Starting phenix.real_space_refine on Sat Mar 16 13:00:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/03_2024/6fhl_4259_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/03_2024/6fhl_4259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/03_2024/6fhl_4259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/03_2024/6fhl_4259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/03_2024/6fhl_4259_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/03_2024/6fhl_4259_updated.pdb" } resolution = 3.3 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= 0.015 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 15 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2835 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 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "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 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "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 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "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 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "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 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "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 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14665 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.62, per 1000 atoms: 0.52 Number of scatterers: 14665 At special positions: 0 Unit cell: (96.8, 92.4, 187, 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 15 15.00 Mg 5 11.99 O 2835 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: 6.21 Conformation dependent library (CDL) restraints added in 2.9 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: 100 helices and 25 sheets defined 45.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.567A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 287 through 294 removed outlier: 5.113A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.219A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.564A pdb=" N ARG A 372 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.566A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 294 removed outlier: 5.112A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.218A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.564A pdb=" N ARG B 372 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.567A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 294 removed outlier: 5.112A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.219A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.564A pdb=" N ARG C 372 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.567A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 287 through 294 removed outlier: 5.112A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.218A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.564A pdb=" N ARG D 372 " --> pdb=" O ILE D 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.567A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 287 through 294 removed outlier: 5.113A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.218A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.564A pdb=" N ARG E 372 " --> pdb=" O ILE E 369 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.807A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 240 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'B' and resid 297 through 300 removed outlier: 5.807A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 238 through 240 Processing sheet with id= K, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= L, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'C' and resid 297 through 300 removed outlier: 5.807A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= P, first strand: chain 'D' and resid 8 through 12 Processing sheet with id= Q, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= R, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= S, first strand: chain 'D' and resid 297 through 300 removed outlier: 5.807A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 238 through 240 Processing sheet with id= U, first strand: chain 'E' and resid 8 through 12 Processing sheet with id= V, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= X, first strand: chain 'E' and resid 297 through 300 removed outlier: 5.808A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 238 through 240 590 hydrogen bonds defined for protein. 1350 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: 4.43 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3476 1.32 - 1.44: 3303 1.44 - 1.56: 8006 1.56 - 1.68: 10 1.68 - 1.80: 185 Bond restraints: 14980 Sorted by residual: bond pdb=" CA ILE C 151 " pdb=" C ILE C 151 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.26e-02 6.30e+03 2.07e+01 bond pdb=" CA ILE E 151 " pdb=" C ILE E 151 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.26e-02 6.30e+03 2.05e+01 bond pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.26e-02 6.30e+03 1.99e+01 bond pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.26e-02 6.30e+03 1.99e+01 bond pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.26e-02 6.30e+03 1.97e+01 ... (remaining 14975 not shown) Histogram of bond angle deviations from ideal: 95.81 - 103.94: 301 103.94 - 112.06: 7341 112.06 - 120.19: 6755 120.19 - 128.31: 5838 128.31 - 136.44: 100 Bond angle restraints: 20335 Sorted by residual: angle pdb=" C ALA D 331 " pdb=" N PRO D 332 " pdb=" CA PRO D 332 " ideal model delta sigma weight residual 119.66 126.92 -7.26 7.20e-01 1.93e+00 1.02e+02 angle pdb=" C ALA B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta sigma weight residual 119.66 126.91 -7.25 7.20e-01 1.93e+00 1.01e+02 angle pdb=" C ALA A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta sigma weight residual 119.66 126.89 -7.23 7.20e-01 1.93e+00 1.01e+02 angle pdb=" C ALA C 331 " pdb=" N PRO C 332 " pdb=" CA PRO C 332 " ideal model delta sigma weight residual 119.66 126.88 -7.22 7.20e-01 1.93e+00 1.01e+02 angle pdb=" C ALA E 331 " pdb=" N PRO E 332 " pdb=" CA PRO E 332 " ideal model delta sigma weight residual 119.66 126.88 -7.22 7.20e-01 1.93e+00 1.01e+02 ... (remaining 20330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.17: 8805 30.17 - 60.34: 150 60.34 - 90.51: 30 90.51 - 120.68: 0 120.68 - 150.85: 10 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.85 -150.85 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.82 -150.82 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.82 -150.82 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 946 0.051 - 0.101: 821 0.101 - 0.152: 368 0.152 - 0.203: 90 0.203 - 0.253: 30 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA PRO D 32 " pdb=" N PRO D 32 " pdb=" C PRO D 32 " pdb=" CB PRO D 32 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 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 2.47 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" C PRO C 32 " pdb=" CB PRO C 32 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.085 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO A 164 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " 0.085 5.00e-02 4.00e+02 1.30e-01 2.69e+01 pdb=" N PRO B 164 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.085 5.00e-02 4.00e+02 1.30e-01 2.69e+01 pdb=" N PRO C 164 " 0.224 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.066 5.00e-02 4.00e+02 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 43 2.57 - 3.15: 13962 3.15 - 3.73: 23514 3.73 - 4.32: 35887 4.32 - 4.90: 55587 Nonbonded interactions: 128993 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O3 PO4 C 403 " model vdw 1.986 2.170 nonbonded pdb="MG MG B 402 " pdb=" O3 PO4 B 403 " model vdw 1.986 2.170 nonbonded pdb="MG MG A 402 " pdb=" O3 PO4 A 403 " model vdw 1.986 2.170 nonbonded pdb="MG MG E 402 " pdb=" O3 PO4 E 403 " model vdw 1.986 2.170 nonbonded pdb="MG MG D 402 " pdb=" O3 PO4 D 403 " model vdw 1.987 2.170 ... (remaining 128988 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.140 Process input model: 41.210 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.018 0.083 14980 Z= 1.180 Angle : 1.586 10.050 20335 Z= 1.024 Chirality : 0.083 0.253 2255 Planarity : 0.017 0.130 2595 Dihedral : 13.072 150.851 5565 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 2.19 % Allowed : 5.46 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.84 (0.18), residues: 1830 helix: -1.41 (0.14), residues: 780 sheet: -1.14 (0.31), residues: 225 loop : -0.85 (0.24), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP E 340 HIS 0.005 0.002 HIS A 275 PHE 0.013 0.002 PHE E 375 TYR 0.020 0.004 TYR B 198 ARG 0.004 0.001 ARG E 256 *********************** 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 502 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6253 (tpt) cc_final: 0.5784 (tpt) REVERT: A 68 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8467 (mmtm) REVERT: A 132 MET cc_start: 0.8124 (tmm) cc_final: 0.7855 (ttt) REVERT: A 165 ILE cc_start: 0.9379 (mt) cc_final: 0.9135 (mt) REVERT: A 206 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7635 (ttp80) REVERT: A 328 LYS cc_start: 0.8514 (tttt) cc_final: 0.8254 (tptt) REVERT: B 47 MET cc_start: 0.2763 (tpt) cc_final: 0.2269 (tpt) REVERT: B 184 ASP cc_start: 0.7650 (m-30) cc_final: 0.7288 (m-30) REVERT: B 191 LYS cc_start: 0.8486 (tttm) cc_final: 0.8141 (ttmm) REVERT: B 205 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 325 MET cc_start: 0.7776 (mmp) cc_final: 0.7576 (mmt) REVERT: C 118 LYS cc_start: 0.8656 (tppt) cc_final: 0.8368 (mttt) REVERT: C 132 MET cc_start: 0.8404 (tmm) cc_final: 0.8190 (ttp) REVERT: C 191 LYS cc_start: 0.8199 (tttm) cc_final: 0.7881 (tttp) REVERT: C 206 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7833 (ttp80) REVERT: C 214 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 344 SER cc_start: 0.8766 (t) cc_final: 0.8338 (p) REVERT: D 113 LYS cc_start: 0.8746 (mttt) cc_final: 0.8474 (mmtt) REVERT: D 123 MET cc_start: 0.8611 (mmp) cc_final: 0.8361 (mmm) REVERT: D 132 MET cc_start: 0.8488 (tmm) cc_final: 0.8240 (ttp) REVERT: D 171 LEU cc_start: 0.9320 (mt) cc_final: 0.9072 (mt) REVERT: D 291 LYS cc_start: 0.8842 (tttt) cc_final: 0.8571 (ttpt) REVERT: E 66 THR cc_start: 0.8894 (m) cc_final: 0.8521 (p) REVERT: E 82 MET cc_start: 0.8315 (tpt) cc_final: 0.8079 (tpt) REVERT: E 132 MET cc_start: 0.8215 (tmm) cc_final: 0.8004 (ttp) REVERT: E 328 LYS cc_start: 0.8747 (tttt) cc_final: 0.8504 (ttpp) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.2945 time to fit residues: 207.5898 Evaluate side-chains 254 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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: 0.8980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN B 161 HIS C 12 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14980 Z= 0.240 Angle : 0.655 6.517 20335 Z= 0.334 Chirality : 0.046 0.192 2255 Planarity : 0.008 0.069 2595 Dihedral : 12.427 169.475 2085 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.80 % Favored : 97.92 % Rotamer: Outliers : 1.53 % Allowed : 9.46 % Favored : 89.01 % 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: -0.45 (0.20), residues: 1830 helix: 0.07 (0.18), residues: 785 sheet: -0.84 (0.31), residues: 295 loop : -0.24 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.005 0.001 HIS D 101 PHE 0.008 0.001 PHE B 255 TYR 0.016 0.001 TYR A 306 ARG 0.005 0.001 ARG B 206 *********************** 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 354 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 330 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6022 (tpt) cc_final: 0.5590 (tpt) REVERT: A 50 LYS cc_start: 0.8209 (mttt) cc_final: 0.7882 (mmtt) REVERT: A 68 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8567 (mmtp) REVERT: A 206 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7833 (ttp80) REVERT: A 284 LYS cc_start: 0.9084 (mttt) cc_final: 0.8856 (mtmt) REVERT: A 296 ASN cc_start: 0.8784 (m-40) cc_final: 0.8516 (m-40) REVERT: A 328 LYS cc_start: 0.8462 (tttt) cc_final: 0.8139 (tptt) REVERT: A 334 GLU cc_start: 0.7099 (tp30) cc_final: 0.6820 (tp30) REVERT: A 355 MET cc_start: 0.7791 (mmm) cc_final: 0.7269 (mtm) REVERT: A 360 GLN cc_start: 0.8475 (tp40) cc_final: 0.8195 (mm-40) REVERT: B 123 MET cc_start: 0.8384 (mmp) cc_final: 0.8106 (mmt) REVERT: B 184 ASP cc_start: 0.7593 (m-30) cc_final: 0.7247 (m-30) REVERT: B 318 THR cc_start: 0.8920 (m) cc_final: 0.8638 (m) REVERT: C 83 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7947 (tm-30) REVERT: C 118 LYS cc_start: 0.8340 (tppt) cc_final: 0.8107 (mttt) REVERT: C 132 MET cc_start: 0.8168 (tmm) cc_final: 0.7902 (ttp) REVERT: C 344 SER cc_start: 0.8685 (t) cc_final: 0.8240 (p) REVERT: D 123 MET cc_start: 0.8485 (mmp) cc_final: 0.8144 (mmm) REVERT: D 328 LYS cc_start: 0.8793 (tttt) cc_final: 0.8558 (ttmt) REVERT: D 355 MET cc_start: 0.8069 (mmm) cc_final: 0.7604 (mmm) REVERT: E 44 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.5161 (mpp) REVERT: E 82 MET cc_start: 0.7896 (tpt) cc_final: 0.7627 (tpt) REVERT: E 132 MET cc_start: 0.8455 (tmm) cc_final: 0.8225 (ttp) REVERT: E 169 TYR cc_start: 0.9193 (m-80) cc_final: 0.8900 (m-80) REVERT: E 191 LYS cc_start: 0.8659 (tttm) cc_final: 0.8386 (ttmm) REVERT: E 192 ILE cc_start: 0.8976 (mm) cc_final: 0.8653 (pt) REVERT: E 207 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: E 225 ASN cc_start: 0.8292 (m-40) cc_final: 0.8086 (m-40) REVERT: E 315 LYS cc_start: 0.8568 (tttm) cc_final: 0.8353 (ttmm) REVERT: E 328 LYS cc_start: 0.8858 (tttt) cc_final: 0.8568 (ttpt) outliers start: 24 outliers final: 13 residues processed: 342 average time/residue: 0.2476 time to fit residues: 126.2962 Evaluate side-chains 259 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 168 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 354 GLN B 296 ASN C 12 ASN C 161 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 87 HIS D 161 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14980 Z= 0.199 Angle : 0.586 7.352 20335 Z= 0.290 Chirality : 0.044 0.167 2255 Planarity : 0.005 0.053 2595 Dihedral : 12.066 179.842 2085 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.31 % Favored : 98.42 % Rotamer: Outliers : 1.92 % Allowed : 11.95 % Favored : 86.13 % 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: 0.08 (0.20), residues: 1830 helix: 0.29 (0.18), residues: 785 sheet: -0.62 (0.31), residues: 285 loop : 0.33 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.003 0.001 HIS C 88 PHE 0.040 0.001 PHE A 352 TYR 0.011 0.001 TYR E 143 ARG 0.004 0.000 ARG D 28 *********************** 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 321 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 291 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5981 (tpt) cc_final: 0.5571 (tpt) REVERT: A 50 LYS cc_start: 0.8272 (mttt) cc_final: 0.8017 (mmmt) REVERT: A 68 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8602 (mmtp) REVERT: A 206 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7747 (ttp80) REVERT: A 296 ASN cc_start: 0.8748 (m-40) cc_final: 0.8477 (m-40) REVERT: A 325 MET cc_start: 0.4813 (mmt) cc_final: 0.3725 (mmt) REVERT: A 328 LYS cc_start: 0.8474 (tttt) cc_final: 0.8155 (tptt) REVERT: A 355 MET cc_start: 0.7848 (mmm) cc_final: 0.7402 (mtm) REVERT: B 184 ASP cc_start: 0.7485 (m-30) cc_final: 0.7136 (m-30) REVERT: B 318 THR cc_start: 0.8891 (m) cc_final: 0.8637 (m) REVERT: C 83 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7961 (tm-30) REVERT: C 118 LYS cc_start: 0.8345 (tppt) cc_final: 0.8104 (mttt) REVERT: C 132 MET cc_start: 0.8227 (tmm) cc_final: 0.7861 (ttp) REVERT: C 207 GLU cc_start: 0.7640 (tp30) cc_final: 0.7397 (mm-30) REVERT: C 225 ASN cc_start: 0.8151 (m-40) cc_final: 0.7930 (m-40) REVERT: C 344 SER cc_start: 0.8672 (t) cc_final: 0.8282 (p) REVERT: C 354 GLN cc_start: 0.8187 (mm110) cc_final: 0.7805 (mt0) REVERT: D 143 TYR cc_start: 0.8690 (m-80) cc_final: 0.8356 (m-80) REVERT: D 328 LYS cc_start: 0.8782 (tttt) cc_final: 0.8537 (ttpp) REVERT: D 355 MET cc_start: 0.8004 (mmm) cc_final: 0.7543 (mmm) REVERT: E 82 MET cc_start: 0.7919 (tpt) cc_final: 0.7599 (tpt) REVERT: E 132 MET cc_start: 0.8579 (tmm) cc_final: 0.8241 (ttp) REVERT: E 169 TYR cc_start: 0.9170 (m-80) cc_final: 0.8889 (m-80) REVERT: E 191 LYS cc_start: 0.8639 (tttm) cc_final: 0.8374 (ttmm) REVERT: E 207 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: E 313 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7834 (ttm) REVERT: E 328 LYS cc_start: 0.8951 (tttt) cc_final: 0.8715 (ttpt) outliers start: 30 outliers final: 20 residues processed: 308 average time/residue: 0.2512 time to fit residues: 117.2705 Evaluate side-chains 271 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 313 MET 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: 7.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 0.0010 chunk 113 optimal weight: 0.0270 chunk 168 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.5446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 49 GLN A 101 HIS A 354 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN E 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14980 Z= 0.162 Angle : 0.551 6.942 20335 Z= 0.267 Chirality : 0.043 0.163 2255 Planarity : 0.005 0.046 2595 Dihedral : 10.124 154.389 2085 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.15 % Favored : 98.58 % Rotamer: Outliers : 2.11 % Allowed : 12.59 % Favored : 85.30 % 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: 0.21 (0.20), residues: 1830 helix: 0.37 (0.18), residues: 785 sheet: -0.63 (0.31), residues: 285 loop : 0.48 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 340 HIS 0.005 0.001 HIS D 87 PHE 0.022 0.001 PHE A 352 TYR 0.011 0.001 TYR C 198 ARG 0.009 0.000 ARG D 28 *********************** 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 318 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 285 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5809 (tpt) cc_final: 0.5561 (tpt) REVERT: A 50 LYS cc_start: 0.8267 (mttt) cc_final: 0.7916 (mmtt) REVERT: A 284 LYS cc_start: 0.9026 (mttt) cc_final: 0.8819 (mtpp) REVERT: A 296 ASN cc_start: 0.8710 (m-40) cc_final: 0.8392 (m-40) REVERT: A 325 MET cc_start: 0.4910 (mmt) cc_final: 0.4026 (mmt) REVERT: A 328 LYS cc_start: 0.8565 (tttt) cc_final: 0.8251 (tptt) REVERT: A 355 MET cc_start: 0.7760 (mmm) cc_final: 0.7301 (mtm) REVERT: B 184 ASP cc_start: 0.7529 (m-30) cc_final: 0.7151 (m-30) REVERT: B 292 ASP cc_start: 0.7990 (m-30) cc_final: 0.7735 (m-30) REVERT: B 318 THR cc_start: 0.8893 (m) cc_final: 0.8660 (m) REVERT: C 6 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8469 (p) REVERT: C 83 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7909 (tm-30) REVERT: C 118 LYS cc_start: 0.8332 (tppt) cc_final: 0.8049 (mttt) REVERT: C 132 MET cc_start: 0.8208 (tmm) cc_final: 0.7814 (ttp) REVERT: C 225 ASN cc_start: 0.8255 (m-40) cc_final: 0.8000 (m-40) REVERT: C 344 SER cc_start: 0.8627 (t) cc_final: 0.8217 (p) REVERT: C 354 GLN cc_start: 0.8203 (mm110) cc_final: 0.7872 (mt0) REVERT: D 132 MET cc_start: 0.7926 (ttt) cc_final: 0.7703 (ttt) REVERT: D 143 TYR cc_start: 0.8657 (m-80) cc_final: 0.8270 (m-80) REVERT: D 328 LYS cc_start: 0.8775 (tttt) cc_final: 0.8515 (ttpp) REVERT: D 355 MET cc_start: 0.7941 (mmm) cc_final: 0.7523 (mmm) REVERT: E 82 MET cc_start: 0.7920 (tpt) cc_final: 0.7490 (tpt) REVERT: E 132 MET cc_start: 0.8566 (tmm) cc_final: 0.8198 (ttp) REVERT: E 169 TYR cc_start: 0.9129 (m-80) cc_final: 0.8833 (m-80) REVERT: E 191 LYS cc_start: 0.8618 (tttm) cc_final: 0.8369 (ttmm) REVERT: E 328 LYS cc_start: 0.8927 (tttt) cc_final: 0.8697 (ttpt) outliers start: 33 outliers final: 17 residues processed: 302 average time/residue: 0.2420 time to fit residues: 111.0124 Evaluate side-chains 276 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 258 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 311 ASP 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: 3.9990 chunk 2 optimal weight: 0.0170 chunk 133 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 123 optimal weight: 0.0040 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14980 Z= 0.373 Angle : 0.622 9.055 20335 Z= 0.301 Chirality : 0.047 0.154 2255 Planarity : 0.005 0.043 2595 Dihedral : 8.641 120.015 2085 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.19 % Favored : 97.65 % Rotamer: Outliers : 2.94 % Allowed : 12.52 % Favored : 84.54 % 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: -0.06 (0.20), residues: 1830 helix: 0.23 (0.18), residues: 785 sheet: -1.02 (0.34), residues: 225 loop : 0.21 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.009 0.001 HIS C 88 PHE 0.021 0.002 PHE A 352 TYR 0.013 0.001 TYR E 143 ARG 0.007 0.001 ARG A 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 318 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 272 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5823 (tpt) cc_final: 0.5373 (tpt) REVERT: A 50 LYS cc_start: 0.8474 (mttt) cc_final: 0.8181 (mmmt) REVERT: A 78 ASN cc_start: 0.8627 (t0) cc_final: 0.8196 (t0) REVERT: A 151 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 328 LYS cc_start: 0.8610 (tttt) cc_final: 0.8316 (tptt) REVERT: A 355 MET cc_start: 0.8031 (mmm) cc_final: 0.7761 (mtt) REVERT: B 292 ASP cc_start: 0.7964 (m-30) cc_final: 0.7682 (m-30) REVERT: C 6 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8556 (p) REVERT: C 83 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7942 (tm-30) REVERT: C 118 LYS cc_start: 0.8505 (tppt) cc_final: 0.8164 (mttt) REVERT: C 123 MET cc_start: 0.8674 (mmm) cc_final: 0.8449 (mmt) REVERT: C 225 ASN cc_start: 0.8290 (m-40) cc_final: 0.8013 (m-40) REVERT: C 249 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8654 (p) REVERT: C 344 SER cc_start: 0.8694 (t) cc_final: 0.8308 (p) REVERT: C 354 GLN cc_start: 0.8352 (mm110) cc_final: 0.8005 (mt0) REVERT: D 143 TYR cc_start: 0.8735 (m-80) cc_final: 0.8425 (m-80) REVERT: D 328 LYS cc_start: 0.8899 (tttt) cc_final: 0.8547 (ttpp) REVERT: D 355 MET cc_start: 0.7930 (mmm) cc_final: 0.7536 (mmm) REVERT: E 68 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8305 (mmtp) REVERT: E 132 MET cc_start: 0.8566 (tmm) cc_final: 0.8194 (ttp) REVERT: E 169 TYR cc_start: 0.9253 (m-80) cc_final: 0.8945 (m-80) REVERT: E 189 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8889 (tt) REVERT: E 191 LYS cc_start: 0.8695 (tttm) cc_final: 0.8413 (ttmm) REVERT: E 207 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: E 328 LYS cc_start: 0.8981 (tttt) cc_final: 0.8721 (ttpt) outliers start: 46 outliers final: 27 residues processed: 302 average time/residue: 0.2263 time to fit residues: 104.7262 Evaluate side-chains 272 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 277 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 101 HIS A 115 ASN A 162 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14980 Z= 0.325 Angle : 0.598 7.015 20335 Z= 0.289 Chirality : 0.046 0.157 2255 Planarity : 0.005 0.041 2595 Dihedral : 8.207 108.927 2085 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.81 % Rotamer: Outliers : 3.64 % Allowed : 13.10 % Favored : 83.26 % 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: -0.22 (0.20), residues: 1830 helix: 0.18 (0.18), residues: 785 sheet: -1.04 (0.31), residues: 295 loop : 0.14 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 79 HIS 0.008 0.001 HIS C 88 PHE 0.016 0.001 PHE A 352 TYR 0.013 0.001 TYR E 143 ARG 0.007 0.000 ARG A 206 *********************** 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 320 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 263 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8533 (mttt) cc_final: 0.8187 (mmmt) REVERT: A 78 ASN cc_start: 0.8653 (t0) cc_final: 0.8209 (t0) REVERT: A 311 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: A 328 LYS cc_start: 0.8562 (tttt) cc_final: 0.8231 (tptt) REVERT: B 292 ASP cc_start: 0.7950 (m-30) cc_final: 0.7668 (m-30) REVERT: B 305 MET cc_start: 0.8759 (mmm) cc_final: 0.8402 (mmt) REVERT: C 6 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8540 (p) REVERT: C 118 LYS cc_start: 0.8573 (tppt) cc_final: 0.8231 (mttt) REVERT: C 189 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8772 (tt) REVERT: C 225 ASN cc_start: 0.8280 (m-40) cc_final: 0.7998 (m-40) REVERT: C 249 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8632 (p) REVERT: C 299 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8154 (mtm) REVERT: C 344 SER cc_start: 0.8696 (t) cc_final: 0.8319 (p) REVERT: C 354 GLN cc_start: 0.8355 (mm110) cc_final: 0.8013 (mt0) REVERT: D 119 MET cc_start: 0.8365 (ttm) cc_final: 0.8109 (ttm) REVERT: D 143 TYR cc_start: 0.8679 (m-80) cc_final: 0.8396 (m-80) REVERT: D 328 LYS cc_start: 0.8908 (tttt) cc_final: 0.8529 (ttpp) REVERT: D 355 MET cc_start: 0.7924 (mmm) cc_final: 0.7577 (mmm) REVERT: E 68 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8338 (mmtp) REVERT: E 132 MET cc_start: 0.8546 (tmm) cc_final: 0.8135 (ttp) REVERT: E 169 TYR cc_start: 0.9222 (m-80) cc_final: 0.8920 (m-80) REVERT: E 189 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8895 (tt) REVERT: E 191 LYS cc_start: 0.8697 (tttm) cc_final: 0.8415 (ttmm) REVERT: E 305 MET cc_start: 0.8431 (mmm) cc_final: 0.8129 (mmm) REVERT: E 328 LYS cc_start: 0.8948 (tttt) cc_final: 0.8692 (ttpt) outliers start: 57 outliers final: 40 residues processed: 304 average time/residue: 0.2270 time to fit residues: 107.3427 Evaluate side-chains 288 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 242 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 101 HIS A 115 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14980 Z= 0.205 Angle : 0.558 6.978 20335 Z= 0.267 Chirality : 0.043 0.171 2255 Planarity : 0.004 0.041 2595 Dihedral : 7.755 101.334 2085 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.88 % Allowed : 13.55 % Favored : 83.58 % 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: 0.27 (0.18), residues: 785 sheet: -1.01 (0.31), residues: 295 loop : 0.15 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.006 0.001 HIS A 101 PHE 0.014 0.001 PHE A 352 TYR 0.010 0.001 TYR E 198 ARG 0.006 0.000 ARG C 206 *********************** 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 307 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 262 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5546 (tpt) cc_final: 0.5147 (tpt) REVERT: A 78 ASN cc_start: 0.8621 (t0) cc_final: 0.8260 (t0) REVERT: A 311 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: A 328 LYS cc_start: 0.8526 (tttt) cc_final: 0.8189 (tptt) REVERT: B 78 ASN cc_start: 0.8211 (t0) cc_final: 0.7930 (p0) REVERT: B 292 ASP cc_start: 0.7963 (m-30) cc_final: 0.7680 (m-30) REVERT: B 305 MET cc_start: 0.8718 (mmm) cc_final: 0.8358 (mmt) REVERT: C 118 LYS cc_start: 0.8521 (tppt) cc_final: 0.8172 (mttt) REVERT: C 192 ILE cc_start: 0.8478 (tt) cc_final: 0.8239 (pt) REVERT: C 225 ASN cc_start: 0.8250 (m-40) cc_final: 0.7988 (m-40) REVERT: C 299 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8216 (mmm) REVERT: C 344 SER cc_start: 0.8527 (t) cc_final: 0.8161 (p) REVERT: C 354 GLN cc_start: 0.8332 (mm110) cc_final: 0.8012 (mt0) REVERT: D 143 TYR cc_start: 0.8628 (m-80) cc_final: 0.8325 (m-80) REVERT: D 328 LYS cc_start: 0.8872 (tttt) cc_final: 0.8473 (ttpp) REVERT: D 355 MET cc_start: 0.7918 (mmm) cc_final: 0.7591 (mmm) REVERT: E 68 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8356 (mmtp) REVERT: E 132 MET cc_start: 0.8542 (tmm) cc_final: 0.8171 (ttp) REVERT: E 169 TYR cc_start: 0.9161 (m-80) cc_final: 0.8649 (m-80) REVERT: E 191 LYS cc_start: 0.8664 (tttm) cc_final: 0.8411 (ttmm) REVERT: E 328 LYS cc_start: 0.8924 (tttt) cc_final: 0.8609 (ttpt) outliers start: 45 outliers final: 30 residues processed: 292 average time/residue: 0.2366 time to fit residues: 106.8749 Evaluate side-chains 279 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 311 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 113 optimal weight: 0.1980 chunk 121 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14980 Z= 0.164 Angle : 0.558 9.940 20335 Z= 0.262 Chirality : 0.043 0.144 2255 Planarity : 0.004 0.042 2595 Dihedral : 7.334 93.657 2085 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.30 % Allowed : 14.50 % Favored : 83.19 % 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: 0.36 (0.19), residues: 785 sheet: -0.93 (0.31), residues: 295 loop : 0.17 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 356 HIS 0.003 0.001 HIS D 87 PHE 0.013 0.001 PHE A 352 TYR 0.011 0.001 TYR E 198 ARG 0.006 0.000 ARG C 206 *********************** 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 306 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 270 time to evaluate : 1.834 Fit side-chains REVERT: A 47 MET cc_start: 0.5381 (tpt) cc_final: 0.5050 (tpt) REVERT: A 78 ASN cc_start: 0.8584 (t0) cc_final: 0.8262 (t0) REVERT: A 82 MET cc_start: 0.8121 (tpt) cc_final: 0.7848 (tpt) REVERT: A 128 ASN cc_start: 0.8065 (t0) cc_final: 0.7620 (t0) REVERT: A 280 ASN cc_start: 0.9101 (m-40) cc_final: 0.8838 (m-40) REVERT: A 311 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: A 328 LYS cc_start: 0.8507 (tttt) cc_final: 0.8155 (tptt) REVERT: A 355 MET cc_start: 0.7726 (mtt) cc_final: 0.7443 (mtp) REVERT: B 8 LEU cc_start: 0.8899 (mp) cc_final: 0.8615 (mt) REVERT: B 292 ASP cc_start: 0.7909 (m-30) cc_final: 0.7673 (m-30) REVERT: B 305 MET cc_start: 0.8658 (mmm) cc_final: 0.8286 (mmt) REVERT: B 353 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8175 (mp10) REVERT: C 82 MET cc_start: 0.8448 (tpt) cc_final: 0.8186 (mmm) REVERT: C 118 LYS cc_start: 0.8444 (tppt) cc_final: 0.8106 (mttt) REVERT: C 132 MET cc_start: 0.8207 (tmm) cc_final: 0.7782 (ttp) REVERT: C 205 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7665 (mt-10) REVERT: C 206 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7225 (tpp80) REVERT: C 269 MET cc_start: 0.8459 (mtp) cc_final: 0.8155 (mtp) REVERT: C 344 SER cc_start: 0.8485 (t) cc_final: 0.8139 (p) REVERT: C 354 GLN cc_start: 0.8310 (mm110) cc_final: 0.8013 (mt0) REVERT: D 143 TYR cc_start: 0.8602 (m-80) cc_final: 0.8345 (m-80) REVERT: D 328 LYS cc_start: 0.8848 (tttt) cc_final: 0.8459 (ttpp) REVERT: D 355 MET cc_start: 0.7884 (mmm) cc_final: 0.7550 (mmm) REVERT: E 68 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8333 (mmtp) REVERT: E 132 MET cc_start: 0.8560 (tmm) cc_final: 0.7920 (ttp) REVERT: E 169 TYR cc_start: 0.9150 (m-80) cc_final: 0.8648 (m-80) REVERT: E 191 LYS cc_start: 0.8632 (tttm) cc_final: 0.8389 (ttmm) REVERT: E 328 LYS cc_start: 0.8902 (tttt) cc_final: 0.8587 (ttpt) REVERT: E 355 MET cc_start: 0.8620 (mpp) cc_final: 0.8118 (mtp) outliers start: 36 outliers final: 28 residues processed: 294 average time/residue: 0.2329 time to fit residues: 105.2102 Evaluate side-chains 280 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 277 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14980 Z= 0.229 Angle : 0.580 7.842 20335 Z= 0.273 Chirality : 0.044 0.168 2255 Planarity : 0.004 0.043 2595 Dihedral : 7.147 90.196 2085 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.04 % Allowed : 15.27 % Favored : 82.68 % 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: -0.07 (0.20), residues: 1830 helix: 0.35 (0.19), residues: 785 sheet: -0.88 (0.31), residues: 295 loop : 0.11 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS D 87 PHE 0.013 0.001 PHE C 223 TYR 0.016 0.001 TYR B 198 ARG 0.006 0.000 ARG C 206 *********************** 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 287 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 255 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.7914 (p0) cc_final: 0.7709 (p0) REVERT: A 47 MET cc_start: 0.5369 (tpt) cc_final: 0.5161 (tpt) REVERT: A 78 ASN cc_start: 0.8578 (t0) cc_final: 0.8211 (t0) REVERT: A 82 MET cc_start: 0.8189 (tpt) cc_final: 0.7890 (tpt) REVERT: A 128 ASN cc_start: 0.8095 (t0) cc_final: 0.7660 (t0) REVERT: A 280 ASN cc_start: 0.9073 (m-40) cc_final: 0.8825 (m-40) REVERT: A 311 ASP cc_start: 0.8288 (m-30) cc_final: 0.8031 (m-30) REVERT: A 325 MET cc_start: 0.4578 (mtt) cc_final: 0.4191 (mtt) REVERT: A 328 LYS cc_start: 0.8547 (tttt) cc_final: 0.8218 (tptt) REVERT: B 269 MET cc_start: 0.8591 (mmm) cc_final: 0.8202 (mtp) REVERT: B 292 ASP cc_start: 0.7954 (m-30) cc_final: 0.7636 (m-30) REVERT: B 305 MET cc_start: 0.8702 (mmm) cc_final: 0.8345 (mmt) REVERT: C 82 MET cc_start: 0.8620 (tpt) cc_final: 0.8266 (mmm) REVERT: C 118 LYS cc_start: 0.8466 (tppt) cc_final: 0.8132 (mttt) REVERT: C 344 SER cc_start: 0.8484 (t) cc_final: 0.8171 (p) REVERT: C 354 GLN cc_start: 0.8349 (mm110) cc_final: 0.8029 (mt0) REVERT: D 143 TYR cc_start: 0.8650 (m-80) cc_final: 0.8405 (m-80) REVERT: D 328 LYS cc_start: 0.8859 (tttt) cc_final: 0.8471 (ttpp) REVERT: D 355 MET cc_start: 0.7853 (mmm) cc_final: 0.7560 (mmm) REVERT: E 68 LYS cc_start: 0.8663 (mmtt) cc_final: 0.8382 (mmtp) REVERT: E 132 MET cc_start: 0.8571 (tmm) cc_final: 0.7977 (ttp) REVERT: E 169 TYR cc_start: 0.9176 (m-80) cc_final: 0.8741 (m-80) REVERT: E 191 LYS cc_start: 0.8662 (tttm) cc_final: 0.8420 (ttmm) REVERT: E 328 LYS cc_start: 0.8919 (tttt) cc_final: 0.8654 (ttpt) REVERT: E 355 MET cc_start: 0.8619 (mpp) cc_final: 0.8114 (mtp) outliers start: 32 outliers final: 27 residues processed: 276 average time/residue: 0.2240 time to fit residues: 96.0167 Evaluate side-chains 277 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 250 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 146 optimal weight: 0.0040 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 12 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14980 Z= 0.201 Angle : 0.577 8.424 20335 Z= 0.271 Chirality : 0.044 0.145 2255 Planarity : 0.004 0.042 2595 Dihedral : 6.975 85.632 2085 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.98 % Allowed : 15.65 % Favored : 82.36 % 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: 0.03 (0.20), residues: 1830 helix: 0.42 (0.19), residues: 785 sheet: -0.81 (0.31), residues: 295 loop : 0.19 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 79 HIS 0.004 0.001 HIS D 87 PHE 0.011 0.001 PHE A 352 TYR 0.017 0.001 TYR A 279 ARG 0.005 0.000 ARG C 206 ********************** 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 293 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 262 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.7926 (p0) cc_final: 0.7720 (p0) REVERT: A 78 ASN cc_start: 0.8578 (t0) cc_final: 0.8231 (t0) REVERT: A 82 MET cc_start: 0.8186 (tpt) cc_final: 0.7885 (tpt) REVERT: A 128 ASN cc_start: 0.8100 (t0) cc_final: 0.7682 (t0) REVERT: A 280 ASN cc_start: 0.9025 (m-40) cc_final: 0.8736 (m-40) REVERT: A 311 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: A 325 MET cc_start: 0.4688 (mtt) cc_final: 0.4327 (mtt) REVERT: A 328 LYS cc_start: 0.8558 (tttt) cc_final: 0.8188 (tptt) REVERT: B 269 MET cc_start: 0.8557 (mmm) cc_final: 0.8199 (mtp) REVERT: B 292 ASP cc_start: 0.7880 (m-30) cc_final: 0.7593 (m-30) REVERT: B 305 MET cc_start: 0.8688 (mmm) cc_final: 0.8373 (mmt) REVERT: C 82 MET cc_start: 0.8588 (tpt) cc_final: 0.8287 (mmm) REVERT: C 118 LYS cc_start: 0.8460 (tppt) cc_final: 0.8131 (mttt) REVERT: C 344 SER cc_start: 0.8446 (t) cc_final: 0.8136 (p) REVERT: C 354 GLN cc_start: 0.8339 (mm110) cc_final: 0.8028 (mt0) REVERT: D 143 TYR cc_start: 0.8644 (m-80) cc_final: 0.8214 (m-80) REVERT: D 328 LYS cc_start: 0.8838 (tttt) cc_final: 0.8488 (ttpp) REVERT: D 355 MET cc_start: 0.7837 (mmm) cc_final: 0.7562 (mmm) REVERT: E 68 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8411 (mmtp) REVERT: E 132 MET cc_start: 0.8580 (tmm) cc_final: 0.7971 (ttp) REVERT: E 169 TYR cc_start: 0.9160 (m-80) cc_final: 0.8718 (m-80) REVERT: E 191 LYS cc_start: 0.8655 (tttm) cc_final: 0.8414 (ttmm) REVERT: E 315 LYS cc_start: 0.8612 (tttm) cc_final: 0.8403 (ttmm) REVERT: E 328 LYS cc_start: 0.8843 (tttt) cc_final: 0.8565 (ttpt) REVERT: E 355 MET cc_start: 0.8593 (mpp) cc_final: 0.8133 (mtp) outliers start: 31 outliers final: 28 residues processed: 283 average time/residue: 0.2261 time to fit residues: 99.1859 Evaluate side-chains 282 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 135 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.0170 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106934 restraints weight = 19261.513| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.04 r_work: 0.3040 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14980 Z= 0.164 Angle : 0.572 8.667 20335 Z= 0.267 Chirality : 0.043 0.141 2255 Planarity : 0.004 0.045 2595 Dihedral : 6.691 77.438 2085 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.73 % Allowed : 16.55 % Favored : 81.73 % 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: 0.54 (0.19), residues: 775 sheet: -0.63 (0.31), residues: 310 loop : 0.16 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.004 0.001 HIS D 87 PHE 0.012 0.001 PHE A 352 TYR 0.012 0.001 TYR E 198 ARG 0.005 0.000 ARG C 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3305.71 seconds wall clock time: 60 minutes 23.89 seconds (3623.89 seconds total)