Starting phenix.real_space_refine on Fri Feb 16 09:29:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/02_2024/5ooc_3836_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.022 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 9425 2.51 5 N 2495 2.21 5 O 2845 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 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "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 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "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 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "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 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "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 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14885 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, '9ZK': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 7.97, per 1000 atoms: 0.54 Number of scatterers: 14885 At special positions: 0 Unit cell: (100.32, 85.5, 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 2845 8.00 N 2495 7.00 C 9425 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: 6.31 Conformation dependent library (CDL) restraints added in 3.1 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 20 sheets defined 44.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.126A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.400A 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: 3.508A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 5.311A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.485A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.260A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (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 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 92 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.127A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.399A 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: 3.508A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 5.312A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.485A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.261A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (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 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 92 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.127A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.399A 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: 3.509A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 5.312A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.484A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.261A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (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 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 92 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.127A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.400A 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: 3.508A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 5.313A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.485A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.261A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (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 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 92 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.127A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.399A 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: 3.508A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 5.311A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.485A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.261A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (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: 6.565A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.761A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.564A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.761A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.564A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.760A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.564A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.761A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.565A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.761A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 555 hydrogen bonds defined for protein. 1335 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: 4.60 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2455 1.28 - 1.41: 3835 1.41 - 1.54: 8721 1.54 - 1.68: 24 1.68 - 1.81: 185 Bond restraints: 15220 Sorted by residual: bond pdb=" C07 9ZK D 403 " pdb=" C08 9ZK D 403 " ideal model delta sigma weight residual 2.679 1.510 1.169 2.00e-02 2.50e+03 3.41e+03 bond pdb=" C07 9ZK A 404 " pdb=" C08 9ZK A 404 " ideal model delta sigma weight residual 2.679 1.511 1.168 2.00e-02 2.50e+03 3.41e+03 bond pdb=" C07 9ZK A 402 " pdb=" C08 9ZK A 402 " ideal model delta sigma weight residual 2.679 1.511 1.168 2.00e-02 2.50e+03 3.41e+03 bond pdb=" C07 9ZK C 403 " pdb=" C08 9ZK C 403 " ideal model delta sigma weight residual 2.679 1.511 1.168 2.00e-02 2.50e+03 3.41e+03 bond pdb=" C07 9ZK B 403 " pdb=" C08 9ZK B 403 " ideal model delta sigma weight residual 2.679 1.511 1.168 2.00e-02 2.50e+03 3.41e+03 ... (remaining 15215 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.41: 479 105.41 - 113.14: 8139 113.14 - 120.87: 7657 120.87 - 128.59: 4275 128.59 - 136.32: 110 Bond angle restraints: 20660 Sorted by residual: angle pdb=" C09 9ZK C 403 " pdb=" C11 9ZK C 403 " pdb=" C12 9ZK C 403 " ideal model delta sigma weight residual 180.00 111.17 68.83 3.00e+00 1.11e-01 5.26e+02 angle pdb=" C09 9ZK A 404 " pdb=" C11 9ZK A 404 " pdb=" C12 9ZK A 404 " ideal model delta sigma weight residual 180.00 111.18 68.82 3.00e+00 1.11e-01 5.26e+02 angle pdb=" C09 9ZK B 403 " pdb=" C11 9ZK B 403 " pdb=" C12 9ZK B 403 " ideal model delta sigma weight residual 180.00 111.18 68.82 3.00e+00 1.11e-01 5.26e+02 angle pdb=" C09 9ZK A 402 " pdb=" C11 9ZK A 402 " pdb=" C12 9ZK A 402 " ideal model delta sigma weight residual 180.00 111.24 68.76 3.00e+00 1.11e-01 5.25e+02 angle pdb=" C09 9ZK D 403 " pdb=" C11 9ZK D 403 " pdb=" C12 9ZK D 403 " ideal model delta sigma weight residual 180.00 111.24 68.76 3.00e+00 1.11e-01 5.25e+02 ... (remaining 20655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 8900 35.02 - 70.03: 120 70.03 - 105.05: 35 105.05 - 140.06: 15 140.06 - 175.08: 25 Dihedral angle restraints: 9095 sinusoidal: 3735 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 89.22 -149.23 1 2.00e+01 2.50e-03 4.46e+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 89.20 -149.20 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.20 -149.20 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 9092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.835: 2270 0.835 - 1.669: 5 1.669 - 2.504: 0 2.504 - 3.339: 0 3.339 - 4.173: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C16 9ZK D 403 " pdb=" C17 9ZK D 403 " pdb=" C22 9ZK D 403 " pdb=" N15 9ZK D 403 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.17 2.00e-01 2.50e+01 4.35e+02 chirality pdb=" C16 9ZK A 402 " pdb=" C17 9ZK A 402 " pdb=" C22 9ZK A 402 " pdb=" N15 9ZK A 402 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.17 2.00e-01 2.50e+01 4.35e+02 chirality pdb=" C16 9ZK C 403 " pdb=" C17 9ZK C 403 " pdb=" C22 9ZK C 403 " pdb=" N15 9ZK C 403 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.17 2.00e-01 2.50e+01 4.35e+02 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO A 164 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO B 164 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.097 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C 164 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.075 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 175 2.62 - 3.19: 14984 3.19 - 3.76: 23185 3.76 - 4.33: 34919 4.33 - 4.90: 53410 Nonbonded interactions: 126673 Sorted by model distance: nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 403 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.051 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 2.051 2.170 ... (remaining 126668 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' and (resid 5 through 375 or resid 401)) selection = (chain 'B' and (resid 5 through 375 or resid 401)) selection = (chain 'C' and (resid 5 through 375 or resid 401)) selection = (chain 'D' and (resid 5 through 375 or resid 401)) selection = (chain 'E' and (resid 5 through 375 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 4.580 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 43.440 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.049 1.169 15220 Z= 3.142 Angle : 3.107 68.833 20660 Z= 1.335 Chirality : 0.220 4.173 2280 Planarity : 0.018 0.147 2630 Dihedral : 17.808 175.080 5665 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 2.73 % Allowed : 4.37 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.20), residues: 1830 helix: -1.31 (0.16), residues: 715 sheet: -0.73 (0.26), residues: 310 loop : -0.45 (0.26), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP C 340 HIS 0.007 0.002 HIS B 88 PHE 0.010 0.003 PHE C 90 TYR 0.021 0.004 TYR B 198 ARG 0.005 0.001 ARG D 39 *********************** 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 500 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7640 (mtm) cc_final: 0.7218 (mpp) REVERT: A 103 THR cc_start: 0.9206 (m) cc_final: 0.8897 (p) REVERT: A 154 ASP cc_start: 0.8393 (t70) cc_final: 0.8127 (t70) REVERT: A 269 MET cc_start: 0.7298 (tpp) cc_final: 0.7007 (tpt) REVERT: A 283 MET cc_start: 0.9125 (mmp) cc_final: 0.8878 (mmp) REVERT: A 286 ASP cc_start: 0.7035 (t70) cc_final: 0.6770 (m-30) REVERT: A 355 MET cc_start: 0.7554 (mmm) cc_final: 0.7148 (mmm) REVERT: B 80 ASP cc_start: 0.8525 (m-30) cc_final: 0.8295 (t0) REVERT: B 154 ASP cc_start: 0.7274 (t70) cc_final: 0.6704 (t0) REVERT: C 47 MET cc_start: 0.5942 (mmt) cc_final: 0.5665 (mmt) REVERT: C 78 ASN cc_start: 0.8532 (t0) cc_final: 0.8238 (t0) REVERT: C 82 MET cc_start: 0.9167 (tpt) cc_final: 0.8963 (tpt) REVERT: C 178 LEU cc_start: 0.8698 (mt) cc_final: 0.8479 (mp) REVERT: C 191 LYS cc_start: 0.8573 (mttt) cc_final: 0.8257 (ttmm) REVERT: C 224 GLU cc_start: 0.8133 (tp30) cc_final: 0.7932 (tm-30) REVERT: C 238 LYS cc_start: 0.8849 (tptt) cc_final: 0.8527 (ttmt) REVERT: C 296 ASN cc_start: 0.8426 (m-40) cc_final: 0.8199 (m-40) REVERT: C 336 LYS cc_start: 0.8136 (mttt) cc_final: 0.7368 (ttmt) REVERT: D 44 MET cc_start: 0.7083 (mtm) cc_final: 0.6057 (ttt) REVERT: D 128 ASN cc_start: 0.7985 (m-40) cc_final: 0.7209 (t0) REVERT: D 201 VAL cc_start: 0.9460 (m) cc_final: 0.9046 (p) REVERT: D 211 ASP cc_start: 0.8788 (t70) cc_final: 0.8299 (t0) REVERT: D 222 ASP cc_start: 0.7416 (t0) cc_final: 0.7195 (p0) REVERT: D 249 THR cc_start: 0.9206 (m) cc_final: 0.9005 (p) REVERT: D 296 ASN cc_start: 0.8373 (m-40) cc_final: 0.7825 (m-40) REVERT: E 120 THR cc_start: 0.8371 (m) cc_final: 0.8151 (p) REVERT: E 227 MET cc_start: 0.8305 (mmm) cc_final: 0.8011 (mmm) REVERT: E 244 ASP cc_start: 0.8851 (p0) cc_final: 0.8577 (p0) REVERT: E 249 THR cc_start: 0.8795 (m) cc_final: 0.8563 (p) REVERT: E 353 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8189 (mm-40) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.3143 time to fit residues: 217.7582 Evaluate side-chains 243 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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: 0.7980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN E 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15220 Z= 0.222 Angle : 1.592 32.827 20660 Z= 0.590 Chirality : 0.049 0.285 2280 Planarity : 0.009 0.062 2630 Dihedral : 24.414 179.623 2185 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 1.09 % Allowed : 2.19 % Favored : 96.72 % Rotamer: Outliers : 1.73 % Allowed : 7.86 % Favored : 90.42 % 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: -0.29 (0.20), residues: 1830 helix: 0.27 (0.19), residues: 765 sheet: -0.64 (0.27), residues: 280 loop : -0.31 (0.25), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 340 HIS 0.007 0.001 HIS A 101 PHE 0.008 0.001 PHE E 127 TYR 0.018 0.001 TYR A 166 ARG 0.007 0.001 ARG D 147 *********************** 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 358 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 331 time to evaluate : 1.940 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8660 (tpt) cc_final: 0.8042 (tmm) REVERT: A 101 HIS cc_start: 0.7794 (m-70) cc_final: 0.7587 (m-70) REVERT: A 103 THR cc_start: 0.9159 (m) cc_final: 0.8944 (p) REVERT: A 167 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8079 (mp0) REVERT: A 222 ASP cc_start: 0.7433 (t0) cc_final: 0.6865 (t0) REVERT: A 225 ASN cc_start: 0.8628 (t0) cc_final: 0.8288 (p0) REVERT: A 238 LYS cc_start: 0.8614 (tptt) cc_final: 0.8350 (tttt) REVERT: A 269 MET cc_start: 0.7420 (tpp) cc_final: 0.6759 (tpt) REVERT: A 283 MET cc_start: 0.9047 (mmp) cc_final: 0.8836 (mmp) REVERT: B 24 ASP cc_start: 0.7616 (m-30) cc_final: 0.7375 (m-30) REVERT: B 78 ASN cc_start: 0.8380 (t0) cc_final: 0.7705 (t0) REVERT: B 80 ASP cc_start: 0.8598 (m-30) cc_final: 0.8187 (t0) REVERT: B 100 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7201 (mm-30) REVERT: B 269 MET cc_start: 0.7678 (mmm) cc_final: 0.7134 (tpp) REVERT: C 34 ILE cc_start: 0.9453 (mt) cc_final: 0.9209 (pt) REVERT: C 78 ASN cc_start: 0.8693 (t0) cc_final: 0.8423 (t0) REVERT: C 82 MET cc_start: 0.8880 (tpt) cc_final: 0.8649 (mmm) REVERT: C 191 LYS cc_start: 0.8613 (mttt) cc_final: 0.8400 (ttmm) REVERT: C 238 LYS cc_start: 0.8845 (tptt) cc_final: 0.8446 (ttmt) REVERT: C 305 MET cc_start: 0.8434 (mmm) cc_final: 0.8143 (mmm) REVERT: C 336 LYS cc_start: 0.8060 (mttt) cc_final: 0.7624 (mttt) REVERT: D 161 HIS cc_start: 0.8942 (p90) cc_final: 0.8511 (p-80) REVERT: D 201 VAL cc_start: 0.9250 (m) cc_final: 0.9044 (p) REVERT: D 211 ASP cc_start: 0.8849 (t70) cc_final: 0.8591 (m-30) REVERT: D 336 LYS cc_start: 0.8447 (mttt) cc_final: 0.7666 (ttmt) REVERT: D 355 MET cc_start: 0.9083 (mmm) cc_final: 0.8870 (mmm) REVERT: E 57 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8031 (mm-30) REVERT: E 82 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8580 (tpt) REVERT: E 132 MET cc_start: 0.8003 (ptm) cc_final: 0.6985 (ttp) REVERT: E 206 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7576 (ttm170) REVERT: E 246 GLN cc_start: 0.8865 (mt0) cc_final: 0.8526 (mt0) REVERT: E 249 THR cc_start: 0.8938 (m) cc_final: 0.8699 (p) REVERT: E 313 MET cc_start: 0.8630 (tpp) cc_final: 0.8148 (ttm) outliers start: 27 outliers final: 16 residues processed: 352 average time/residue: 0.2767 time to fit residues: 146.7898 Evaluate side-chains 262 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 181 optimal weight: 0.0870 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS E 115 ASN E 162 ASN E 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15220 Z= 0.197 Angle : 1.537 32.441 20660 Z= 0.561 Chirality : 0.045 0.174 2280 Planarity : 0.006 0.054 2630 Dihedral : 23.291 172.016 2185 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.28 % Favored : 95.63 % Rotamer: Outliers : 2.88 % Allowed : 11.57 % Favored : 85.56 % 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: 0.20 (0.20), residues: 1830 helix: 0.67 (0.19), residues: 770 sheet: -0.22 (0.30), residues: 250 loop : -0.12 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 86 HIS 0.006 0.001 HIS C 40 PHE 0.023 0.001 PHE A 352 TYR 0.012 0.001 TYR A 166 ARG 0.008 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8783 (tpt) cc_final: 0.8234 (tmm) REVERT: A 101 HIS cc_start: 0.7749 (m-70) cc_final: 0.7148 (m-70) REVERT: A 103 THR cc_start: 0.9166 (m) cc_final: 0.8942 (p) REVERT: A 238 LYS cc_start: 0.8554 (tptt) cc_final: 0.8304 (tttt) REVERT: A 269 MET cc_start: 0.7363 (tpp) cc_final: 0.6775 (tpt) REVERT: A 283 MET cc_start: 0.9051 (mmp) cc_final: 0.8850 (mmt) REVERT: A 298 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 328 LYS cc_start: 0.8608 (tmtt) cc_final: 0.8237 (tmtt) REVERT: B 24 ASP cc_start: 0.7768 (m-30) cc_final: 0.7476 (m-30) REVERT: B 78 ASN cc_start: 0.8482 (t0) cc_final: 0.7713 (t0) REVERT: B 80 ASP cc_start: 0.8523 (m-30) cc_final: 0.8214 (t0) REVERT: B 100 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 269 MET cc_start: 0.7867 (mmm) cc_final: 0.7355 (tpp) REVERT: B 355 MET cc_start: 0.8418 (mmp) cc_final: 0.8147 (mmm) REVERT: C 34 ILE cc_start: 0.9455 (mt) cc_final: 0.9255 (pt) REVERT: C 47 MET cc_start: 0.6520 (tpp) cc_final: 0.6054 (tpp) REVERT: C 66 THR cc_start: 0.9235 (m) cc_final: 0.8988 (p) REVERT: C 78 ASN cc_start: 0.8601 (t0) cc_final: 0.8298 (t0) REVERT: C 222 ASP cc_start: 0.7856 (t0) cc_final: 0.7392 (p0) REVERT: C 238 LYS cc_start: 0.8809 (tptt) cc_final: 0.8400 (ttmt) REVERT: C 305 MET cc_start: 0.8498 (mmm) cc_final: 0.8083 (mmm) REVERT: C 336 LYS cc_start: 0.8209 (mttt) cc_final: 0.7536 (ttpt) REVERT: C 349 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8484 (mp) REVERT: D 192 ILE cc_start: 0.9055 (mm) cc_final: 0.8810 (tp) REVERT: D 201 VAL cc_start: 0.9263 (m) cc_final: 0.9057 (p) REVERT: D 211 ASP cc_start: 0.8854 (t70) cc_final: 0.8576 (m-30) REVERT: D 227 MET cc_start: 0.8154 (mmm) cc_final: 0.7907 (mmm) REVERT: D 289 ILE cc_start: 0.8492 (mm) cc_final: 0.8146 (tt) REVERT: D 336 LYS cc_start: 0.8570 (mttt) cc_final: 0.8112 (mttp) REVERT: E 47 MET cc_start: 0.1951 (mtt) cc_final: 0.1618 (mtt) REVERT: E 57 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8190 (mm-30) REVERT: E 192 ILE cc_start: 0.9154 (mm) cc_final: 0.8929 (tp) REVERT: E 206 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7974 (ttm-80) REVERT: E 246 GLN cc_start: 0.8929 (mt0) cc_final: 0.8657 (mt0) REVERT: E 249 THR cc_start: 0.8968 (m) cc_final: 0.8736 (p) REVERT: E 313 MET cc_start: 0.8557 (tpp) cc_final: 0.8246 (ttm) outliers start: 45 outliers final: 29 residues processed: 309 average time/residue: 0.2294 time to fit residues: 109.7530 Evaluate side-chains 272 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 191 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 113 optimal weight: 0.0270 chunk 168 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15220 Z= 0.150 Angle : 1.514 32.449 20660 Z= 0.548 Chirality : 0.043 0.153 2280 Planarity : 0.005 0.050 2630 Dihedral : 22.834 178.346 2185 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 1.09 % Allowed : 2.79 % Favored : 96.12 % Rotamer: Outliers : 2.49 % Allowed : 13.74 % Favored : 83.77 % 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: 0.55 (0.20), residues: 1830 helix: 0.99 (0.19), residues: 740 sheet: 0.30 (0.29), residues: 275 loop : -0.08 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 86 HIS 0.005 0.001 HIS C 40 PHE 0.013 0.001 PHE B 223 TYR 0.017 0.001 TYR A 166 ARG 0.004 0.000 ARG D 372 *********************** 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 303 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 264 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8840 (mt) cc_final: 0.8620 (mt) REVERT: A 82 MET cc_start: 0.8922 (tpt) cc_final: 0.8294 (tmm) REVERT: A 238 LYS cc_start: 0.8592 (tptt) cc_final: 0.8322 (tttt) REVERT: A 269 MET cc_start: 0.7416 (tpp) cc_final: 0.6852 (tpt) REVERT: A 283 MET cc_start: 0.9012 (mmp) cc_final: 0.8668 (mmt) REVERT: A 328 LYS cc_start: 0.8559 (tmtt) cc_final: 0.8203 (tmtt) REVERT: A 360 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 24 ASP cc_start: 0.7780 (m-30) cc_final: 0.7514 (m-30) REVERT: B 80 ASP cc_start: 0.8519 (m-30) cc_final: 0.8293 (t0) REVERT: B 100 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7473 (tp30) REVERT: B 269 MET cc_start: 0.8001 (mmm) cc_final: 0.7463 (tpp) REVERT: C 47 MET cc_start: 0.6580 (tpp) cc_final: 0.6208 (tpp) REVERT: C 78 ASN cc_start: 0.8499 (t0) cc_final: 0.8179 (t0) REVERT: C 82 MET cc_start: 0.8876 (tpt) cc_final: 0.8642 (mmm) REVERT: C 140 LEU cc_start: 0.9227 (mm) cc_final: 0.9012 (mt) REVERT: C 238 LYS cc_start: 0.8845 (tptt) cc_final: 0.8439 (ttmt) REVERT: C 336 LYS cc_start: 0.8135 (mttt) cc_final: 0.7837 (mttt) REVERT: C 349 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 44 MET cc_start: 0.5176 (mmt) cc_final: 0.4933 (mtt) REVERT: D 82 MET cc_start: 0.8920 (tpt) cc_final: 0.8668 (mmm) REVERT: D 161 HIS cc_start: 0.9078 (p90) cc_final: 0.8623 (p90) REVERT: D 211 ASP cc_start: 0.8879 (t70) cc_final: 0.8607 (m-30) REVERT: D 269 MET cc_start: 0.7640 (tpp) cc_final: 0.7380 (tpt) REVERT: D 316 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7391 (mm-30) REVERT: D 336 LYS cc_start: 0.8242 (mttt) cc_final: 0.8014 (ttmt) REVERT: E 206 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7930 (ttm-80) REVERT: E 246 GLN cc_start: 0.8830 (mt0) cc_final: 0.8533 (mt0) REVERT: E 313 MET cc_start: 0.8440 (tpp) cc_final: 0.8203 (ttm) outliers start: 39 outliers final: 27 residues processed: 288 average time/residue: 0.2443 time to fit residues: 110.6344 Evaluate side-chains 271 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 9.9990 chunk 101 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 0.0670 chunk 73 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15220 Z= 0.337 Angle : 1.541 32.199 20660 Z= 0.566 Chirality : 0.047 0.196 2280 Planarity : 0.005 0.048 2630 Dihedral : 22.528 178.365 2185 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.55 % Favored : 95.36 % Rotamer: Outliers : 3.32 % Allowed : 14.19 % Favored : 82.49 % 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: 0.30 (0.20), residues: 1830 helix: 0.89 (0.19), residues: 730 sheet: -0.07 (0.30), residues: 280 loop : -0.21 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.007 0.001 HIS C 40 PHE 0.022 0.002 PHE B 223 TYR 0.018 0.001 TYR A 166 ARG 0.008 0.001 ARG E 116 *********************** 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 305 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 253 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.8641 (tptt) cc_final: 0.8336 (tttt) REVERT: A 269 MET cc_start: 0.7522 (tpp) cc_final: 0.6982 (tpt) REVERT: A 283 MET cc_start: 0.8875 (mmp) cc_final: 0.8610 (mmt) REVERT: A 328 LYS cc_start: 0.8641 (tmtt) cc_final: 0.8272 (tmtt) REVERT: A 360 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 24 ASP cc_start: 0.7852 (m-30) cc_final: 0.7608 (m-30) REVERT: B 78 ASN cc_start: 0.8561 (t0) cc_final: 0.7716 (t0) REVERT: B 80 ASP cc_start: 0.8597 (m-30) cc_final: 0.8278 (t0) REVERT: B 100 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7661 (tp30) REVERT: B 269 MET cc_start: 0.8038 (mmm) cc_final: 0.7438 (tpp) REVERT: C 47 MET cc_start: 0.7214 (tpp) cc_final: 0.6783 (tpp) REVERT: C 66 THR cc_start: 0.9354 (m) cc_final: 0.8976 (p) REVERT: C 78 ASN cc_start: 0.8466 (t0) cc_final: 0.7722 (t0) REVERT: C 81 ASP cc_start: 0.8778 (m-30) cc_final: 0.8453 (m-30) REVERT: C 132 MET cc_start: 0.8466 (ppp) cc_final: 0.8038 (ptt) REVERT: C 238 LYS cc_start: 0.8879 (tptt) cc_final: 0.8480 (ttmt) REVERT: C 336 LYS cc_start: 0.8205 (mttt) cc_final: 0.7791 (mttt) REVERT: C 349 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8629 (mp) REVERT: D 192 ILE cc_start: 0.9075 (mm) cc_final: 0.8848 (tp) REVERT: D 211 ASP cc_start: 0.8857 (t70) cc_final: 0.8621 (m-30) REVERT: D 269 MET cc_start: 0.7803 (tpp) cc_final: 0.7540 (tpt) REVERT: D 316 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7536 (mm-30) REVERT: E 246 GLN cc_start: 0.8894 (mt0) cc_final: 0.8609 (mt0) REVERT: E 313 MET cc_start: 0.8780 (tpp) cc_final: 0.8472 (ttm) REVERT: E 325 MET cc_start: 0.8006 (mmt) cc_final: 0.7378 (mmm) REVERT: E 354 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8326 (tp-100) outliers start: 52 outliers final: 42 residues processed: 289 average time/residue: 0.2270 time to fit residues: 102.8772 Evaluate side-chains 279 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.0050 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 59 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15220 Z= 0.332 Angle : 1.541 32.196 20660 Z= 0.566 Chirality : 0.046 0.199 2280 Planarity : 0.005 0.046 2630 Dihedral : 22.598 178.434 2185 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.50 % Favored : 95.41 % Rotamer: Outliers : 2.81 % Allowed : 15.53 % Favored : 81.66 % 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: 0.29 (0.20), residues: 1830 helix: 0.88 (0.19), residues: 730 sheet: -0.07 (0.30), residues: 280 loop : -0.22 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 86 HIS 0.007 0.001 HIS C 40 PHE 0.020 0.001 PHE B 223 TYR 0.021 0.001 TYR A 166 ARG 0.007 0.000 ARG E 116 *********************** 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 279 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.8635 (tptt) cc_final: 0.8335 (tttt) REVERT: A 269 MET cc_start: 0.7521 (tpp) cc_final: 0.6981 (tpt) REVERT: A 283 MET cc_start: 0.8877 (mmp) cc_final: 0.8610 (mmt) REVERT: A 328 LYS cc_start: 0.8654 (tmtt) cc_final: 0.8269 (tmtt) REVERT: A 360 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 24 ASP cc_start: 0.7852 (m-30) cc_final: 0.7606 (m-30) REVERT: B 78 ASN cc_start: 0.8567 (t0) cc_final: 0.7715 (t0) REVERT: B 80 ASP cc_start: 0.8594 (m-30) cc_final: 0.8278 (t0) REVERT: B 100 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7662 (tp30) REVERT: B 269 MET cc_start: 0.8056 (mmm) cc_final: 0.7439 (tpp) REVERT: C 47 MET cc_start: 0.7208 (tpp) cc_final: 0.6784 (tpp) REVERT: C 66 THR cc_start: 0.9356 (m) cc_final: 0.8974 (p) REVERT: C 78 ASN cc_start: 0.8451 (t0) cc_final: 0.7720 (t0) REVERT: C 81 ASP cc_start: 0.8760 (m-30) cc_final: 0.8447 (m-30) REVERT: C 132 MET cc_start: 0.8461 (ppp) cc_final: 0.8037 (ptt) REVERT: C 238 LYS cc_start: 0.8883 (tptt) cc_final: 0.8478 (ttmt) REVERT: C 336 LYS cc_start: 0.8205 (mttt) cc_final: 0.7783 (mttt) REVERT: C 349 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8627 (mp) REVERT: D 192 ILE cc_start: 0.9073 (mm) cc_final: 0.8846 (tp) REVERT: D 211 ASP cc_start: 0.8871 (t70) cc_final: 0.8619 (m-30) REVERT: D 269 MET cc_start: 0.7798 (tpp) cc_final: 0.7538 (tpt) REVERT: D 316 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7534 (mm-30) REVERT: E 246 GLN cc_start: 0.8895 (mt0) cc_final: 0.8610 (mt0) REVERT: E 313 MET cc_start: 0.8781 (tpp) cc_final: 0.8471 (ttm) REVERT: E 325 MET cc_start: 0.8011 (mmt) cc_final: 0.7381 (mmm) REVERT: E 354 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8328 (tp-100) outliers start: 44 outliers final: 42 residues processed: 265 average time/residue: 0.2206 time to fit residues: 92.0411 Evaluate side-chains 278 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 235 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 0.0070 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15220 Z= 0.161 Angle : 1.512 32.169 20660 Z= 0.547 Chirality : 0.043 0.147 2280 Planarity : 0.005 0.045 2630 Dihedral : 22.351 179.168 2185 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.01 % Favored : 95.90 % Rotamer: Outliers : 2.62 % Allowed : 15.46 % Favored : 81.92 % 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: 0.93 (0.19), residues: 740 sheet: 0.48 (0.31), residues: 270 loop : -0.24 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 86 HIS 0.004 0.001 HIS C 40 PHE 0.011 0.001 PHE B 223 TYR 0.027 0.001 TYR A 166 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 236 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8367 (tt0) cc_final: 0.8157 (mt-10) REVERT: A 238 LYS cc_start: 0.8614 (tptt) cc_final: 0.8328 (tttt) REVERT: A 283 MET cc_start: 0.8903 (mmp) cc_final: 0.8601 (mmt) REVERT: A 328 LYS cc_start: 0.8542 (tmtt) cc_final: 0.8132 (tmtt) REVERT: B 24 ASP cc_start: 0.7791 (m-30) cc_final: 0.7510 (m-30) REVERT: B 80 ASP cc_start: 0.8519 (m-30) cc_final: 0.8223 (t0) REVERT: B 100 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7617 (tp30) REVERT: B 269 MET cc_start: 0.8067 (mmm) cc_final: 0.7458 (tpp) REVERT: C 47 MET cc_start: 0.7187 (tpp) cc_final: 0.6846 (tpp) REVERT: C 78 ASN cc_start: 0.8459 (t0) cc_final: 0.8237 (t0) REVERT: C 82 MET cc_start: 0.9074 (mmm) cc_final: 0.8803 (tpp) REVERT: C 132 MET cc_start: 0.8586 (ppp) cc_final: 0.8184 (ptt) REVERT: C 140 LEU cc_start: 0.9298 (mm) cc_final: 0.8944 (mt) REVERT: C 238 LYS cc_start: 0.8900 (tptt) cc_final: 0.8497 (ttmt) REVERT: C 336 LYS cc_start: 0.8022 (mttt) cc_final: 0.7475 (ttpt) REVERT: D 211 ASP cc_start: 0.8844 (t70) cc_final: 0.8587 (m-30) REVERT: D 316 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7510 (mm-30) REVERT: E 82 MET cc_start: 0.8963 (tpt) cc_final: 0.8587 (tpt) REVERT: E 246 GLN cc_start: 0.8848 (mt0) cc_final: 0.8529 (mt0) REVERT: E 325 MET cc_start: 0.7955 (mmt) cc_final: 0.7393 (mmm) REVERT: E 354 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8337 (tp-100) outliers start: 41 outliers final: 29 residues processed: 259 average time/residue: 0.2196 time to fit residues: 89.1331 Evaluate side-chains 254 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 334 GLU 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: 0.0970 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 0.0870 chunk 113 optimal weight: 0.0980 chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15220 Z= 0.158 Angle : 1.513 32.214 20660 Z= 0.546 Chirality : 0.044 0.207 2280 Planarity : 0.005 0.044 2630 Dihedral : 22.309 179.936 2185 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.17 % Favored : 95.74 % Rotamer: Outliers : 2.62 % Allowed : 15.91 % Favored : 81.47 % 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: 0.91 (0.19), residues: 740 sheet: 0.50 (0.32), residues: 270 loop : -0.23 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 86 HIS 0.004 0.001 HIS C 40 PHE 0.012 0.001 PHE E 31 TYR 0.030 0.001 TYR A 166 ARG 0.007 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.8616 (tptt) cc_final: 0.8332 (tttt) REVERT: A 283 MET cc_start: 0.8898 (mmp) cc_final: 0.8609 (mmt) REVERT: A 328 LYS cc_start: 0.8519 (tmtt) cc_final: 0.8115 (tmtt) REVERT: B 24 ASP cc_start: 0.7794 (m-30) cc_final: 0.7508 (m-30) REVERT: B 80 ASP cc_start: 0.8525 (m-30) cc_final: 0.8229 (t0) REVERT: B 100 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7626 (tp30) REVERT: C 47 MET cc_start: 0.7192 (tpp) cc_final: 0.6864 (tpp) REVERT: C 82 MET cc_start: 0.9084 (mmm) cc_final: 0.8211 (tpt) REVERT: C 132 MET cc_start: 0.8608 (ppp) cc_final: 0.8207 (ptt) REVERT: C 238 LYS cc_start: 0.8881 (tptt) cc_final: 0.8475 (ttmt) REVERT: C 336 LYS cc_start: 0.7998 (mttt) cc_final: 0.7409 (ttpt) REVERT: D 44 MET cc_start: 0.5362 (mmt) cc_final: 0.5000 (mtt) REVERT: D 82 MET cc_start: 0.8893 (tpt) cc_final: 0.8675 (tpt) REVERT: D 211 ASP cc_start: 0.8841 (t70) cc_final: 0.8585 (m-30) REVERT: D 227 MET cc_start: 0.8294 (mmm) cc_final: 0.8082 (mmm) REVERT: D 316 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 82 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8587 (tpt) REVERT: E 246 GLN cc_start: 0.8840 (mt0) cc_final: 0.8517 (mt0) REVERT: E 313 MET cc_start: 0.8590 (ttm) cc_final: 0.8127 (ttm) REVERT: E 325 MET cc_start: 0.7969 (mmt) cc_final: 0.7406 (mmm) REVERT: E 354 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8329 (tp-100) outliers start: 41 outliers final: 35 residues processed: 259 average time/residue: 0.2228 time to fit residues: 90.2520 Evaluate side-chains 259 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 0.0870 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15220 Z= 0.158 Angle : 1.512 32.214 20660 Z= 0.546 Chirality : 0.044 0.206 2280 Planarity : 0.005 0.044 2630 Dihedral : 22.322 179.936 2185 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.17 % Favored : 95.74 % Rotamer: Outliers : 2.30 % Allowed : 16.55 % Favored : 81.15 % 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: 0.45 (0.20), residues: 1830 helix: 0.91 (0.19), residues: 740 sheet: 0.50 (0.32), residues: 270 loop : -0.23 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 86 HIS 0.004 0.001 HIS C 40 PHE 0.012 0.001 PHE E 31 TYR 0.030 0.001 TYR A 166 ARG 0.007 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.8628 (tptt) cc_final: 0.8332 (tttt) REVERT: A 283 MET cc_start: 0.8897 (mmp) cc_final: 0.8609 (mmt) REVERT: A 328 LYS cc_start: 0.8524 (tmtt) cc_final: 0.8115 (tmtt) REVERT: B 24 ASP cc_start: 0.7795 (m-30) cc_final: 0.7508 (m-30) REVERT: B 80 ASP cc_start: 0.8526 (m-30) cc_final: 0.8229 (t0) REVERT: B 100 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7627 (tp30) REVERT: C 47 MET cc_start: 0.7184 (tpp) cc_final: 0.6864 (tpp) REVERT: C 82 MET cc_start: 0.9095 (mmm) cc_final: 0.8212 (tpt) REVERT: C 132 MET cc_start: 0.8610 (ppp) cc_final: 0.8207 (ptt) REVERT: C 238 LYS cc_start: 0.8880 (tptt) cc_final: 0.8475 (ttmt) REVERT: C 336 LYS cc_start: 0.7998 (mttt) cc_final: 0.7409 (ttpt) REVERT: D 44 MET cc_start: 0.5355 (mmt) cc_final: 0.5000 (mtt) REVERT: D 82 MET cc_start: 0.8893 (tpt) cc_final: 0.8676 (tpt) REVERT: D 211 ASP cc_start: 0.8844 (t70) cc_final: 0.8585 (m-30) REVERT: D 227 MET cc_start: 0.8294 (mmm) cc_final: 0.8082 (mmm) REVERT: D 316 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 82 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8587 (tpt) REVERT: E 246 GLN cc_start: 0.8842 (mt0) cc_final: 0.8517 (mt0) REVERT: E 313 MET cc_start: 0.8582 (ttm) cc_final: 0.8127 (ttm) REVERT: E 325 MET cc_start: 0.7971 (mmt) cc_final: 0.7406 (mmm) REVERT: E 354 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8329 (tp-100) outliers start: 36 outliers final: 35 residues processed: 246 average time/residue: 0.2214 time to fit residues: 85.4401 Evaluate side-chains 259 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 122 optimal weight: 0.7980 chunk 184 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15220 Z= 0.158 Angle : 1.512 32.214 20660 Z= 0.546 Chirality : 0.044 0.206 2280 Planarity : 0.005 0.044 2630 Dihedral : 22.310 179.936 2185 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.17 % Favored : 95.74 % Rotamer: Outliers : 2.30 % Allowed : 16.55 % Favored : 81.15 % 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: 0.45 (0.20), residues: 1830 helix: 0.91 (0.19), residues: 740 sheet: 0.50 (0.32), residues: 270 loop : -0.23 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 86 HIS 0.004 0.001 HIS C 40 PHE 0.012 0.001 PHE E 31 TYR 0.030 0.001 TYR A 166 ARG 0.007 0.000 ARG E 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.8628 (tptt) cc_final: 0.8332 (tttt) REVERT: A 283 MET cc_start: 0.8897 (mmp) cc_final: 0.8609 (mmt) REVERT: A 328 LYS cc_start: 0.8524 (tmtt) cc_final: 0.8115 (tmtt) REVERT: B 24 ASP cc_start: 0.7795 (m-30) cc_final: 0.7508 (m-30) REVERT: B 80 ASP cc_start: 0.8526 (m-30) cc_final: 0.8229 (t0) REVERT: B 100 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7627 (tp30) REVERT: C 47 MET cc_start: 0.7184 (tpp) cc_final: 0.6864 (tpp) REVERT: C 82 MET cc_start: 0.9095 (mmm) cc_final: 0.8212 (tpt) REVERT: C 132 MET cc_start: 0.8610 (ppp) cc_final: 0.8207 (ptt) REVERT: C 238 LYS cc_start: 0.8880 (tptt) cc_final: 0.8475 (ttmt) REVERT: C 336 LYS cc_start: 0.7998 (mttt) cc_final: 0.7409 (ttpt) REVERT: D 44 MET cc_start: 0.5355 (mmt) cc_final: 0.5000 (mtt) REVERT: D 82 MET cc_start: 0.8893 (tpt) cc_final: 0.8676 (tpt) REVERT: D 211 ASP cc_start: 0.8844 (t70) cc_final: 0.8585 (m-30) REVERT: D 227 MET cc_start: 0.8294 (mmm) cc_final: 0.8082 (mmm) REVERT: D 316 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 82 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8587 (tpt) REVERT: E 246 GLN cc_start: 0.8842 (mt0) cc_final: 0.8517 (mt0) REVERT: E 313 MET cc_start: 0.8582 (ttm) cc_final: 0.8127 (ttm) REVERT: E 325 MET cc_start: 0.7971 (mmt) cc_final: 0.7406 (mmm) REVERT: E 354 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8329 (tp-100) outliers start: 36 outliers final: 35 residues processed: 246 average time/residue: 0.2235 time to fit residues: 86.5563 Evaluate side-chains 259 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 61 optimal weight: 0.0170 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 0.1980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104097 restraints weight = 23198.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107137 restraints weight = 12148.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109111 restraints weight = 7602.949| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15220 Z= 0.157 Angle : 1.517 32.187 20660 Z= 0.548 Chirality : 0.044 0.189 2280 Planarity : 0.005 0.050 2630 Dihedral : 22.277 179.492 2185 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 1.04 % Allowed : 3.06 % Favored : 95.90 % Rotamer: Outliers : 2.56 % Allowed : 16.36 % Favored : 81.09 % 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: 0.44 (0.20), residues: 1830 helix: 0.89 (0.19), residues: 740 sheet: 0.52 (0.32), residues: 270 loop : -0.23 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 86 HIS 0.004 0.001 HIS C 40 PHE 0.016 0.001 PHE D 375 TYR 0.034 0.001 TYR A 166 ARG 0.008 0.000 ARG E 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3067.35 seconds wall clock time: 56 minutes 48.90 seconds (3408.90 seconds total)