Starting phenix.real_space_refine on Fri Feb 16 07:24:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oof_3839/02_2024/5oof_3839_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oof_3839/02_2024/5oof_3839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oof_3839/02_2024/5oof_3839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oof_3839/02_2024/5oof_3839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oof_3839/02_2024/5oof_3839_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oof_3839/02_2024/5oof_3839_updated.pdb" } resolution = 3.4 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "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 "A GLU 361": "OE1" <-> "OE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "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 "B GLU 361": "OE1" <-> "OE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "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 "C GLU 361": "OE1" <-> "OE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "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 "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "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" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.03, per 1000 atoms: 0.55 Number of scatterers: 14640 At special positions: 0 Unit cell: (98.04, 91.2, 190.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2815 8.00 N 2470 7.00 C 9235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.91 Conformation dependent library (CDL) restraints added in 2.5 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 20 sheets defined 45.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 55 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 removed outlier: 4.286A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.834A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 267 removed outlier: 5.211A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.680A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A 292 " --> 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: 5.669A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.526A 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 371 Processing helix chain 'B' and resid 55 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 removed outlier: 4.287A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.834A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 267 removed outlier: 5.210A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Proline residue: B 264 - end of helix Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.681A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP B 292 " --> 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: 5.670A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.526A 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 371 Processing helix chain 'C' and resid 55 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 removed outlier: 4.287A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.835A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 267 removed outlier: 5.210A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.680A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP C 292 " --> 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: 5.669A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.526A 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 371 Processing helix chain 'D' and resid 55 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 removed outlier: 4.287A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.834A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 267 removed outlier: 5.210A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Proline residue: D 264 - end of helix Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.680A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP D 292 " --> 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: 5.670A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.525A 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 371 Processing helix chain 'E' and resid 55 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 removed outlier: 4.287A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.834A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 267 removed outlier: 5.211A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.680A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP E 292 " --> 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: 5.669A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.526A 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 371 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.497A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) 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 297 through 299 removed outlier: 5.923A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.497A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 299 removed outlier: 5.924A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.498A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 299 removed outlier: 5.923A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.498A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 299 removed outlier: 5.923A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.496A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 299 removed outlier: 5.922A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 580 hydrogen bonds defined for protein. 1305 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: 4.72 Time building geometry restraints manager: 6.17 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: 3328 1.32 - 1.44: 3451 1.44 - 1.56: 7996 1.56 - 1.69: 0 1.69 - 1.81: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.86e+01 bond pdb=" CA SER B 155 " pdb=" C SER B 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.84e+01 bond pdb=" CA SER E 155 " pdb=" C SER E 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.81e+01 bond pdb=" CA SER D 155 " pdb=" C SER D 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.79e+01 bond pdb=" CA SER A 155 " pdb=" C SER A 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.79e+01 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 97.12 - 104.88: 403 104.88 - 112.65: 7767 112.65 - 120.41: 6855 120.41 - 128.17: 5185 128.17 - 135.94: 95 Bond angle restraints: 20305 Sorted by residual: angle pdb=" C GLY B 366 " pdb=" N PRO B 367 " pdb=" CA PRO B 367 " ideal model delta sigma weight residual 119.84 129.55 -9.71 1.25e+00 6.40e-01 6.04e+01 angle pdb=" C GLY D 366 " pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 119.84 129.54 -9.70 1.25e+00 6.40e-01 6.02e+01 angle pdb=" C GLY E 366 " pdb=" N PRO E 367 " pdb=" CA PRO E 367 " ideal model delta sigma weight residual 119.84 129.53 -9.69 1.25e+00 6.40e-01 6.02e+01 angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.84 129.53 -9.69 1.25e+00 6.40e-01 6.00e+01 angle pdb=" C GLY C 366 " pdb=" N PRO C 367 " pdb=" CA PRO C 367 " ideal model delta sigma weight residual 119.84 129.48 -9.64 1.25e+00 6.40e-01 5.95e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.52: 8835 29.52 - 59.04: 135 59.04 - 88.56: 20 88.56 - 118.08: 0 118.08 - 147.61: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.61 -147.61 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.57 -147.57 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.56 -147.56 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 907 0.047 - 0.094: 909 0.094 - 0.140: 308 0.140 - 0.187: 93 0.187 - 0.234: 38 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA ASP A 157 " pdb=" N ASP A 157 " pdb=" C ASP A 157 " pdb=" CB ASP A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ASP B 157 " pdb=" N ASP B 157 " pdb=" C ASP B 157 " pdb=" CB ASP B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASP E 157 " pdb=" N ASP E 157 " pdb=" C ASP E 157 " pdb=" CB ASP E 157 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 375 " -0.033 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C PHE D 375 " 0.114 2.00e-02 2.50e+03 pdb=" O PHE D 375 " -0.041 2.00e-02 2.50e+03 pdb=" OXT PHE D 375 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 375 " 0.032 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" C PHE E 375 " -0.114 2.00e-02 2.50e+03 pdb=" O PHE E 375 " 0.041 2.00e-02 2.50e+03 pdb=" OXT PHE E 375 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 375 " -0.032 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" C PHE B 375 " 0.114 2.00e-02 2.50e+03 pdb=" O PHE B 375 " -0.041 2.00e-02 2.50e+03 pdb=" OXT PHE B 375 " -0.040 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 71 2.59 - 3.17: 14073 3.17 - 3.74: 22350 3.74 - 4.32: 34646 4.32 - 4.90: 53474 Nonbonded interactions: 124614 Sorted by model distance: nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.010 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.010 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.011 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.011 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.011 2.170 ... (remaining 124609 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: 0.700 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: 4.470 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 40.850 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.015 0.052 14960 Z= 1.010 Angle : 1.532 14.555 20305 Z= 0.993 Chirality : 0.075 0.234 2255 Planarity : 0.016 0.143 2595 Dihedral : 11.806 147.605 5565 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 2.73 % Allowed : 6.28 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 1830 helix: -1.44 (0.16), residues: 780 sheet: -1.22 (0.28), residues: 235 loop : -0.01 (0.25), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.006 TRP C 340 HIS 0.010 0.002 HIS D 101 PHE 0.013 0.003 PHE C 375 TYR 0.030 0.005 TYR B 69 ARG 0.004 0.001 ARG E 183 *********************** 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 408 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: A 76 ILE cc_start: 0.9238 (mt) cc_final: 0.8981 (mp) REVERT: A 176 MET cc_start: 0.8871 (mmm) cc_final: 0.8640 (mmt) REVERT: A 283 MET cc_start: 0.9192 (mmp) cc_final: 0.8962 (mmt) REVERT: A 328 LYS cc_start: 0.8714 (tttt) cc_final: 0.8452 (tttm) REVERT: A 355 MET cc_start: 0.8432 (mmm) cc_final: 0.8217 (mmm) REVERT: B 47 MET cc_start: 0.5700 (mtm) cc_final: 0.5438 (tpt) REVERT: C 123 MET cc_start: 0.8724 (mmp) cc_final: 0.8482 (mmt) REVERT: D 51 ASP cc_start: 0.7474 (p0) cc_final: 0.6842 (p0) REVERT: D 113 LYS cc_start: 0.8803 (mttt) cc_final: 0.8112 (mtpp) REVERT: E 12 ASN cc_start: 0.8292 (t0) cc_final: 0.8005 (p0) REVERT: E 78 ASN cc_start: 0.8630 (t0) cc_final: 0.8177 (t0) REVERT: E 269 MET cc_start: 0.8429 (tpp) cc_final: 0.8210 (mmt) REVERT: E 354 GLN cc_start: 0.8334 (pt0) cc_final: 0.7932 (pt0) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3285 time to fit residues: 183.3413 Evaluate side-chains 184 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 162 ASN A 246 GLN B 121 GLN B 162 ASN B 314 GLN C 92 ASN C 162 ASN C 246 GLN D 162 ASN D 371 HIS E 162 ASN E 371 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14960 Z= 0.205 Angle : 0.622 7.780 20305 Z= 0.320 Chirality : 0.044 0.157 2255 Planarity : 0.007 0.071 2595 Dihedral : 7.126 90.100 2085 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.44 % Favored : 96.01 % Rotamer: Outliers : 1.28 % Allowed : 8.37 % Favored : 90.35 % 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 (0.20), residues: 1830 helix: -0.01 (0.18), residues: 780 sheet: -1.09 (0.28), residues: 260 loop : 0.39 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 79 HIS 0.006 0.002 HIS D 40 PHE 0.023 0.002 PHE A 352 TYR 0.015 0.001 TYR D 306 ARG 0.007 0.001 ARG C 210 *********************** 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 286 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 266 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.9064 (mm) cc_final: 0.8801 (tp) REVERT: A 355 MET cc_start: 0.8582 (mmm) cc_final: 0.8304 (mmm) REVERT: B 9 VAL cc_start: 0.9038 (t) cc_final: 0.8821 (m) REVERT: B 192 ILE cc_start: 0.9113 (mm) cc_final: 0.8760 (pt) REVERT: C 10 CYS cc_start: 0.8302 (t) cc_final: 0.8050 (t) REVERT: C 269 MET cc_start: 0.8478 (tpt) cc_final: 0.8129 (tpt) REVERT: D 9 VAL cc_start: 0.9068 (t) cc_final: 0.8713 (m) REVERT: D 47 MET cc_start: 0.3350 (OUTLIER) cc_final: 0.0534 (mmp) REVERT: D 51 ASP cc_start: 0.7452 (p0) cc_final: 0.7191 (p0) REVERT: D 103 THR cc_start: 0.9417 (m) cc_final: 0.9199 (p) REVERT: D 113 LYS cc_start: 0.8772 (mttt) cc_final: 0.8393 (mttp) REVERT: D 132 MET cc_start: 0.8519 (tmm) cc_final: 0.8087 (ppp) REVERT: D 227 MET cc_start: 0.8444 (tpp) cc_final: 0.8200 (mtp) REVERT: E 82 MET cc_start: 0.8822 (tpt) cc_final: 0.8160 (tpt) outliers start: 20 outliers final: 10 residues processed: 278 average time/residue: 0.2684 time to fit residues: 109.4190 Evaluate side-chains 188 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 0.0020 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN C 246 GLN D 12 ASN E 162 ASN E 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14960 Z= 0.226 Angle : 0.582 6.044 20305 Z= 0.290 Chirality : 0.044 0.149 2255 Planarity : 0.005 0.051 2595 Dihedral : 5.992 61.269 2085 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.33 % Favored : 96.12 % Rotamer: Outliers : 2.36 % Allowed : 9.65 % Favored : 87.99 % 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: 0.38 (0.20), residues: 1830 helix: 0.46 (0.19), residues: 750 sheet: -0.66 (0.29), residues: 260 loop : 0.62 (0.24), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.006 0.001 HIS C 275 PHE 0.011 0.001 PHE A 352 TYR 0.011 0.001 TYR D 306 ARG 0.011 0.001 ARG D 147 *********************** 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 238 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.720 Fit side-chains REVERT: A 12 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8343 (t160) REVERT: A 151 ILE cc_start: 0.9096 (mm) cc_final: 0.8784 (tp) REVERT: A 285 CYS cc_start: 0.7100 (m) cc_final: 0.6866 (m) REVERT: A 355 MET cc_start: 0.8539 (mmm) cc_final: 0.8119 (mmm) REVERT: B 9 VAL cc_start: 0.9313 (t) cc_final: 0.9079 (m) REVERT: B 132 MET cc_start: 0.7867 (ptm) cc_final: 0.7418 (ttp) REVERT: B 192 ILE cc_start: 0.9142 (mm) cc_final: 0.8793 (pt) REVERT: C 9 VAL cc_start: 0.9283 (t) cc_final: 0.9017 (m) REVERT: C 355 MET cc_start: 0.8108 (tpp) cc_final: 0.7861 (tpp) REVERT: D 9 VAL cc_start: 0.9271 (t) cc_final: 0.8959 (m) REVERT: D 47 MET cc_start: 0.2494 (OUTLIER) cc_final: -0.0182 (mmp) REVERT: D 51 ASP cc_start: 0.7399 (p0) cc_final: 0.6937 (p0) REVERT: D 82 MET cc_start: 0.8845 (tpt) cc_final: 0.8419 (tpt) REVERT: D 103 THR cc_start: 0.9385 (m) cc_final: 0.9160 (p) REVERT: D 132 MET cc_start: 0.8451 (tmm) cc_final: 0.8108 (ppp) REVERT: E 120 THR cc_start: 0.9002 (m) cc_final: 0.8785 (p) REVERT: E 269 MET cc_start: 0.8822 (tpp) cc_final: 0.8406 (mmt) outliers start: 37 outliers final: 20 residues processed: 223 average time/residue: 0.2405 time to fit residues: 81.9503 Evaluate side-chains 198 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14960 Z= 0.233 Angle : 0.571 7.680 20305 Z= 0.279 Chirality : 0.044 0.148 2255 Planarity : 0.005 0.042 2595 Dihedral : 5.800 56.455 2085 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.90 % Favored : 96.56 % Rotamer: Outliers : 2.49 % Allowed : 11.50 % Favored : 86.01 % 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: 0.65 (0.20), residues: 1830 helix: 0.88 (0.19), residues: 710 sheet: -0.44 (0.30), residues: 260 loop : 0.53 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.007 0.001 HIS E 275 PHE 0.008 0.001 PHE A 255 TYR 0.009 0.001 TYR D 306 ARG 0.007 0.000 ARG D 147 *********************** 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 231 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.9088 (mm) cc_final: 0.8773 (tp) REVERT: A 355 MET cc_start: 0.8565 (mmm) cc_final: 0.8296 (mmm) REVERT: B 9 VAL cc_start: 0.9350 (t) cc_final: 0.9119 (m) REVERT: B 71 ILE cc_start: 0.9340 (mt) cc_final: 0.9099 (mt) REVERT: B 192 ILE cc_start: 0.9103 (mm) cc_final: 0.8788 (pt) REVERT: D 9 VAL cc_start: 0.9292 (t) cc_final: 0.9022 (m) REVERT: D 47 MET cc_start: 0.2766 (OUTLIER) cc_final: 0.0389 (mmt) REVERT: D 51 ASP cc_start: 0.7475 (p0) cc_final: 0.6979 (p0) REVERT: D 82 MET cc_start: 0.8844 (tpt) cc_final: 0.8399 (tpt) REVERT: D 250 ILE cc_start: 0.8685 (mm) cc_final: 0.8436 (mt) REVERT: D 263 GLN cc_start: 0.8407 (mt0) cc_final: 0.8188 (mt0) REVERT: E 47 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.3617 (tpt) REVERT: E 120 THR cc_start: 0.9001 (m) cc_final: 0.8795 (p) outliers start: 39 outliers final: 27 residues processed: 214 average time/residue: 0.2383 time to fit residues: 78.9134 Evaluate side-chains 195 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS E 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14960 Z= 0.343 Angle : 0.621 7.276 20305 Z= 0.305 Chirality : 0.045 0.150 2255 Planarity : 0.005 0.037 2595 Dihedral : 6.018 57.709 2085 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.83 % Favored : 95.63 % Rotamer: Outliers : 2.88 % Allowed : 12.33 % Favored : 84.79 % 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: 0.50 (0.20), residues: 1830 helix: 0.77 (0.19), residues: 710 sheet: -0.44 (0.28), residues: 330 loop : 0.51 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 79 HIS 0.006 0.001 HIS C 40 PHE 0.013 0.001 PHE A 255 TYR 0.013 0.001 TYR D 166 ARG 0.005 0.000 ARG A 372 *********************** 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 234 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.9057 (mm) cc_final: 0.8760 (tp) REVERT: B 71 ILE cc_start: 0.9407 (mt) cc_final: 0.9126 (mt) REVERT: B 192 ILE cc_start: 0.9108 (mm) cc_final: 0.8770 (pt) REVERT: D 47 MET cc_start: 0.2380 (OUTLIER) cc_final: 0.0044 (mmt) REVERT: D 51 ASP cc_start: 0.7795 (p0) cc_final: 0.7251 (p0) REVERT: D 82 MET cc_start: 0.8900 (tpt) cc_final: 0.8434 (tpt) REVERT: D 263 GLN cc_start: 0.8567 (mt0) cc_final: 0.8278 (mt0) REVERT: E 47 MET cc_start: 0.5469 (OUTLIER) cc_final: 0.3592 (tpt) REVERT: E 120 THR cc_start: 0.9132 (m) cc_final: 0.8930 (p) outliers start: 45 outliers final: 31 residues processed: 219 average time/residue: 0.2288 time to fit residues: 77.3895 Evaluate side-chains 204 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS C 101 HIS D 40 HIS D 354 GLN E 40 HIS E 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14960 Z= 0.165 Angle : 0.549 7.041 20305 Z= 0.266 Chirality : 0.042 0.146 2255 Planarity : 0.004 0.039 2595 Dihedral : 5.654 51.143 2085 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.95 % Favored : 96.50 % Rotamer: Outliers : 1.92 % Allowed : 14.57 % Favored : 83.51 % 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: 0.80 (0.20), residues: 1830 helix: 0.92 (0.19), residues: 710 sheet: -0.00 (0.28), residues: 335 loop : 0.63 (0.25), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.005 0.001 HIS C 275 PHE 0.007 0.001 PHE B 31 TYR 0.009 0.001 TYR C 306 ARG 0.005 0.000 ARG A 372 *********************** 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 224 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.705 Fit side-chains REVERT: A 151 ILE cc_start: 0.9027 (mm) cc_final: 0.8730 (tp) REVERT: B 132 MET cc_start: 0.7739 (ptm) cc_final: 0.7256 (ttp) REVERT: B 192 ILE cc_start: 0.9061 (mm) cc_final: 0.8855 (pt) REVERT: B 355 MET cc_start: 0.7831 (tpp) cc_final: 0.7169 (mmt) REVERT: D 47 MET cc_start: 0.2930 (OUTLIER) cc_final: 0.0541 (mmt) REVERT: D 51 ASP cc_start: 0.7741 (p0) cc_final: 0.7251 (p0) REVERT: D 132 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7970 (ppp) REVERT: E 47 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.3572 (tpt) REVERT: E 120 THR cc_start: 0.9088 (m) cc_final: 0.8830 (p) outliers start: 30 outliers final: 21 residues processed: 211 average time/residue: 0.2403 time to fit residues: 77.5637 Evaluate side-chains 201 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS D 40 HIS E 40 HIS E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14960 Z= 0.243 Angle : 0.574 6.681 20305 Z= 0.278 Chirality : 0.043 0.145 2255 Planarity : 0.004 0.045 2595 Dihedral : 5.698 52.129 2085 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.55 % Favored : 95.90 % Rotamer: Outliers : 2.62 % Allowed : 14.38 % Favored : 83.00 % 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: 0.79 (0.20), residues: 1830 helix: 0.90 (0.19), residues: 710 sheet: -0.06 (0.28), residues: 350 loop : 0.69 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 86 HIS 0.004 0.001 HIS E 173 PHE 0.008 0.001 PHE A 255 TYR 0.007 0.001 TYR D 166 ARG 0.012 0.000 ARG A 372 *********************** 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 219 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 1.810 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.9037 (mm) cc_final: 0.8743 (tp) REVERT: A 294 TYR cc_start: 0.8539 (m-10) cc_final: 0.8245 (m-10) REVERT: B 192 ILE cc_start: 0.9059 (mm) cc_final: 0.8798 (pt) REVERT: B 355 MET cc_start: 0.7904 (tpp) cc_final: 0.7256 (mmt) REVERT: D 47 MET cc_start: 0.2873 (OUTLIER) cc_final: 0.0526 (mmt) REVERT: D 51 ASP cc_start: 0.7872 (p0) cc_final: 0.7390 (p0) REVERT: D 132 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7955 (ppp) REVERT: D 263 GLN cc_start: 0.8454 (mt0) cc_final: 0.8193 (mt0) REVERT: D 325 MET cc_start: 0.8228 (mmp) cc_final: 0.7978 (mmp) REVERT: E 47 MET cc_start: 0.5340 (OUTLIER) cc_final: 0.3619 (tpt) REVERT: E 120 THR cc_start: 0.9122 (m) cc_final: 0.8861 (p) REVERT: E 325 MET cc_start: 0.8035 (mmm) cc_final: 0.7694 (mmm) outliers start: 41 outliers final: 29 residues processed: 206 average time/residue: 0.2334 time to fit residues: 73.8164 Evaluate side-chains 205 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 53 optimal weight: 0.3980 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS D 40 HIS E 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14960 Z= 0.199 Angle : 0.562 6.477 20305 Z= 0.272 Chirality : 0.042 0.144 2255 Planarity : 0.004 0.052 2595 Dihedral : 5.633 51.874 2085 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.84 % Favored : 96.61 % Rotamer: Outliers : 2.62 % Allowed : 14.44 % Favored : 82.94 % 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: 0.87 (0.20), residues: 1830 helix: 0.92 (0.19), residues: 710 sheet: 0.13 (0.29), residues: 325 loop : 0.68 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.004 0.001 HIS C 275 PHE 0.006 0.001 PHE A 255 TYR 0.007 0.001 TYR C 198 ARG 0.013 0.000 ARG A 372 *********************** 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 220 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 1.559 Fit side-chains REVERT: A 151 ILE cc_start: 0.9034 (mm) cc_final: 0.8728 (tp) REVERT: B 82 MET cc_start: 0.8733 (tpp) cc_final: 0.7978 (tpt) REVERT: B 192 ILE cc_start: 0.9063 (mm) cc_final: 0.8808 (pt) REVERT: B 355 MET cc_start: 0.7884 (tpp) cc_final: 0.7241 (mmt) REVERT: C 9 VAL cc_start: 0.9380 (t) cc_final: 0.9148 (m) REVERT: D 47 MET cc_start: 0.2873 (OUTLIER) cc_final: 0.0544 (mmt) REVERT: D 51 ASP cc_start: 0.7872 (p0) cc_final: 0.7401 (p0) REVERT: D 132 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7892 (ppp) REVERT: D 263 GLN cc_start: 0.8406 (mt0) cc_final: 0.8143 (mt0) REVERT: E 47 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.3626 (tpt) REVERT: E 120 THR cc_start: 0.9126 (m) cc_final: 0.8890 (p) REVERT: E 325 MET cc_start: 0.7973 (mmm) cc_final: 0.7696 (mmm) outliers start: 41 outliers final: 29 residues processed: 207 average time/residue: 0.2441 time to fit residues: 78.2382 Evaluate side-chains 207 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 40 HIS C 101 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS E 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14960 Z= 0.355 Angle : 0.626 7.117 20305 Z= 0.307 Chirality : 0.045 0.169 2255 Planarity : 0.005 0.056 2595 Dihedral : 5.894 51.766 2085 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.93 % Favored : 95.52 % Rotamer: Outliers : 2.43 % Allowed : 14.63 % Favored : 82.94 % 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: 0.55 (0.19), residues: 740 sheet: -0.05 (0.29), residues: 325 loop : 0.44 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 86 HIS 0.005 0.001 HIS C 40 PHE 0.011 0.001 PHE E 223 TYR 0.011 0.001 TYR D 166 ARG 0.014 0.001 ARG A 372 *********************** 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 213 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.588 Fit side-chains REVERT: A 151 ILE cc_start: 0.9045 (mm) cc_final: 0.8773 (tp) REVERT: A 294 TYR cc_start: 0.8611 (m-10) cc_final: 0.8387 (m-10) REVERT: B 192 ILE cc_start: 0.9108 (mm) cc_final: 0.8814 (pt) REVERT: B 355 MET cc_start: 0.7965 (tpp) cc_final: 0.7335 (mmt) REVERT: C 9 VAL cc_start: 0.9434 (t) cc_final: 0.9173 (m) REVERT: D 47 MET cc_start: 0.2884 (OUTLIER) cc_final: 0.0432 (mmt) REVERT: D 51 ASP cc_start: 0.7975 (p0) cc_final: 0.7481 (p0) REVERT: D 82 MET cc_start: 0.8923 (tpt) cc_final: 0.8416 (tpt) REVERT: D 132 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7894 (ppp) REVERT: D 176 MET cc_start: 0.8766 (mmm) cc_final: 0.8260 (mtp) REVERT: E 47 MET cc_start: 0.5356 (OUTLIER) cc_final: 0.3642 (tpt) REVERT: E 120 THR cc_start: 0.9133 (m) cc_final: 0.8932 (m) REVERT: E 325 MET cc_start: 0.8081 (mmm) cc_final: 0.7743 (mmm) outliers start: 38 outliers final: 30 residues processed: 201 average time/residue: 0.2319 time to fit residues: 71.7155 Evaluate side-chains 202 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 146 optimal weight: 0.0170 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS C 101 HIS E 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14960 Z= 0.161 Angle : 0.563 6.510 20305 Z= 0.274 Chirality : 0.043 0.168 2255 Planarity : 0.004 0.059 2595 Dihedral : 5.608 50.931 2085 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.95 % Favored : 96.50 % Rotamer: Outliers : 1.98 % Allowed : 15.34 % 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: 0.60 (0.20), residues: 1830 helix: 0.62 (0.19), residues: 745 sheet: 0.13 (0.30), residues: 325 loop : 0.55 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.009 0.001 HIS C 101 PHE 0.012 0.001 PHE E 223 TYR 0.008 0.001 TYR C 306 ARG 0.014 0.000 ARG A 372 ********************** 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 215 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 1.986 Fit side-chains REVERT: A 151 ILE cc_start: 0.9020 (mm) cc_final: 0.8700 (tp) REVERT: A 294 TYR cc_start: 0.8563 (m-10) cc_final: 0.8213 (m-10) REVERT: B 82 MET cc_start: 0.8714 (tpp) cc_final: 0.7994 (tpt) REVERT: B 132 MET cc_start: 0.7784 (ptm) cc_final: 0.7336 (ttp) REVERT: B 192 ILE cc_start: 0.9053 (mm) cc_final: 0.8850 (pt) REVERT: B 227 MET cc_start: 0.8734 (ttm) cc_final: 0.8500 (ttm) REVERT: B 355 MET cc_start: 0.7854 (tpp) cc_final: 0.7235 (mmt) REVERT: C 9 VAL cc_start: 0.9370 (t) cc_final: 0.9128 (m) REVERT: D 9 VAL cc_start: 0.9239 (t) cc_final: 0.8985 (m) REVERT: D 47 MET cc_start: 0.2877 (OUTLIER) cc_final: 0.0545 (mmt) REVERT: D 51 ASP cc_start: 0.7904 (p0) cc_final: 0.7483 (p0) REVERT: D 132 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7880 (ppp) REVERT: D 176 MET cc_start: 0.8756 (mmm) cc_final: 0.8288 (mtp) REVERT: E 47 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.3619 (tpt) REVERT: E 120 THR cc_start: 0.9118 (m) cc_final: 0.8850 (p) REVERT: E 325 MET cc_start: 0.7914 (mmm) cc_final: 0.7654 (mmm) outliers start: 31 outliers final: 23 residues processed: 201 average time/residue: 0.2408 time to fit residues: 74.5133 Evaluate side-chains 195 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS C 101 HIS E 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.085713 restraints weight = 25925.761| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.22 r_work: 0.2913 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14960 Z= 0.181 Angle : 0.566 6.316 20305 Z= 0.275 Chirality : 0.043 0.167 2255 Planarity : 0.004 0.059 2595 Dihedral : 5.520 49.590 2085 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.33 % Favored : 96.12 % Rotamer: Outliers : 1.85 % Allowed : 15.72 % Favored : 82.43 % 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: 0.63 (0.20), residues: 1830 helix: 0.65 (0.19), residues: 745 sheet: 0.21 (0.30), residues: 325 loop : 0.51 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 86 HIS 0.008 0.001 HIS C 40 PHE 0.018 0.001 PHE E 223 TYR 0.008 0.001 TYR A 337 ARG 0.014 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3071.69 seconds wall clock time: 56 minutes 47.94 seconds (3407.94 seconds total)