Starting phenix.real_space_refine (version: dev) on Fri May 13 21:06:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/05_2022/6fhl_4259_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/05_2022/6fhl_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_4259/05_2022/6fhl_4259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/05_2022/6fhl_4259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/05_2022/6fhl_4259_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhl_4259/05_2022/6fhl_4259_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 Convert atoms to be neutral 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PO4': 1, ' MG': 1, 'ADP': 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: {'PO4': 1, ' MG': 1, 'ADP': 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: {'PO4': 1, ' MG': 1, 'ADP': 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: {'PO4': 1, ' MG': 1, 'ADP': 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: {'PO4': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.86, per 1000 atoms: 0.60 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: 6.42 Conformation dependent library (CDL) restraints added in 2.4 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: 1.56 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: 4.64 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 947 0.051 - 0.101: 820 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 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. 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.110 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 41.580 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 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= 1.187 Angle : 1.597 10.050 20335 Z= 1.026 Chirality : 0.083 0.253 2255 Planarity : 0.017 0.130 2595 Dihedral : 13.054 150.851 5565 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 2.19 % Allowed : 5.46 % Favored : 92.35 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.2843 time to fit residues: 201.3547 Evaluate side-chains 247 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2022 ------------------------------------------------------------------------------- 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: 0.9980 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8508 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14980 Z= 0.238 Angle : 0.674 6.830 20335 Z= 0.338 Chirality : 0.047 0.188 2255 Planarity : 0.008 0.101 2595 Dihedral : 12.419 168.917 2085 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.69 % Favored : 98.03 % Rotamer Outliers : 1.73 % 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: -0.46 (0.20), residues: 1830 helix: 0.04 (0.18), residues: 785 sheet: -0.80 (0.31), residues: 295 loop : -0.25 (0.24), residues: 750 *********************** 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 352 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 325 time to evaluate : 1.706 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 339 average time/residue: 0.2366 time to fit residues: 119.6022 Evaluate side-chains 239 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1355 time to fit residues: 5.4958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 161 HIS B 296 ASN C 12 ASN C 161 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS D 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 14980 Z= 0.327 Angle : 0.636 7.388 20335 Z= 0.314 Chirality : 0.047 0.171 2255 Planarity : 0.006 0.083 2595 Dihedral : 12.071 179.156 2085 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.91 % Favored : 97.81 % Rotamer Outliers : 1.66 % 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: 0.17 (0.18), residues: 785 sheet: -0.83 (0.31), residues: 295 loop : 0.30 (0.23), residues: 750 *********************** 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 283 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 257 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 272 average time/residue: 0.2343 time to fit residues: 97.9982 Evaluate side-chains 251 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 237 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1513 time to fit residues: 6.1566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN D 12 ASN D 353 GLN ** 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: 0.8547 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14980 Z= 0.196 Angle : 0.575 7.382 20335 Z= 0.277 Chirality : 0.043 0.149 2255 Planarity : 0.005 0.072 2595 Dihedral : 10.285 154.662 2085 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.31 % Favored : 98.42 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1830 helix: 0.23 (0.18), residues: 785 sheet: -0.69 (0.31), residues: 285 loop : 0.33 (0.23), residues: 760 *********************** 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 297 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 1.490 Fit side-chains outliers start: 18 outliers final: 5 residues processed: 288 average time/residue: 0.2316 time to fit residues: 103.3650 Evaluate side-chains 250 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1317 time to fit residues: 3.6756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS C 12 ASN D 12 ASN D 59 GLN D 353 GLN E 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.110 14980 Z= 0.618 Angle : 0.745 9.059 20335 Z= 0.368 Chirality : 0.052 0.182 2255 Planarity : 0.006 0.086 2595 Dihedral : 9.258 131.888 2085 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.28 % Favored : 96.50 % Rotamer Outliers : 2.68 % 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: -0.58 (0.19), residues: 1830 helix: -0.14 (0.18), residues: 785 sheet: -1.19 (0.34), residues: 225 loop : -0.18 (0.22), residues: 820 *********************** 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 314 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 272 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 301 average time/residue: 0.2193 time to fit residues: 104.2574 Evaluate side-chains 243 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1332 time to fit residues: 8.1922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN A 162 ASN B 162 ASN B 225 ASN D 12 ASN D 162 ASN E 59 GLN E 78 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14980 Z= 0.209 Angle : 0.586 7.018 20335 Z= 0.281 Chirality : 0.044 0.148 2255 Planarity : 0.005 0.072 2595 Dihedral : 8.070 105.781 2085 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.53 % Favored : 98.42 % Rotamer Outliers : 1.15 % 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: -0.33 (0.19), residues: 1830 helix: 0.15 (0.19), residues: 780 sheet: -1.22 (0.35), residues: 225 loop : -0.09 (0.21), residues: 825 *********************** 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 273 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 265 average time/residue: 0.2199 time to fit residues: 91.9407 Evaluate side-chains 244 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 234 time to evaluate : 1.920 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1331 time to fit residues: 5.0069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 115 ASN A 162 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 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: 0.8588 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 : 0.004 0.059 14980 Z= 0.240 Angle : 0.582 7.715 20335 Z= 0.276 Chirality : 0.045 0.217 2255 Planarity : 0.005 0.063 2595 Dihedral : 7.807 102.575 2085 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.43 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 1830 helix: 0.20 (0.19), residues: 780 sheet: -1.15 (0.35), residues: 225 loop : -0.15 (0.21), residues: 825 *********************** 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 268 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 265 average time/residue: 0.2336 time to fit residues: 95.0474 Evaluate side-chains 235 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1264 time to fit residues: 3.1487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 121 optimal weight: 0.0060 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN C 49 GLN D 12 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 14980 Z= 0.161 Angle : 0.560 7.624 20335 Z= 0.265 Chirality : 0.043 0.182 2255 Planarity : 0.005 0.060 2595 Dihedral : 7.293 92.633 2085 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.37 % Favored : 98.58 % Rotamer Outliers : 0.70 % 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: -0.17 (0.19), residues: 1830 helix: 0.28 (0.19), residues: 780 sheet: -0.73 (0.36), residues: 215 loop : -0.15 (0.21), residues: 835 *********************** 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 280 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 269 time to evaluate : 1.717 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 273 average time/residue: 0.2307 time to fit residues: 98.1867 Evaluate side-chains 245 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 240 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1345 time to fit residues: 3.6408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14980 Z= 0.200 Angle : 0.580 7.659 20335 Z= 0.273 Chirality : 0.044 0.174 2255 Planarity : 0.005 0.058 2595 Dihedral : 7.074 87.550 2085 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.51 % 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: -0.18 (0.19), residues: 1830 helix: 0.31 (0.19), residues: 780 sheet: -0.90 (0.35), residues: 225 loop : -0.12 (0.21), residues: 825 *********************** 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 251 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 243 time to evaluate : 1.792 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 246 average time/residue: 0.2179 time to fit residues: 84.2302 Evaluate side-chains 236 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1460 time to fit residues: 3.2363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.0170 chunk 122 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 0.0770 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.3780 ------------------------------------------------------------------------------- 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** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN ** 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: 0.8580 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 14980 Z= 0.263 Angle : 0.607 9.485 20335 Z= 0.285 Chirality : 0.045 0.197 2255 Planarity : 0.005 0.057 2595 Dihedral : 6.939 85.697 2085 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.32 % 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: -0.13 (0.20), residues: 1830 helix: 0.35 (0.19), residues: 780 sheet: -0.88 (0.35), residues: 225 loop : -0.10 (0.22), residues: 825 ********************** 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 239 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 234 time to evaluate : 1.908 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 238 average time/residue: 0.2315 time to fit residues: 85.9160 Evaluate side-chains 231 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1247 time to fit residues: 2.3511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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** D 12 ASN D 296 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.112621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.095998 restraints weight = 19857.318| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.14 r_work: 0.3075 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3046 rms_B_bonded: 1.96 restraints_weight: 0.1250 r_work: 0.3030 rms_B_bonded: 2.06 restraints_weight: 0.0625 r_work: 0.3013 rms_B_bonded: 2.20 restraints_weight: 0.0312 r_work: 0.2995 rms_B_bonded: 2.39 restraints_weight: 0.0156 r_work: 0.2976 rms_B_bonded: 2.61 restraints_weight: 0.0078 r_work: 0.2955 rms_B_bonded: 2.88 restraints_weight: 0.0039 r_work: 0.2932 rms_B_bonded: 3.19 restraints_weight: 0.0020 r_work: 0.2907 rms_B_bonded: 3.55 restraints_weight: 0.0010 r_work: 0.2879 rms_B_bonded: 3.97 restraints_weight: 0.0005 r_work: 0.2849 rms_B_bonded: 4.45 restraints_weight: 0.0002 r_work: 0.2816 rms_B_bonded: 4.99 restraints_weight: 0.0001 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 14980 Z= 0.313 Angle : 0.630 10.015 20335 Z= 0.297 Chirality : 0.046 0.208 2255 Planarity : 0.005 0.056 2595 Dihedral : 6.944 87.084 2085 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.26 % 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: -0.25 (0.19), residues: 1830 helix: 0.26 (0.19), residues: 780 sheet: -0.92 (0.34), residues: 225 loop : -0.17 (0.22), residues: 825 =============================================================================== Job complete usr+sys time: 2827.08 seconds wall clock time: 52 minutes 32.66 seconds (3152.66 seconds total)