Starting phenix.real_space_refine on Fri Feb 16 09:51:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t24_10366/02_2024/6t24_10366_updated.pdb" } resolution = 3.7 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2865 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 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 375": "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: 14910 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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.83, per 1000 atoms: 0.53 Number of scatterers: 14910 At special positions: 0 Unit cell: (96.32, 92.96, 192.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 15 15.00 Mg 5 11.99 O 2865 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: 5.38 Conformation dependent library (CDL) restraints added in 2.8 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: 105 helices and 20 sheets defined 45.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.826A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.542A 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 232 removed outlier: 3.921A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 252 through 261 removed outlier: 4.840A 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 295 removed outlier: 4.421A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.231A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' 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 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.826A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.542A 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 232 removed outlier: 3.921A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 252 through 261 removed outlier: 4.840A 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 295 removed outlier: 4.422A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.231A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' 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 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.826A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.543A 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 232 removed outlier: 3.921A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.839A 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 295 removed outlier: 4.422A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.230A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' 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 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.826A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.543A 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 232 removed outlier: 3.921A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 252 through 261 removed outlier: 4.840A 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 295 removed outlier: 4.422A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.231A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' 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 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.827A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.542A 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 232 removed outlier: 3.920A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 252 through 261 removed outlier: 4.839A 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 295 removed outlier: 4.421A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.230A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' 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: 6.684A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.142A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.191A 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: 6.684A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.190A 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: 6.684A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.191A 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: 6.684A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.192A 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: 6.684A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.190A 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: 4.59 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2478 1.29 - 1.43: 3885 1.43 - 1.56: 8566 1.56 - 1.69: 126 1.69 - 1.83: 185 Bond restraints: 15240 Sorted by residual: bond pdb=" C07 9ZK E 379 " pdb=" C08 9ZK E 379 " ideal model delta sigma weight residual 2.679 1.524 1.155 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C07 9ZK C 379 " pdb=" C08 9ZK C 379 " ideal model delta sigma weight residual 2.679 1.525 1.154 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C07 9ZK A 379 " pdb=" C08 9ZK A 379 " ideal model delta sigma weight residual 2.679 1.525 1.154 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C07 9ZK D 379 " pdb=" C08 9ZK D 379 " ideal model delta sigma weight residual 2.679 1.525 1.154 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C07 9ZK B 379 " pdb=" C08 9ZK B 379 " ideal model delta sigma weight residual 2.679 1.525 1.154 2.00e-02 2.50e+03 3.33e+03 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 97.35 - 105.03: 442 105.03 - 112.72: 7399 112.72 - 120.40: 7408 120.40 - 128.09: 5300 128.09 - 135.77: 141 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C41 9ZK B 379 " pdb=" C42 9ZK B 379 " pdb=" O43 9ZK B 379 " ideal model delta sigma weight residual 59.79 118.00 -58.21 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C41 9ZK C 379 " pdb=" C42 9ZK C 379 " pdb=" O43 9ZK C 379 " ideal model delta sigma weight residual 59.79 117.99 -58.20 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C41 9ZK A 379 " pdb=" C42 9ZK A 379 " pdb=" O43 9ZK A 379 " ideal model delta sigma weight residual 59.79 117.98 -58.19 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C41 9ZK E 379 " pdb=" C42 9ZK E 379 " pdb=" O43 9ZK E 379 " ideal model delta sigma weight residual 59.79 117.98 -58.19 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C41 9ZK D 379 " pdb=" C42 9ZK D 379 " pdb=" O43 9ZK D 379 " ideal model delta sigma weight residual 59.79 117.97 -58.18 3.00e+00 1.11e-01 3.76e+02 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 8915 35.09 - 70.17: 110 70.17 - 105.26: 30 105.26 - 140.35: 25 140.35 - 175.44: 15 Dihedral angle restraints: 9095 sinusoidal: 3735 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP A 376 " pdb=" O3A ADP A 376 " pdb=" PB ADP A 376 " pdb=" PA ADP A 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.82 -149.83 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP D 376 " pdb=" O3A ADP D 376 " pdb=" PB ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.80 -149.81 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP C 376 " pdb=" O3A ADP C 376 " pdb=" PB ADP C 376 " pdb=" PA ADP C 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.80 -149.80 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 9092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.860: 2270 0.860 - 1.720: 5 1.720 - 2.580: 0 2.580 - 3.440: 0 3.440 - 4.300: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C16 9ZK E 379 " pdb=" C17 9ZK E 379 " pdb=" C22 9ZK E 379 " pdb=" N15 9ZK E 379 " both_signs ideal model delta sigma weight residual False 1.76 -2.54 4.30 2.00e-01 2.50e+01 4.62e+02 chirality pdb=" C16 9ZK C 379 " pdb=" C17 9ZK C 379 " pdb=" C22 9ZK C 379 " pdb=" N15 9ZK C 379 " both_signs ideal model delta sigma weight residual False 1.76 -2.53 4.30 2.00e-01 2.50e+01 4.62e+02 chirality pdb=" C16 9ZK D 379 " pdb=" C17 9ZK D 379 " pdb=" C22 9ZK D 379 " pdb=" N15 9ZK D 379 " both_signs ideal model delta sigma weight residual False 1.76 -2.53 4.30 2.00e-01 2.50e+01 4.61e+02 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 375 " -0.031 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" C PHE A 375 " 0.110 2.00e-02 2.50e+03 pdb=" O PHE A 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE A 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 375 " -0.031 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C PHE E 375 " 0.110 2.00e-02 2.50e+03 pdb=" O PHE E 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE E 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 375 " 0.031 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C PHE B 375 " -0.110 2.00e-02 2.50e+03 pdb=" O PHE B 375 " 0.039 2.00e-02 2.50e+03 pdb=" OXT PHE B 375 " 0.039 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 490 2.66 - 3.22: 14875 3.22 - 3.78: 23761 3.78 - 4.34: 34300 4.34 - 4.90: 53677 Nonbonded interactions: 127103 Sorted by model distance: nonbonded pdb=" N SER B 14 " pdb=" O1 PO4 B 377 " model vdw 2.104 2.520 nonbonded pdb=" N SER E 14 " pdb=" O1 PO4 E 377 " model vdw 2.104 2.520 nonbonded pdb=" N SER C 14 " pdb=" O1 PO4 C 377 " model vdw 2.104 2.520 nonbonded pdb=" N SER A 14 " pdb=" O1 PO4 A 377 " model vdw 2.104 2.520 nonbonded pdb=" N SER D 14 " pdb=" O1 PO4 D 377 " model vdw 2.105 2.520 ... (remaining 127098 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) selection = (chain 'B' and resid 5 through 375) selection = (chain 'C' and resid 5 through 375) selection = (chain 'D' and resid 5 through 375) selection = (chain 'E' and resid 5 through 375) } 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.310 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 41.470 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 1.155 15240 Z= 3.061 Angle : 3.181 58.206 20690 Z= 1.455 Chirality : 0.234 4.300 2280 Planarity : 0.009 0.063 2630 Dihedral : 16.985 175.435 5665 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1830 helix: -0.66 (0.16), residues: 760 sheet: 0.72 (0.31), residues: 270 loop : 2.00 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.013 TRP A 340 HIS 0.004 0.001 HIS B 161 PHE 0.030 0.005 PHE A 200 TYR 0.045 0.008 TYR B 188 ARG 0.007 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 619 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8886 (mt) cc_final: 0.8578 (mp) REVERT: A 226 GLU cc_start: 0.8228 (tp30) cc_final: 0.7823 (mm-30) REVERT: A 259 GLU cc_start: 0.8580 (tp30) cc_final: 0.7698 (tp30) REVERT: A 283 MET cc_start: 0.7975 (mmm) cc_final: 0.7616 (mmm) REVERT: A 290 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7838 (mtm180) REVERT: B 25 ASP cc_start: 0.7361 (p0) cc_final: 0.7070 (t0) REVERT: B 118 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7850 (mmtt) REVERT: B 157 ASP cc_start: 0.6615 (t70) cc_final: 0.5983 (t0) REVERT: B 269 MET cc_start: 0.7406 (mtt) cc_final: 0.7160 (mtp) REVERT: B 283 MET cc_start: 0.8554 (mmm) cc_final: 0.8336 (mmt) REVERT: B 284 LYS cc_start: 0.8204 (mttm) cc_final: 0.7868 (tptp) REVERT: B 309 ILE cc_start: 0.8527 (tp) cc_final: 0.8260 (tt) REVERT: B 316 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8174 (mm-30) REVERT: C 39 ARG cc_start: 0.6726 (ttp-170) cc_final: 0.6134 (ttp80) REVERT: C 123 MET cc_start: 0.8212 (mmt) cc_final: 0.7938 (mmm) REVERT: C 152 VAL cc_start: 0.9026 (t) cc_final: 0.8776 (p) REVERT: C 187 ASP cc_start: 0.8049 (t70) cc_final: 0.7841 (m-30) REVERT: C 190 MET cc_start: 0.8412 (mtp) cc_final: 0.8198 (mtp) REVERT: D 64 ILE cc_start: 0.8925 (tt) cc_final: 0.8691 (mt) REVERT: D 81 ASP cc_start: 0.7872 (m-30) cc_final: 0.7637 (m-30) REVERT: D 116 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7427 (mtm-85) REVERT: D 152 VAL cc_start: 0.9503 (t) cc_final: 0.9291 (p) REVERT: D 180 LEU cc_start: 0.8111 (tp) cc_final: 0.7799 (pp) REVERT: D 283 MET cc_start: 0.7688 (mmm) cc_final: 0.7236 (ttp) REVERT: D 346 LEU cc_start: 0.8679 (tp) cc_final: 0.8292 (tp) REVERT: E 104 LEU cc_start: 0.8917 (tp) cc_final: 0.8679 (tt) outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.2961 time to fit residues: 261.4237 Evaluate side-chains 301 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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: 1.9990 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN D 225 ASN D 371 HIS E 12 ASN E 111 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15240 Z= 0.232 Angle : 1.551 32.511 20690 Z= 0.568 Chirality : 0.048 0.211 2280 Planarity : 0.005 0.039 2630 Dihedral : 20.663 152.566 2185 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.00 % Allowed : 12.20 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1830 helix: 0.58 (0.18), residues: 720 sheet: 0.92 (0.29), residues: 320 loop : 2.16 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 340 HIS 0.007 0.002 HIS E 173 PHE 0.014 0.001 PHE C 255 TYR 0.023 0.002 TYR E 294 ARG 0.008 0.001 ARG E 254 *********************** 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 374 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 327 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7994 (mm-30) REVERT: A 154 ASP cc_start: 0.8819 (t0) cc_final: 0.8316 (t70) REVERT: A 259 GLU cc_start: 0.8643 (tp30) cc_final: 0.7886 (tp30) REVERT: A 283 MET cc_start: 0.8154 (mmm) cc_final: 0.7795 (mmm) REVERT: A 290 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7672 (mtm180) REVERT: A 355 MET cc_start: 0.8305 (mmm) cc_final: 0.8098 (mmt) REVERT: B 47 MET cc_start: 0.3175 (mtt) cc_final: 0.2615 (ptp) REVERT: B 118 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7898 (mmtt) REVERT: B 179 ASP cc_start: 0.7451 (m-30) cc_final: 0.7127 (m-30) REVERT: B 244 ASP cc_start: 0.8322 (p0) cc_final: 0.7725 (t0) REVERT: B 259 GLU cc_start: 0.8347 (tp30) cc_final: 0.7970 (tp30) REVERT: B 269 MET cc_start: 0.7463 (mtt) cc_final: 0.7199 (mtp) REVERT: B 284 LYS cc_start: 0.8275 (mttm) cc_final: 0.7888 (tptp) REVERT: C 244 ASP cc_start: 0.8845 (p0) cc_final: 0.7683 (t0) REVERT: D 115 ASN cc_start: 0.8546 (t0) cc_final: 0.8323 (t0) REVERT: D 167 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7368 (mp0) REVERT: D 246 GLN cc_start: 0.8530 (mt0) cc_final: 0.8251 (mt0) REVERT: D 283 MET cc_start: 0.7837 (mmm) cc_final: 0.7421 (ttp) REVERT: D 346 LEU cc_start: 0.8692 (tp) cc_final: 0.8382 (tp) REVERT: E 14 SER cc_start: 0.7800 (m) cc_final: 0.7271 (p) outliers start: 47 outliers final: 31 residues processed: 362 average time/residue: 0.2542 time to fit residues: 140.8114 Evaluate side-chains 284 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 168 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 115 ASN D 162 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN E 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15240 Z= 0.180 Angle : 1.502 32.335 20690 Z= 0.538 Chirality : 0.044 0.154 2280 Planarity : 0.004 0.032 2630 Dihedral : 19.249 173.032 2185 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.07 % Allowed : 13.99 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1830 helix: 0.69 (0.18), residues: 755 sheet: 0.88 (0.29), residues: 325 loop : 2.00 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 79 HIS 0.004 0.001 HIS A 371 PHE 0.021 0.001 PHE E 352 TYR 0.014 0.001 TYR C 294 ARG 0.004 0.000 ARG C 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 341 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 293 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8761 (mttt) cc_final: 0.8406 (mtpt) REVERT: A 259 GLU cc_start: 0.8648 (tp30) cc_final: 0.7845 (tp30) REVERT: A 269 MET cc_start: 0.8018 (mtt) cc_final: 0.7764 (mtt) REVERT: A 355 MET cc_start: 0.8356 (mmm) cc_final: 0.8075 (mmt) REVERT: B 118 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7777 (mmtp) REVERT: B 244 ASP cc_start: 0.8556 (p0) cc_final: 0.7907 (t0) REVERT: B 259 GLU cc_start: 0.8345 (tp30) cc_final: 0.7944 (tp30) REVERT: B 283 MET cc_start: 0.8542 (mmt) cc_final: 0.8329 (mmt) REVERT: B 284 LYS cc_start: 0.8163 (mttm) cc_final: 0.7924 (tptp) REVERT: B 369 ILE cc_start: 0.9083 (tp) cc_final: 0.8883 (tp) REVERT: C 225 ASN cc_start: 0.7666 (m-40) cc_final: 0.7385 (t0) REVERT: C 244 ASP cc_start: 0.8847 (p0) cc_final: 0.7705 (t0) REVERT: D 115 ASN cc_start: 0.8407 (t0) cc_final: 0.7944 (t0) REVERT: D 167 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7265 (mp0) REVERT: D 176 MET cc_start: 0.8618 (mtp) cc_final: 0.8417 (ttm) REVERT: D 283 MET cc_start: 0.7826 (mmm) cc_final: 0.7378 (ttp) REVERT: D 346 LEU cc_start: 0.8741 (tp) cc_final: 0.8431 (tp) REVERT: E 14 SER cc_start: 0.7658 (m) cc_final: 0.7239 (p) REVERT: E 67 LEU cc_start: 0.8892 (mp) cc_final: 0.8682 (mp) REVERT: E 123 MET cc_start: 0.7627 (mmp) cc_final: 0.7109 (tpp) REVERT: E 226 GLU cc_start: 0.7604 (tp30) cc_final: 0.7286 (tp30) outliers start: 48 outliers final: 33 residues processed: 328 average time/residue: 0.2391 time to fit residues: 121.3746 Evaluate side-chains 283 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 0.0870 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 137 GLN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15240 Z= 0.452 Angle : 1.558 32.409 20690 Z= 0.578 Chirality : 0.050 0.269 2280 Planarity : 0.005 0.043 2630 Dihedral : 19.522 168.554 2185 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 5.11 % Allowed : 14.70 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1830 helix: 0.36 (0.19), residues: 730 sheet: 0.51 (0.29), residues: 315 loop : 1.13 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 79 HIS 0.005 0.001 HIS C 88 PHE 0.018 0.002 PHE E 352 TYR 0.019 0.002 TYR C 294 ARG 0.008 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 246 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8782 (mttt) cc_final: 0.8514 (mmtp) REVERT: A 178 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8039 (mm) REVERT: A 259 GLU cc_start: 0.8599 (tp30) cc_final: 0.7893 (tp30) REVERT: A 299 MET cc_start: 0.7959 (tpp) cc_final: 0.7732 (tpp) REVERT: A 352 PHE cc_start: 0.8594 (t80) cc_final: 0.8365 (t80) REVERT: B 64 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8675 (tp) REVERT: B 81 ASP cc_start: 0.8199 (m-30) cc_final: 0.7843 (m-30) REVERT: B 82 MET cc_start: 0.8264 (tpt) cc_final: 0.7849 (tpt) REVERT: B 118 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7969 (mmtt) REVERT: B 176 MET cc_start: 0.8228 (mmm) cc_final: 0.7788 (mpp) REVERT: B 244 ASP cc_start: 0.8445 (p0) cc_final: 0.7991 (t0) REVERT: B 284 LYS cc_start: 0.8283 (mttm) cc_final: 0.8064 (tptp) REVERT: D 283 MET cc_start: 0.7948 (mmm) cc_final: 0.7476 (ttp) REVERT: D 346 LEU cc_start: 0.8835 (tp) cc_final: 0.8296 (tp) REVERT: E 14 SER cc_start: 0.7646 (m) cc_final: 0.7008 (p) REVERT: E 271 SER cc_start: 0.8705 (m) cc_final: 0.8335 (p) outliers start: 80 outliers final: 56 residues processed: 301 average time/residue: 0.2260 time to fit residues: 105.4564 Evaluate side-chains 282 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 152 optimal weight: 0.0670 chunk 123 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 173 HIS E 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15240 Z= 0.199 Angle : 1.498 32.236 20690 Z= 0.535 Chirality : 0.044 0.140 2280 Planarity : 0.004 0.043 2630 Dihedral : 18.878 148.322 2185 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.90 % Allowed : 15.97 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1830 helix: 0.60 (0.19), residues: 725 sheet: 0.37 (0.29), residues: 325 loop : 1.32 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.003 0.001 HIS C 161 PHE 0.016 0.001 PHE E 352 TYR 0.013 0.001 TYR C 294 ARG 0.003 0.000 ARG E 254 *********************** 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 304 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 243 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8753 (mttt) cc_final: 0.8483 (mmtp) REVERT: A 259 GLU cc_start: 0.8565 (tp30) cc_final: 0.7848 (tp30) REVERT: A 299 MET cc_start: 0.7838 (tpp) cc_final: 0.7579 (tpp) REVERT: A 352 PHE cc_start: 0.8638 (t80) cc_final: 0.8413 (t80) REVERT: B 81 ASP cc_start: 0.8053 (m-30) cc_final: 0.7626 (m-30) REVERT: B 82 MET cc_start: 0.8271 (tpt) cc_final: 0.7939 (tpt) REVERT: B 118 LYS cc_start: 0.8311 (mmmt) cc_final: 0.8090 (mttt) REVERT: B 244 ASP cc_start: 0.8565 (p0) cc_final: 0.8152 (t0) REVERT: C 167 GLU cc_start: 0.7978 (mp0) cc_final: 0.7670 (mp0) REVERT: C 244 ASP cc_start: 0.8933 (p0) cc_final: 0.7905 (t0) REVERT: C 288 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: D 283 MET cc_start: 0.7828 (mmm) cc_final: 0.7337 (ttp) REVERT: D 346 LEU cc_start: 0.8883 (tp) cc_final: 0.8524 (tp) REVERT: E 14 SER cc_start: 0.7081 (m) cc_final: 0.6728 (p) REVERT: E 121 GLN cc_start: 0.8680 (tp40) cc_final: 0.8328 (tp40) REVERT: E 123 MET cc_start: 0.7476 (mmp) cc_final: 0.7204 (tpp) outliers start: 61 outliers final: 36 residues processed: 281 average time/residue: 0.2226 time to fit residues: 97.8820 Evaluate side-chains 264 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 227 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.0980 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS D 173 HIS E 173 HIS ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15240 Z= 0.215 Angle : 1.500 32.320 20690 Z= 0.535 Chirality : 0.044 0.148 2280 Planarity : 0.004 0.041 2630 Dihedral : 18.660 150.964 2185 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.83 % Allowed : 17.06 % Favored : 79.11 % 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: 1.25 (0.20), residues: 1830 helix: 0.94 (0.20), residues: 685 sheet: 0.10 (0.29), residues: 315 loop : 1.32 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.008 0.001 HIS E 173 PHE 0.015 0.001 PHE E 352 TYR 0.013 0.001 TYR C 166 ARG 0.003 0.000 ARG E 254 *********************** 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 291 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 231 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8769 (mttt) cc_final: 0.8489 (mmtp) REVERT: A 299 MET cc_start: 0.7807 (tpp) cc_final: 0.7545 (tpp) REVERT: A 352 PHE cc_start: 0.8740 (t80) cc_final: 0.8516 (t80) REVERT: B 64 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8642 (tp) REVERT: B 81 ASP cc_start: 0.8091 (m-30) cc_final: 0.7702 (m-30) REVERT: B 82 MET cc_start: 0.8282 (tpt) cc_final: 0.7938 (tpt) REVERT: B 118 LYS cc_start: 0.8310 (mmmt) cc_final: 0.8093 (mttt) REVERT: B 173 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6874 (m90) REVERT: B 244 ASP cc_start: 0.8488 (p0) cc_final: 0.8124 (t0) REVERT: B 305 MET cc_start: 0.8009 (mmm) cc_final: 0.7736 (tpt) REVERT: C 244 ASP cc_start: 0.8906 (p0) cc_final: 0.7939 (t0) REVERT: D 241 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 283 MET cc_start: 0.7764 (mmm) cc_final: 0.7308 (ttp) REVERT: D 346 LEU cc_start: 0.8840 (tp) cc_final: 0.8528 (tp) REVERT: E 14 SER cc_start: 0.7832 (m) cc_final: 0.7260 (p) REVERT: E 123 MET cc_start: 0.7544 (mmp) cc_final: 0.7131 (tpp) REVERT: E 143 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7469 (m-10) outliers start: 60 outliers final: 41 residues processed: 266 average time/residue: 0.2208 time to fit residues: 92.4602 Evaluate side-chains 261 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15240 Z= 0.227 Angle : 1.499 32.287 20690 Z= 0.535 Chirality : 0.045 0.151 2280 Planarity : 0.004 0.039 2630 Dihedral : 18.410 152.635 2185 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.64 % Allowed : 17.25 % Favored : 79.11 % 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: 0.86 (0.20), residues: 1830 helix: 0.51 (0.19), residues: 750 sheet: 0.03 (0.29), residues: 315 loop : 1.19 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS C 88 PHE 0.014 0.001 PHE E 352 TYR 0.017 0.001 TYR C 166 ARG 0.004 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 222 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8787 (mttt) cc_final: 0.8490 (mmtp) REVERT: A 299 MET cc_start: 0.7773 (tpp) cc_final: 0.7519 (tpp) REVERT: A 352 PHE cc_start: 0.8827 (t80) cc_final: 0.8585 (t80) REVERT: B 64 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 81 ASP cc_start: 0.8064 (m-30) cc_final: 0.7687 (m-30) REVERT: B 82 MET cc_start: 0.8292 (tpt) cc_final: 0.7933 (tpt) REVERT: B 118 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8109 (mttt) REVERT: B 173 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6898 (m90) REVERT: B 244 ASP cc_start: 0.8493 (p0) cc_final: 0.8122 (t0) REVERT: B 305 MET cc_start: 0.8073 (mmm) cc_final: 0.7810 (tpt) REVERT: D 283 MET cc_start: 0.7794 (mmm) cc_final: 0.7326 (ttp) REVERT: D 346 LEU cc_start: 0.8859 (tp) cc_final: 0.8490 (tp) REVERT: E 14 SER cc_start: 0.7944 (m) cc_final: 0.7396 (p) REVERT: E 121 GLN cc_start: 0.8719 (tp40) cc_final: 0.8450 (mm110) REVERT: E 123 MET cc_start: 0.7549 (mmp) cc_final: 0.7156 (tpp) REVERT: E 143 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: E 179 ASP cc_start: 0.8038 (t0) cc_final: 0.7734 (t0) outliers start: 57 outliers final: 42 residues processed: 256 average time/residue: 0.2218 time to fit residues: 89.4851 Evaluate side-chains 258 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 213 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 350 SER 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: 4.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15240 Z= 0.289 Angle : 1.511 32.250 20690 Z= 0.545 Chirality : 0.046 0.170 2280 Planarity : 0.004 0.040 2630 Dihedral : 18.360 154.547 2185 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.83 % Allowed : 17.57 % Favored : 78.59 % 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: 0.85 (0.20), residues: 1830 helix: 0.63 (0.20), residues: 720 sheet: -0.05 (0.29), residues: 315 loop : 1.04 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 79 HIS 0.004 0.001 HIS C 88 PHE 0.012 0.001 PHE C 31 TYR 0.015 0.001 TYR C 166 ARG 0.004 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 220 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8741 (mttt) cc_final: 0.8513 (mmtp) REVERT: A 283 MET cc_start: 0.8589 (mmt) cc_final: 0.8168 (mmp) REVERT: A 299 MET cc_start: 0.7808 (tpp) cc_final: 0.7593 (tpp) REVERT: B 64 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8659 (tp) REVERT: B 81 ASP cc_start: 0.8100 (m-30) cc_final: 0.7735 (m-30) REVERT: B 82 MET cc_start: 0.8316 (tpt) cc_final: 0.7952 (tpt) REVERT: B 118 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8149 (mttt) REVERT: B 173 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.6939 (m90) REVERT: B 244 ASP cc_start: 0.8586 (p0) cc_final: 0.8162 (t0) REVERT: B 305 MET cc_start: 0.8008 (mmm) cc_final: 0.7611 (tpt) REVERT: C 166 TYR cc_start: 0.8655 (t80) cc_final: 0.8397 (t80) REVERT: C 244 ASP cc_start: 0.8937 (p0) cc_final: 0.7995 (t0) REVERT: D 57 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7346 (tt0) REVERT: D 283 MET cc_start: 0.7836 (mmm) cc_final: 0.7435 (ttp) REVERT: D 346 LEU cc_start: 0.8879 (tp) cc_final: 0.8497 (tp) REVERT: E 14 SER cc_start: 0.7983 (m) cc_final: 0.7432 (p) REVERT: E 143 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7570 (m-10) outliers start: 60 outliers final: 48 residues processed: 260 average time/residue: 0.2130 time to fit residues: 88.3046 Evaluate side-chains 261 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 0.0020 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15240 Z= 0.292 Angle : 1.517 32.256 20690 Z= 0.548 Chirality : 0.046 0.196 2280 Planarity : 0.004 0.042 2630 Dihedral : 18.321 154.838 2185 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.71 % Allowed : 18.27 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1830 helix: 0.59 (0.19), residues: 720 sheet: 0.18 (0.28), residues: 345 loop : 0.93 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.004 0.001 HIS C 88 PHE 0.018 0.001 PHE E 223 TYR 0.020 0.001 TYR C 166 ARG 0.004 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 219 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7892 (m-30) cc_final: 0.7688 (m-30) REVERT: A 113 LYS cc_start: 0.8738 (mttt) cc_final: 0.8516 (mmtp) REVERT: A 283 MET cc_start: 0.8588 (mmt) cc_final: 0.8169 (mmp) REVERT: A 299 MET cc_start: 0.7816 (tpp) cc_final: 0.7613 (tpp) REVERT: B 64 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8646 (tp) REVERT: B 81 ASP cc_start: 0.8090 (m-30) cc_final: 0.7724 (m-30) REVERT: B 82 MET cc_start: 0.8318 (tpt) cc_final: 0.7947 (tpt) REVERT: B 118 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8144 (mttt) REVERT: B 173 HIS cc_start: 0.7578 (OUTLIER) cc_final: 0.6962 (m90) REVERT: B 244 ASP cc_start: 0.8583 (p0) cc_final: 0.8163 (t0) REVERT: B 305 MET cc_start: 0.8004 (mmm) cc_final: 0.7598 (tpt) REVERT: C 244 ASP cc_start: 0.8942 (p0) cc_final: 0.7905 (t0) REVERT: D 57 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7357 (tt0) REVERT: D 283 MET cc_start: 0.7838 (mmm) cc_final: 0.7442 (ttp) REVERT: D 346 LEU cc_start: 0.8879 (tp) cc_final: 0.8472 (tp) REVERT: E 14 SER cc_start: 0.8019 (m) cc_final: 0.7613 (p) REVERT: E 143 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7627 (m-10) outliers start: 58 outliers final: 50 residues processed: 261 average time/residue: 0.2292 time to fit residues: 95.6265 Evaluate side-chains 269 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 216 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 184 optimal weight: 0.0370 chunk 169 optimal weight: 1.9990 chunk 146 optimal weight: 0.2980 chunk 15 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15240 Z= 0.219 Angle : 1.497 32.205 20690 Z= 0.535 Chirality : 0.044 0.154 2280 Planarity : 0.004 0.039 2630 Dihedral : 18.080 155.126 2185 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.64 % Allowed : 18.27 % Favored : 78.08 % 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: 0.88 (0.20), residues: 1830 helix: 0.76 (0.20), residues: 710 sheet: 0.00 (0.27), residues: 370 loop : 1.02 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 86 HIS 0.003 0.001 HIS C 88 PHE 0.013 0.001 PHE E 352 TYR 0.046 0.001 TYR C 166 ARG 0.004 0.000 ARG A 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 221 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7900 (m-30) cc_final: 0.7694 (m-30) REVERT: A 113 LYS cc_start: 0.8707 (mttt) cc_final: 0.8481 (mmtp) REVERT: A 283 MET cc_start: 0.8617 (mmt) cc_final: 0.8204 (mmp) REVERT: A 299 MET cc_start: 0.7807 (tpp) cc_final: 0.7575 (tpp) REVERT: A 354 GLN cc_start: 0.7768 (pp30) cc_final: 0.7524 (pp30) REVERT: B 64 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8611 (tp) REVERT: B 81 ASP cc_start: 0.8030 (m-30) cc_final: 0.7774 (m-30) REVERT: B 82 MET cc_start: 0.8294 (tpt) cc_final: 0.7932 (tpt) REVERT: B 118 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8133 (mttt) REVERT: B 173 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.6916 (m90) REVERT: B 244 ASP cc_start: 0.8559 (p0) cc_final: 0.8146 (t0) REVERT: B 305 MET cc_start: 0.8041 (mmm) cc_final: 0.7608 (tpt) REVERT: C 244 ASP cc_start: 0.8867 (p0) cc_final: 0.7825 (t0) REVERT: D 283 MET cc_start: 0.7790 (mmm) cc_final: 0.7405 (ttp) REVERT: D 346 LEU cc_start: 0.8874 (tp) cc_final: 0.8455 (tp) REVERT: E 14 SER cc_start: 0.8061 (m) cc_final: 0.7654 (p) REVERT: E 44 MET cc_start: -0.0827 (tpp) cc_final: -0.2318 (ptp) REVERT: E 143 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7595 (m-10) outliers start: 57 outliers final: 47 residues processed: 259 average time/residue: 0.2224 time to fit residues: 91.8795 Evaluate side-chains 260 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.094997 restraints weight = 23406.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.098153 restraints weight = 13032.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100349 restraints weight = 8370.889| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15240 Z= 0.368 Angle : 1.531 32.363 20690 Z= 0.559 Chirality : 0.047 0.214 2280 Planarity : 0.004 0.043 2630 Dihedral : 18.311 156.401 2185 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.58 % Allowed : 18.91 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1830 helix: 0.47 (0.20), residues: 715 sheet: -0.42 (0.28), residues: 330 loop : 0.70 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 79 HIS 0.005 0.001 HIS C 88 PHE 0.018 0.002 PHE E 223 TYR 0.046 0.002 TYR C 166 ARG 0.004 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.31 seconds wall clock time: 56 minutes 11.45 seconds (3371.45 seconds total)