80) REVERT: B 370 VAL cc_start: 0.9205 (t) cc_final: 0.8988 (t) REVERT: C 21 PHE cc_start: 0.6982 (m-80) cc_final: 0.6700 (m-80) REVERT: C 47 MET cc_start: 0.5790 (mtm) cc_final: 0.5477 (ptp) REVERT: C 78 ASN cc_start: 0.7367 (t0) cc_final: 0.5630 (t0) REVERT: C 81 ASP cc_start: 0.8543 (m-30) cc_final: 0.7808 (m-30) REVERT: C 87 HIS cc_start: 0.8818 (t70) cc_final: 0.8513 (t-170) REVERT: C 157 ASP cc_start: 0.6669 (t70) cc_final: 0.6112 (t0) REVERT: C 161 HIS cc_start: 0.9368 (p90) cc_final: 0.9014 (p90) REVERT: C 165 ILE cc_start: 0.9235 (mt) cc_final: 0.8852 (tp) REVERT: C 176 MET cc_start: 0.7815 (mtt) cc_final: 0.7500 (mtp) REVERT: C 227 MET cc_start: 0.8793 (tmm) cc_final: 0.8510 (tmm) REVERT: C 267 ILE cc_start: 0.9221 (pt) cc_final: 0.8945 (mp) REVERT: C 280 ASN cc_start: 0.8636 (m-40) cc_final: 0.8430 (m-40) REVERT: C 292 ASP cc_start: 0.8383 (m-30) cc_final: 0.7877 (t0) REVERT: C 305 MET cc_start: 0.8730 (mmm) cc_final: 0.8482 (mmt) REVERT: C 340 TRP cc_start: 0.9034 (t60) cc_final: 0.8514 (t60) REVERT: D 43 VAL cc_start: 0.8558 (t) cc_final: 0.7246 (t) REVERT: D 47 MET cc_start: 0.6272 (mtm) cc_final: 0.5204 (ptp) REVERT: D 106 THR cc_start: 0.7793 (t) cc_final: 0.7508 (t) REVERT: D 127 PHE cc_start: 0.8855 (m-80) cc_final: 0.8611 (m-10) REVERT: D 137 GLN cc_start: 0.8093 (mt0) cc_final: 0.7370 (mm-40) REVERT: D 142 LEU cc_start: 0.9277 (mt) cc_final: 0.8956 (mt) REVERT: D 155 SER cc_start: 0.8418 (t) cc_final: 0.8208 (t) REVERT: D 157 ASP cc_start: 0.6757 (t70) cc_final: 0.6545 (t70) REVERT: D 162 ASN cc_start: 0.8722 (t0) cc_final: 0.8289 (p0) REVERT: D 165 ILE cc_start: 0.9133 (mt) cc_final: 0.8684 (tp) REVERT: D 214 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7863 (mt-10) REVERT: D 244 ASP cc_start: 0.9017 (p0) cc_final: 0.8808 (p0) REVERT: D 270 GLU cc_start: 0.7542 (tt0) cc_final: 0.7239 (pt0) REVERT: D 280 ASN cc_start: 0.9029 (m-40) cc_final: 0.7994 (m-40) REVERT: D 288 ASP cc_start: 0.7521 (t70) cc_final: 0.7138 (t0) REVERT: D 299 MET cc_start: 0.8340 (mtp) cc_final: 0.8128 (mtt) REVERT: D 305 MET cc_start: 0.8509 (mmm) cc_final: 0.8294 (tpp) REVERT: D 311 ASP cc_start: 0.8585 (m-30) cc_final: 0.8127 (t70) REVERT: D 358 THR cc_start: 0.8877 (p) cc_final: 0.8601 (t) REVERT: E 11 ASP cc_start: 0.8631 (t0) cc_final: 0.8362 (t0) REVERT: E 21 PHE cc_start: 0.7218 (m-80) cc_final: 0.6828 (m-80) REVERT: E 30 VAL cc_start: 0.9277 (t) cc_final: 0.9027 (m) REVERT: E 43 VAL cc_start: 0.8529 (t) cc_final: 0.7361 (t) REVERT: E 47 MET cc_start: 0.6952 (mtm) cc_final: 0.5809 (ttt) REVERT: E 78 ASN cc_start: 0.8135 (t0) cc_final: 0.7279 (t0) REVERT: E 87 HIS cc_start: 0.8871 (t70) cc_final: 0.8635 (t-170) REVERT: E 104 LEU cc_start: 0.9137 (tp) cc_final: 0.8876 (tp) REVERT: E 137 GLN cc_start: 0.8192 (mt0) cc_final: 0.7966 (mm-40) REVERT: E 205 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6965 (mt-10) REVERT: E 211 ASP cc_start: 0.7563 (t70) cc_final: 0.7012 (t70) REVERT: E 280 ASN cc_start: 0.9023 (m-40) cc_final: 0.7977 (m110) REVERT: E 292 ASP cc_start: 0.8502 (m-30) cc_final: 0.8093 (t70) outliers start: 0 outliers final: 0 residues processed: 729 average time/residue: 0.2681 time to fit residues: 279.7683 Evaluate side-chains 372 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 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 87 HIS A 137 GLN A 263 GLN A 280 ASN B 87 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 40 HIS C 87 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN E 354 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14960 Z= 0.257 Angle : 0.703 7.522 20305 Z= 0.361 Chirality : 0.046 0.175 2255 Planarity : 0.007 0.056 2595 Dihedral : 7.209 90.334 2085 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.97 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.75 (0.19), residues: 1830 helix: 0.38 (0.17), residues: 795 sheet: -0.65 (0.30), residues: 325 loop : -1.34 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 86 HIS 0.011 0.001 HIS C 275 PHE 0.017 0.001 PHE E 255 TYR 0.019 0.002 TYR C 166 ARG 0.006 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 1.766 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: symmetry clash REVERT: A 8 LEU cc_start: 0.9210 (tp) cc_final: 0.8975 (tp) REVERT: A 24 ASP cc_start: 0.7364 (m-30) cc_final: 0.6520 (t70) REVERT: A 34 ILE cc_start: 0.9625 (mt) cc_final: 0.9342 (tp) REVERT: A 41 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 43 VAL cc_start: 0.8487 (t) cc_final: 0.8214 (t) REVERT: A 86 TRP cc_start: 0.9051 (m-10) cc_final: 0.8822 (m-10) REVERT: A 154 ASP cc_start: 0.8227 (t70) cc_final: 0.7623 (t70) REVERT: A 217 CYS cc_start: 0.8696 (m) cc_final: 0.8474 (m) REVERT: A 227 MET cc_start: 0.8691 (ttt) cc_final: 0.8429 (tmm) REVERT: A 229 THR cc_start: 0.8853 (m) cc_final: 0.8598 (p) REVERT: A 291 LYS cc_start: 0.8746 (tmmt) cc_final: 0.8334 (mptt) REVERT: A 292 ASP cc_start: 0.8334 (m-30) cc_final: 0.7649 (t0) REVERT: A 346 LEU cc_start: 0.9511 (tp) cc_final: 0.9270 (tt) REVERT: B 31 PHE cc_start: 0.9087 (p90) cc_final: 0.8870 (p90) REVERT: B 41 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 47 MET cc_start: 0.5669 (mtm) cc_final: 0.5065 (tpt) REVERT: B 106 THR cc_start: 0.8730 (t) cc_final: 0.8467 (p) REVERT: B 113 LYS cc_start: 0.9023 (ptmt) cc_final: 0.8595 (ttpt) REVERT: B 120 THR cc_start: 0.9338 (m) cc_final: 0.9048 (m) REVERT: B 123 MET cc_start: 0.8771 (mmp) cc_final: 0.8373 (mmp) REVERT: B 362 TYR cc_start: 0.8442 (t80) cc_final: 0.8128 (t80) REVERT: C 41 GLN cc_start: 0.8316 (tt0) cc_final: 0.8082 (tm-30) REVERT: C 43 VAL cc_start: 0.8556 (t) cc_final: 0.7495 (t) REVERT: C 80 ASP cc_start: 0.7844 (p0) cc_final: 0.6815 (p0) REVERT: C 81 ASP cc_start: 0.8165 (m-30) cc_final: 0.7753 (m-30) REVERT: C 82 MET cc_start: 0.8132 (tmm) cc_final: 0.7926 (tmm) REVERT: C 121 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 154 ASP cc_start: 0.8534 (t0) cc_final: 0.8278 (t0) REVERT: C 161 HIS cc_start: 0.9186 (p90) cc_final: 0.8423 (p90) REVERT: C 269 MET cc_start: 0.7655 (tpp) cc_final: 0.7418 (tpp) REVERT: C 288 ASP cc_start: 0.6954 (t70) cc_final: 0.6710 (t0) REVERT: C 305 MET cc_start: 0.8631 (mmm) cc_final: 0.8377 (mmt) REVERT: C 340 TRP cc_start: 0.9237 (t60) cc_final: 0.8634 (t60) REVERT: D 43 VAL cc_start: 0.8458 (t) cc_final: 0.8251 (t) REVERT: D 47 MET cc_start: 0.5925 (mtm) cc_final: 0.4708 (ttt) REVERT: D 49 GLN cc_start: 0.7749 (pm20) cc_final: 0.7419 (pm20) REVERT: D 111 ASN cc_start: 0.8321 (p0) cc_final: 0.7553 (p0) REVERT: D 137 GLN cc_start: 0.8182 (mt0) cc_final: 0.7801 (mm-40) REVERT: D 162 ASN cc_start: 0.8585 (t0) cc_final: 0.8346 (p0) REVERT: D 184 ASP cc_start: 0.8195 (t70) cc_final: 0.7979 (t0) REVERT: D 217 CYS cc_start: 0.8311 (m) cc_final: 0.8067 (m) REVERT: D 305 MET cc_start: 0.8593 (mmm) cc_final: 0.7841 (tpp) REVERT: D 316 GLU cc_start: 0.8350 (tp30) cc_final: 0.7937 (tp30) REVERT: D 318 THR cc_start: 0.8954 (m) cc_final: 0.8697 (p) REVERT: D 334 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7402 (tp30) REVERT: D 356 TRP cc_start: 0.8683 (m100) cc_final: 0.8365 (m100) REVERT: D 371 HIS cc_start: 0.7470 (t70) cc_final: 0.7092 (t70) REVERT: E 47 MET cc_start: 0.6969 (mtm) cc_final: 0.6462 (ttt) REVERT: E 51 ASP cc_start: 0.7996 (p0) cc_final: 0.7711 (p0) REVERT: E 56 ASP cc_start: 0.8676 (p0) cc_final: 0.8406 (p0) REVERT: E 80 ASP cc_start: 0.8626 (t70) cc_final: 0.8403 (t0) REVERT: E 154 ASP cc_start: 0.8562 (t0) cc_final: 0.8178 (t0) REVERT: E 190 MET cc_start: 0.8653 (mtm) cc_final: 0.8358 (mtm) REVERT: E 283 MET cc_start: 0.8847 (mmp) cc_final: 0.8367 (tpp) REVERT: E 371 HIS cc_start: 0.8134 (t-90) cc_final: 0.7786 (t-90) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.2409 time to fit residues: 192.1891 Evaluate side-chains 299 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN B 371 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 87 HIS E 137 GLN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14960 Z= 0.274 Angle : 0.686 7.693 20305 Z= 0.346 Chirality : 0.046 0.162 2255 Planarity : 0.005 0.049 2595 Dihedral : 6.637 67.287 2085 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.97 % Favored : 94.48 % Rotamer: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.02 (0.20), residues: 1830 helix: 0.92 (0.18), residues: 770 sheet: -0.40 (0.30), residues: 315 loop : -0.73 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 356 HIS 0.008 0.002 HIS C 275 PHE 0.016 0.001 PHE A 352 TYR 0.030 0.002 TYR A 279 ARG 0.007 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 1.878 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 8 LEU cc_start: 0.9357 (tp) cc_final: 0.9138 (tp) REVERT: A 24 ASP cc_start: 0.7526 (m-30) cc_final: 0.6856 (t0) REVERT: A 34 ILE cc_start: 0.9685 (mt) cc_final: 0.9373 (tp) REVERT: A 121 GLN cc_start: 0.9026 (pp30) cc_final: 0.8628 (pp30) REVERT: A 154 ASP cc_start: 0.8195 (t70) cc_final: 0.7583 (t70) REVERT: A 217 CYS cc_start: 0.8774 (m) cc_final: 0.8551 (m) REVERT: A 291 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8307 (mptt) REVERT: A 292 ASP cc_start: 0.8254 (m-30) cc_final: 0.7526 (t0) REVERT: A 330 ILE cc_start: 0.9151 (mt) cc_final: 0.8881 (tp) REVERT: A 356 TRP cc_start: 0.9102 (m100) cc_final: 0.8779 (m100) REVERT: B 83 GLU cc_start: 0.9097 (pp20) cc_final: 0.8629 (pt0) REVERT: B 113 LYS cc_start: 0.9098 (ptmt) cc_final: 0.8619 (ttpt) REVERT: B 166 TYR cc_start: 0.8585 (t80) cc_final: 0.8221 (t80) REVERT: B 200 PHE cc_start: 0.8912 (m-80) cc_final: 0.8648 (m-80) REVERT: B 283 MET cc_start: 0.8593 (mmm) cc_final: 0.8376 (mmm) REVERT: B 313 MET cc_start: 0.8694 (ttm) cc_final: 0.8474 (ttm) REVERT: C 82 MET cc_start: 0.8363 (tmm) cc_final: 0.8034 (tmm) REVERT: C 119 MET cc_start: 0.9514 (ttp) cc_final: 0.9261 (ttp) REVERT: C 154 ASP cc_start: 0.8736 (t0) cc_final: 0.8371 (t0) REVERT: C 161 HIS cc_start: 0.9342 (p90) cc_final: 0.8584 (p90) REVERT: C 165 ILE cc_start: 0.9235 (mt) cc_final: 0.8957 (tp) REVERT: C 222 ASP cc_start: 0.7428 (p0) cc_final: 0.7096 (p0) REVERT: C 269 MET cc_start: 0.7811 (tpp) cc_final: 0.7413 (tpp) REVERT: C 276 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7949 (tm-30) REVERT: C 305 MET cc_start: 0.8690 (mmm) cc_final: 0.8241 (tpp) REVERT: C 340 TRP cc_start: 0.9335 (t60) cc_final: 0.8832 (t60) REVERT: D 43 VAL cc_start: 0.8316 (t) cc_final: 0.7752 (t) REVERT: D 47 MET cc_start: 0.6210 (mtm) cc_final: 0.4793 (ttt) REVERT: D 49 GLN cc_start: 0.7983 (pm20) cc_final: 0.7632 (pm20) REVERT: D 137 GLN cc_start: 0.8564 (mt0) cc_final: 0.8239 (mm-40) REVERT: D 162 ASN cc_start: 0.8862 (t0) cc_final: 0.8223 (p0) REVERT: D 283 MET cc_start: 0.8465 (mmp) cc_final: 0.7997 (mmp) REVERT: D 305 MET cc_start: 0.8546 (mmm) cc_final: 0.8001 (tpp) REVERT: D 316 GLU cc_start: 0.8275 (tp30) cc_final: 0.7984 (tp30) REVERT: E 43 VAL cc_start: 0.8462 (t) cc_final: 0.8076 (t) REVERT: E 47 MET cc_start: 0.6728 (mtm) cc_final: 0.5642 (ttt) REVERT: E 49 GLN cc_start: 0.7723 (pm20) cc_final: 0.7465 (pm20) REVERT: E 72 GLU cc_start: 0.8992 (pp20) cc_final: 0.8691 (pp20) REVERT: E 80 ASP cc_start: 0.8656 (t70) cc_final: 0.8314 (t0) REVERT: E 154 ASP cc_start: 0.8700 (t0) cc_final: 0.8147 (t0) REVERT: E 283 MET cc_start: 0.8868 (mmp) cc_final: 0.8323 (tpp) REVERT: E 299 MET cc_start: 0.8777 (mtt) cc_final: 0.7751 (mtt) REVERT: E 371 HIS cc_start: 0.7865 (t-90) cc_final: 0.7455 (t-90) outliers start: 1 outliers final: 0 residues processed: 395 average time/residue: 0.2255 time to fit residues: 136.2396 Evaluate side-chains 263 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 115 ASN C 101 HIS ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 40 HIS E 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14960 Z= 0.209 Angle : 0.635 7.465 20305 Z= 0.316 Chirality : 0.045 0.144 2255 Planarity : 0.004 0.043 2595 Dihedral : 6.355 60.041 2085 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.59 % Favored : 94.97 % Rotamer: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1830 helix: 1.09 (0.19), residues: 760 sheet: -0.31 (0.30), residues: 315 loop : -0.34 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.006 0.001 HIS D 275 PHE 0.017 0.001 PHE B 124 TYR 0.023 0.001 TYR A 279 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 376 time to evaluate : 1.918 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: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7608 (m-30) cc_final: 0.7098 (t0) REVERT: A 34 ILE cc_start: 0.9670 (mt) cc_final: 0.9369 (tp) REVERT: A 121 GLN cc_start: 0.9148 (pp30) cc_final: 0.8688 (pp30) REVERT: A 154 ASP cc_start: 0.8228 (t70) cc_final: 0.7584 (t70) REVERT: A 291 LYS cc_start: 0.8708 (tmmt) cc_final: 0.8280 (mptt) REVERT: A 292 ASP cc_start: 0.8251 (m-30) cc_final: 0.7491 (t0) REVERT: A 330 ILE cc_start: 0.9246 (mt) cc_final: 0.9037 (mm) REVERT: B 83 GLU cc_start: 0.8986 (pp20) cc_final: 0.8786 (pt0) REVERT: B 92 ASN cc_start: 0.8490 (m-40) cc_final: 0.8067 (t0) REVERT: B 113 LYS cc_start: 0.9206 (ptmt) cc_final: 0.8643 (ttpt) REVERT: B 132 MET cc_start: 0.8433 (ppp) cc_final: 0.8165 (ptm) REVERT: B 154 ASP cc_start: 0.9241 (t0) cc_final: 0.9020 (t70) REVERT: C 82 MET cc_start: 0.8336 (tmm) cc_final: 0.8028 (tmm) REVERT: C 154 ASP cc_start: 0.8752 (t0) cc_final: 0.8444 (t0) REVERT: C 165 ILE cc_start: 0.9261 (mt) cc_final: 0.9049 (mt) REVERT: C 190 MET cc_start: 0.8526 (mtm) cc_final: 0.8310 (mtt) REVERT: C 222 ASP cc_start: 0.7473 (p0) cc_final: 0.7089 (p0) REVERT: C 269 MET cc_start: 0.7684 (tpp) cc_final: 0.7400 (tpp) REVERT: C 276 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7971 (tm-30) REVERT: D 43 VAL cc_start: 0.8437 (t) cc_final: 0.8175 (t) REVERT: D 224 GLU cc_start: 0.8351 (pm20) cc_final: 0.8090 (pm20) REVERT: D 283 MET cc_start: 0.8448 (mmp) cc_final: 0.8035 (mmp) REVERT: D 305 MET cc_start: 0.8634 (mmm) cc_final: 0.8159 (tpp) REVERT: D 316 GLU cc_start: 0.8271 (tp30) cc_final: 0.8045 (tp30) REVERT: D 369 ILE cc_start: 0.8901 (tp) cc_final: 0.8615 (tt) REVERT: E 39 ARG cc_start: 0.8736 (ttp-170) cc_final: 0.8287 (ttt90) REVERT: E 43 VAL cc_start: 0.8621 (t) cc_final: 0.8329 (t) REVERT: E 47 MET cc_start: 0.6881 (mtm) cc_final: 0.5963 (ttt) REVERT: E 49 GLN cc_start: 0.7949 (pm20) cc_final: 0.7656 (pm20) REVERT: E 72 GLU cc_start: 0.9064 (pp20) cc_final: 0.8752 (pp20) REVERT: E 80 ASP cc_start: 0.8547 (t70) cc_final: 0.8149 (t0) REVERT: E 154 ASP cc_start: 0.8790 (t0) cc_final: 0.8415 (t0) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.2456 time to fit residues: 141.8344 Evaluate side-chains 261 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 160 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN B 12 ASN B 115 ASN C 297 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 40 HIS E 87 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14960 Z= 0.205 Angle : 0.624 7.590 20305 Z= 0.311 Chirality : 0.044 0.143 2255 Planarity : 0.004 0.040 2595 Dihedral : 6.231 60.930 2085 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.43 % Favored : 95.19 % Rotamer: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.31 (0.20), residues: 1830 helix: 1.07 (0.19), residues: 765 sheet: -0.38 (0.30), residues: 320 loop : -0.31 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 86 HIS 0.007 0.001 HIS E 87 PHE 0.012 0.001 PHE B 124 TYR 0.017 0.001 TYR A 337 ARG 0.006 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 1.667 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 24 ASP cc_start: 0.7739 (m-30) cc_final: 0.7142 (t0) REVERT: A 34 ILE cc_start: 0.9616 (mt) cc_final: 0.9362 (tp) REVERT: A 121 GLN cc_start: 0.9080 (pp30) cc_final: 0.8673 (pp30) REVERT: A 154 ASP cc_start: 0.8294 (t70) cc_final: 0.7631 (t70) REVERT: A 162 ASN cc_start: 0.8681 (t0) cc_final: 0.8196 (t0) REVERT: A 291 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8275 (mptt) REVERT: A 292 ASP cc_start: 0.8287 (m-30) cc_final: 0.7429 (t0) REVERT: A 330 ILE cc_start: 0.9267 (mt) cc_final: 0.9040 (mt) REVERT: B 92 ASN cc_start: 0.8507 (m-40) cc_final: 0.8150 (t0) REVERT: B 113 LYS cc_start: 0.9204 (ptmt) cc_final: 0.8691 (ttpt) REVERT: B 123 MET cc_start: 0.9284 (mmp) cc_final: 0.9009 (mmp) REVERT: B 199 SER cc_start: 0.8045 (m) cc_final: 0.7681 (p) REVERT: C 82 MET cc_start: 0.8352 (tmm) cc_final: 0.8036 (tmm) REVERT: C 154 ASP cc_start: 0.8636 (t0) cc_final: 0.8324 (t0) REVERT: C 165 ILE cc_start: 0.9218 (mt) cc_final: 0.8857 (tp) REVERT: C 190 MET cc_start: 0.8510 (mtm) cc_final: 0.8257 (mtt) REVERT: C 222 ASP cc_start: 0.7145 (p0) cc_final: 0.6863 (p0) REVERT: C 269 MET cc_start: 0.7590 (tpp) cc_final: 0.7369 (tpp) REVERT: C 276 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7955 (tm-30) REVERT: C 288 ASP cc_start: 0.7177 (t70) cc_final: 0.6976 (t0) REVERT: D 47 MET cc_start: 0.1612 (ttt) cc_final: 0.1166 (ttt) REVERT: D 283 MET cc_start: 0.8317 (mmp) cc_final: 0.7945 (mmp) REVERT: D 305 MET cc_start: 0.8521 (mmm) cc_final: 0.8135 (tpp) REVERT: D 316 GLU cc_start: 0.8286 (tp30) cc_final: 0.7963 (tp30) REVERT: D 362 TYR cc_start: 0.9022 (t80) cc_final: 0.8647 (t80) REVERT: E 39 ARG cc_start: 0.8713 (ttp-170) cc_final: 0.8256 (ttt90) REVERT: E 47 MET cc_start: 0.7009 (mtm) cc_final: 0.6166 (ttt) REVERT: E 49 GLN cc_start: 0.7942 (pm20) cc_final: 0.7669 (pm20) REVERT: E 72 GLU cc_start: 0.9081 (pp20) cc_final: 0.8779 (pp20) REVERT: E 80 ASP cc_start: 0.8581 (t70) cc_final: 0.8154 (t0) REVERT: E 86 TRP cc_start: 0.8905 (m-10) cc_final: 0.8616 (m-10) REVERT: E 154 ASP cc_start: 0.8790 (t0) cc_final: 0.8390 (t0) REVERT: E 371 HIS cc_start: 0.6921 (t-90) cc_final: 0.6402 (t-90) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.2223 time to fit residues: 130.3607 Evaluate side-chains 265 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 40 HIS E 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14960 Z= 0.423 Angle : 0.764 9.603 20305 Z= 0.383 Chirality : 0.048 0.189 2255 Planarity : 0.005 0.043 2595 Dihedral : 6.754 64.259 2085 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.41 % Favored : 94.21 % Rotamer: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.41 (0.20), residues: 1830 helix: 0.44 (0.18), residues: 800 sheet: -0.54 (0.30), residues: 320 loop : -0.81 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 356 HIS 0.007 0.002 HIS A 101 PHE 0.019 0.002 PHE B 255 TYR 0.022 0.002 TYR B 198 ARG 0.005 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 325 time to evaluate : 1.740 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 43 VAL cc_start: 0.8867 (t) cc_final: 0.8557 (t) REVERT: A 47 MET cc_start: 0.4926 (ptt) cc_final: 0.4551 (ptt) REVERT: A 154 ASP cc_start: 0.8347 (t70) cc_final: 0.7599 (t70) REVERT: A 162 ASN cc_start: 0.8979 (t0) cc_final: 0.8492 (t0) REVERT: A 246 GLN cc_start: 0.8793 (mp-120) cc_final: 0.8456 (mp10) REVERT: B 91 TYR cc_start: 0.9110 (m-80) cc_final: 0.8402 (m-10) REVERT: B 113 LYS cc_start: 0.9256 (ptmt) cc_final: 0.8698 (ttpt) REVERT: B 199 SER cc_start: 0.8256 (m) cc_final: 0.7837 (p) REVERT: C 82 MET cc_start: 0.8554 (tmm) cc_final: 0.8179 (tmm) REVERT: C 154 ASP cc_start: 0.8876 (t0) cc_final: 0.8543 (t0) REVERT: C 176 MET cc_start: 0.8264 (mtp) cc_final: 0.8028 (mtt) REVERT: C 190 MET cc_start: 0.8549 (mtm) cc_final: 0.8249 (mtt) REVERT: C 276 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 288 ASP cc_start: 0.7131 (t70) cc_final: 0.6799 (t0) REVERT: C 316 GLU cc_start: 0.7933 (tp30) cc_final: 0.7634 (tp30) REVERT: D 47 MET cc_start: 0.0392 (ttt) cc_final: -0.0057 (ttt) REVERT: D 224 GLU cc_start: 0.8426 (pm20) cc_final: 0.8168 (pm20) REVERT: D 305 MET cc_start: 0.8609 (mmm) cc_final: 0.8352 (tpp) REVERT: D 316 GLU cc_start: 0.8550 (tp30) cc_final: 0.8026 (tp30) REVERT: D 352 PHE cc_start: 0.9004 (t80) cc_final: 0.8724 (t80) REVERT: E 72 GLU cc_start: 0.9225 (pp20) cc_final: 0.8820 (pp20) REVERT: E 80 ASP cc_start: 0.8789 (t70) cc_final: 0.8247 (t0) REVERT: E 154 ASP cc_start: 0.8830 (t0) cc_final: 0.8226 (t0) REVERT: E 160 THR cc_start: 0.9397 (m) cc_final: 0.9167 (p) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.2125 time to fit residues: 108.5503 Evaluate side-chains 238 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 88 HIS B 115 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14960 Z= 0.191 Angle : 0.641 8.753 20305 Z= 0.317 Chirality : 0.045 0.179 2255 Planarity : 0.004 0.046 2595 Dihedral : 6.322 62.889 2085 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.64 % Favored : 94.97 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1830 helix: 0.89 (0.19), residues: 770 sheet: -0.39 (0.30), residues: 315 loop : -0.56 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 86 HIS 0.005 0.001 HIS A 101 PHE 0.012 0.001 PHE E 255 TYR 0.021 0.001 TYR C 166 ARG 0.003 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 1.761 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 43 VAL cc_start: 0.8798 (t) cc_final: 0.8477 (t) REVERT: A 80 ASP cc_start: 0.8612 (p0) cc_final: 0.8179 (p0) REVERT: A 154 ASP cc_start: 0.8345 (t70) cc_final: 0.7550 (t70) REVERT: A 162 ASN cc_start: 0.8870 (t0) cc_final: 0.8352 (t0) REVERT: A 283 MET cc_start: 0.8361 (mmt) cc_final: 0.7986 (mmm) REVERT: A 292 ASP cc_start: 0.8167 (m-30) cc_final: 0.7577 (t0) REVERT: A 330 ILE cc_start: 0.9088 (pt) cc_final: 0.8884 (tt) REVERT: A 362 TYR cc_start: 0.8053 (t80) cc_final: 0.7671 (t80) REVERT: B 91 TYR cc_start: 0.8931 (m-80) cc_final: 0.8470 (m-10) REVERT: B 113 LYS cc_start: 0.9262 (ptmt) cc_final: 0.8732 (ttpt) REVERT: B 154 ASP cc_start: 0.9162 (t70) cc_final: 0.8235 (t70) REVERT: B 199 SER cc_start: 0.7980 (m) cc_final: 0.7670 (p) REVERT: C 154 ASP cc_start: 0.8663 (t0) cc_final: 0.8252 (t0) REVERT: C 288 ASP cc_start: 0.7042 (t70) cc_final: 0.6766 (t0) REVERT: C 316 GLU cc_start: 0.7864 (tp30) cc_final: 0.7646 (tp30) REVERT: D 47 MET cc_start: -0.0114 (ttt) cc_final: -0.0523 (ttt) REVERT: D 154 ASP cc_start: 0.8336 (t70) cc_final: 0.7959 (t70) REVERT: D 283 MET cc_start: 0.8392 (mmp) cc_final: 0.8038 (mmp) REVERT: D 305 MET cc_start: 0.8593 (mmm) cc_final: 0.8371 (tpp) REVERT: D 316 GLU cc_start: 0.8409 (tp30) cc_final: 0.7988 (tp30) REVERT: E 72 GLU cc_start: 0.9156 (pp20) cc_final: 0.8841 (pp20) REVERT: E 80 ASP cc_start: 0.8689 (t70) cc_final: 0.8256 (t0) REVERT: E 154 ASP cc_start: 0.8612 (t0) cc_final: 0.8242 (t0) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.2091 time to fit residues: 112.5725 Evaluate side-chains 257 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 53 optimal weight: 0.0030 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS B 115 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14960 Z= 0.215 Angle : 0.660 7.966 20305 Z= 0.324 Chirality : 0.045 0.167 2255 Planarity : 0.004 0.047 2595 Dihedral : 6.198 60.943 2085 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.81 % Favored : 94.86 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1830 helix: 0.85 (0.19), residues: 770 sheet: -0.23 (0.30), residues: 305 loop : -0.47 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 86 HIS 0.004 0.001 HIS A 87 PHE 0.010 0.001 PHE E 255 TYR 0.048 0.001 TYR C 279 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 325 time to evaluate : 1.763 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 80 ASP cc_start: 0.8600 (p0) cc_final: 0.8297 (p0) REVERT: A 154 ASP cc_start: 0.8383 (t70) cc_final: 0.7583 (t70) REVERT: A 162 ASN cc_start: 0.8887 (t0) cc_final: 0.8356 (t0) REVERT: A 283 MET cc_start: 0.8302 (mmt) cc_final: 0.7946 (mmm) REVERT: A 292 ASP cc_start: 0.8159 (m-30) cc_final: 0.7531 (t0) REVERT: A 362 TYR cc_start: 0.8126 (t80) cc_final: 0.7727 (t80) REVERT: B 91 TYR cc_start: 0.8946 (m-80) cc_final: 0.8441 (m-10) REVERT: B 113 LYS cc_start: 0.9280 (ptmt) cc_final: 0.8740 (ttpt) REVERT: B 154 ASP cc_start: 0.9184 (t70) cc_final: 0.8419 (t70) REVERT: B 199 SER cc_start: 0.7966 (m) cc_final: 0.7705 (p) REVERT: C 154 ASP cc_start: 0.8867 (t0) cc_final: 0.8458 (t0) REVERT: C 253 GLU cc_start: 0.8186 (mp0) cc_final: 0.7973 (mp0) REVERT: C 269 MET cc_start: 0.7717 (mtp) cc_final: 0.7503 (ttm) REVERT: C 292 ASP cc_start: 0.7458 (t0) cc_final: 0.7252 (t0) REVERT: C 316 GLU cc_start: 0.7875 (tp30) cc_final: 0.7623 (tp30) REVERT: D 47 MET cc_start: -0.0401 (ttt) cc_final: -0.0895 (ttt) REVERT: D 147 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7832 (mtp85) REVERT: D 283 MET cc_start: 0.8384 (mmp) cc_final: 0.7972 (mmp) REVERT: D 292 ASP cc_start: 0.8269 (m-30) cc_final: 0.7923 (t0) REVERT: D 316 GLU cc_start: 0.8424 (tp30) cc_final: 0.7990 (tp30) REVERT: E 72 GLU cc_start: 0.9142 (pp20) cc_final: 0.8813 (pp20) REVERT: E 80 ASP cc_start: 0.8744 (t70) cc_final: 0.8270 (t0) REVERT: E 154 ASP cc_start: 0.8667 (t0) cc_final: 0.8095 (t0) outliers start: 1 outliers final: 1 residues processed: 325 average time/residue: 0.2115 time to fit residues: 107.1572 Evaluate side-chains 245 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 0.0670 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14960 Z= 0.230 Angle : 0.652 7.269 20305 Z= 0.321 Chirality : 0.045 0.210 2255 Planarity : 0.004 0.048 2595 Dihedral : 6.127 60.670 2085 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.75 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1830 helix: 0.61 (0.18), residues: 800 sheet: -0.35 (0.30), residues: 310 loop : -0.63 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 86 HIS 0.007 0.001 HIS C 371 PHE 0.010 0.001 PHE A 255 TYR 0.031 0.001 TYR C 279 ARG 0.003 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8468 (p0) cc_final: 0.8082 (p0) REVERT: A 162 ASN cc_start: 0.8910 (t0) cc_final: 0.8367 (t0) REVERT: A 227 MET cc_start: 0.8721 (ttm) cc_final: 0.8519 (ttm) REVERT: A 292 ASP cc_start: 0.8193 (m-30) cc_final: 0.7609 (t0) REVERT: A 305 MET cc_start: 0.8619 (mmm) cc_final: 0.8047 (ttm) REVERT: A 362 TYR cc_start: 0.8117 (t80) cc_final: 0.7735 (t80) REVERT: B 91 TYR cc_start: 0.8955 (m-80) cc_final: 0.8448 (m-10) REVERT: B 113 LYS cc_start: 0.9284 (ptmt) cc_final: 0.8697 (ttpt) REVERT: B 154 ASP cc_start: 0.9194 (t70) cc_final: 0.8432 (t70) REVERT: B 199 SER cc_start: 0.8054 (m) cc_final: 0.7853 (p) REVERT: C 81 ASP cc_start: 0.8190 (m-30) cc_final: 0.7908 (m-30) REVERT: C 154 ASP cc_start: 0.8934 (t0) cc_final: 0.8498 (t0) REVERT: C 253 GLU cc_start: 0.8158 (mp0) cc_final: 0.7949 (mp0) REVERT: C 305 MET cc_start: 0.8463 (tpt) cc_final: 0.8209 (tpp) REVERT: C 316 GLU cc_start: 0.7894 (tp30) cc_final: 0.7692 (tp30) REVERT: D 47 MET cc_start: -0.0455 (ttt) cc_final: -0.0952 (ttt) REVERT: D 147 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7790 (mtp85) REVERT: D 151 ILE cc_start: 0.9550 (tp) cc_final: 0.9347 (tp) REVERT: D 316 GLU cc_start: 0.8415 (tp30) cc_final: 0.8011 (tp30) REVERT: E 72 GLU cc_start: 0.9137 (pp20) cc_final: 0.8771 (pp20) REVERT: E 80 ASP cc_start: 0.8770 (t70) cc_final: 0.8261 (t0) REVERT: E 154 ASP cc_start: 0.8661 (t0) cc_final: 0.8127 (t0) REVERT: E 283 MET cc_start: 0.8780 (mmt) cc_final: 0.8247 (mpp) REVERT: E 325 MET cc_start: 0.7945 (mmm) cc_final: 0.7131 (mmm) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2145 time to fit residues: 106.2101 Evaluate side-chains 242 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 116 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: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14960 Z= 0.363 Angle : 0.730 8.834 20305 Z= 0.362 Chirality : 0.047 0.172 2255 Planarity : 0.005 0.051 2595 Dihedral : 6.466 60.903 2085 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.46 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.42 (0.20), residues: 1830 helix: 0.39 (0.18), residues: 800 sheet: -0.48 (0.30), residues: 310 loop : -0.81 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 356 HIS 0.009 0.002 HIS C 371 PHE 0.015 0.001 PHE B 255 TYR 0.020 0.002 TYR A 198 ARG 0.004 0.001 ARG E 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.778 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: symmetry clash REVERT: A 80 ASP cc_start: 0.8746 (p0) cc_final: 0.8466 (p0) REVERT: A 162 ASN cc_start: 0.9030 (t0) cc_final: 0.8600 (t0) REVERT: A 246 GLN cc_start: 0.8438 (mp10) cc_final: 0.8112 (mp10) REVERT: A 292 ASP cc_start: 0.8264 (m-30) cc_final: 0.7840 (t0) REVERT: A 305 MET cc_start: 0.8634 (mmm) cc_final: 0.8099 (ttm) REVERT: A 362 TYR cc_start: 0.8276 (t80) cc_final: 0.7763 (t80) REVERT: B 91 TYR cc_start: 0.8948 (m-80) cc_final: 0.8383 (m-10) REVERT: B 113 LYS cc_start: 0.9304 (ptmt) cc_final: 0.8805 (ttpt) REVERT: C 154 ASP cc_start: 0.8910 (t0) cc_final: 0.8476 (t0) REVERT: C 305 MET cc_start: 0.8566 (tpt) cc_final: 0.8302 (tpp) REVERT: C 316 GLU cc_start: 0.7947 (tp30) cc_final: 0.7724 (tp30) REVERT: D 47 MET cc_start: -0.0815 (ttt) cc_final: -0.1149 (ttt) REVERT: D 123 MET cc_start: 0.9217 (mmp) cc_final: 0.8889 (mmp) REVERT: D 316 GLU cc_start: 0.8550 (tp30) cc_final: 0.8088 (tp30) REVERT: E 72 GLU cc_start: 0.9212 (pp20) cc_final: 0.8864 (pp20) REVERT: E 80 ASP cc_start: 0.8808 (t70) cc_final: 0.8187 (t0) REVERT: E 154 ASP cc_start: 0.8766 (t0) cc_final: 0.8198 (t0) REVERT: E 283 MET cc_start: 0.8766 (mmt) cc_final: 0.8145 (mmm) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2283 time to fit residues: 108.0320 Evaluate side-chains 237 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS E 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.074559 restraints weight = 36685.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.077242 restraints weight = 19659.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.079025 restraints weight = 12002.976| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14960 Z= 0.169 Angle : 0.647 8.272 20305 Z= 0.317 Chirality : 0.044 0.174 2255 Planarity : 0.004 0.047 2595 Dihedral : 6.096 63.391 2085 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.86 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1830 helix: 0.71 (0.19), residues: 770 sheet: -0.30 (0.31), residues: 300 loop : -0.48 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 86 HIS 0.008 0.001 HIS C 371 PHE 0.011 0.001 PHE E 255 TYR 0.017 0.001 TYR C 279 ARG 0.004 0.000 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.60 seconds wall clock time: 59 minutes 6.28 seconds (3546.28 seconds total)