Starting phenix.real_space_refine on Sat Mar 16 15:23:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ood_3837/03_2024/5ood_3837_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ood_3837/03_2024/5ood_3837.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ood_3837/03_2024/5ood_3837_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/5ood_3837/03_2024/5ood_3837_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ood_3837/03_2024/5ood_3837_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ood_3837/03_2024/5ood_3837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ood_3837/03_2024/5ood_3837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ood_3837/03_2024/5ood_3837_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ood_3837/03_2024/5ood_3837_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= 0.000 sd= 0.006 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 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "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 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "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 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "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 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "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 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {' MG': 1, '9ZK': 2, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.66, per 1000 atoms: 0.58 Number of scatterers: 14910 At special positions: 0 Unit cell: (91.56, 94.83, 190.75, 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: 6.14 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: 100 helices and 20 sheets defined 44.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 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 90 removed outlier: 3.689A pdb=" N PHE A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) 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: 3.897A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.596A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 5.255A 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: 4.391A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (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: 5.571A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 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 90 removed outlier: 3.689A pdb=" N PHE B 90 " --> pdb=" O TRP B 86 " (cutoff:3.500A) 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: 3.898A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.596A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 5.255A 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: 4.390A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (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: 5.571A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 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 90 removed outlier: 3.688A pdb=" N PHE C 90 " --> pdb=" O TRP C 86 " (cutoff:3.500A) 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: 3.897A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.598A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 5.255A 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: 4.390A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (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: 5.571A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 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 90 removed outlier: 3.690A pdb=" N PHE D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) 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: 3.897A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.597A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 5.255A 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: 4.391A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (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: 5.572A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 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 90 removed outlier: 3.689A pdb=" N PHE E 90 " --> pdb=" O TRP E 86 " (cutoff:3.500A) 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: 3.897A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.597A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 5.255A 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: 4.390A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (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: 5.571A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.685A pdb=" N CYS A 10 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A 104 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N THR A 106 " --> pdb=" O ASN A 12 " (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: 5.784A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.757A 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 29 through 32 removed outlier: 7.685A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASN B 12 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR B 106 " --> pdb=" O ASN B 12 " (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: 5.784A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.757A 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 29 through 32 removed outlier: 7.685A pdb=" N CYS C 10 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU C 104 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN C 12 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR C 106 " --> pdb=" O ASN C 12 " (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: 5.785A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.757A 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 29 through 32 removed outlier: 7.684A pdb=" N CYS D 10 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN D 12 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR D 106 " --> pdb=" O ASN D 12 " (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: 5.784A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.757A 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 29 through 32 removed outlier: 7.685A pdb=" N CYS E 10 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU E 104 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN E 12 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR E 106 " --> pdb=" O ASN E 12 " (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: 5.784A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.757A 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. 1320 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: 5.03 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2460 1.28 - 1.41: 3850 1.41 - 1.54: 8730 1.54 - 1.68: 15 1.68 - 1.81: 185 Bond restraints: 15240 Sorted by residual: bond pdb=" C07 9ZK A 403 " pdb=" C08 9ZK A 403 " ideal model delta sigma weight residual 2.679 1.505 1.174 2.00e-02 2.50e+03 3.45e+03 bond pdb=" C07 9ZK C 404 " pdb=" C08 9ZK C 404 " ideal model delta sigma weight residual 2.679 1.505 1.174 2.00e-02 2.50e+03 3.45e+03 bond pdb=" C07 9ZK A 405 " pdb=" C08 9ZK A 405 " ideal model delta sigma weight residual 2.679 1.505 1.174 2.00e-02 2.50e+03 3.45e+03 bond pdb=" C07 9ZK B 404 " pdb=" C08 9ZK B 404 " ideal model delta sigma weight residual 2.679 1.505 1.174 2.00e-02 2.50e+03 3.44e+03 bond pdb=" C07 9ZK D 404 " pdb=" C08 9ZK D 404 " ideal model delta sigma weight residual 2.679 1.506 1.173 2.00e-02 2.50e+03 3.44e+03 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.90: 458 104.90 - 112.82: 8009 112.82 - 120.75: 7651 120.75 - 128.67: 4467 128.67 - 136.59: 105 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C09 9ZK B 404 " pdb=" C11 9ZK B 404 " pdb=" C12 9ZK B 404 " ideal model delta sigma weight residual 180.00 109.38 70.62 3.00e+00 1.11e-01 5.54e+02 angle pdb=" C09 9ZK A 403 " pdb=" C11 9ZK A 403 " pdb=" C12 9ZK A 403 " ideal model delta sigma weight residual 180.00 109.41 70.59 3.00e+00 1.11e-01 5.54e+02 angle pdb=" C09 9ZK A 405 " pdb=" C11 9ZK A 405 " pdb=" C12 9ZK A 405 " ideal model delta sigma weight residual 180.00 109.41 70.59 3.00e+00 1.11e-01 5.54e+02 angle pdb=" C09 9ZK C 404 " pdb=" C11 9ZK C 404 " pdb=" C12 9ZK C 404 " ideal model delta sigma weight residual 180.00 109.42 70.58 3.00e+00 1.11e-01 5.53e+02 angle pdb=" C09 9ZK D 404 " pdb=" C11 9ZK D 404 " pdb=" C12 9ZK D 404 " ideal model delta sigma weight residual 180.00 109.43 70.57 3.00e+00 1.11e-01 5.53e+02 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 8890 35.52 - 71.04: 120 71.04 - 106.56: 40 106.56 - 142.08: 20 142.08 - 177.60: 25 Dihedral angle restraints: 9095 sinusoidal: 3735 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.40 133.60 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.43 133.57 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.44 133.56 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 9092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.836: 2270 0.836 - 1.671: 5 1.671 - 2.506: 0 2.506 - 3.342: 0 3.342 - 4.177: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C16 9ZK A 405 " pdb=" C17 9ZK A 405 " pdb=" C22 9ZK A 405 " pdb=" N15 9ZK A 405 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.18 2.00e-01 2.50e+01 4.36e+02 chirality pdb=" C16 9ZK C 404 " pdb=" C17 9ZK C 404 " pdb=" C22 9ZK C 404 " pdb=" N15 9ZK C 404 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.18 2.00e-01 2.50e+01 4.36e+02 chirality pdb=" C16 9ZK A 403 " pdb=" C17 9ZK A 403 " pdb=" C22 9ZK A 403 " pdb=" N15 9ZK A 403 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.18 2.00e-01 2.50e+01 4.36e+02 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.095 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO C 164 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.095 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO B 164 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " 0.095 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO E 164 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.073 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 123 2.58 - 3.16: 14282 3.16 - 3.74: 23056 3.74 - 4.32: 36029 4.32 - 4.90: 54934 Nonbonded interactions: 128424 Sorted by model distance: nonbonded pdb=" O3 PO4 A 402 " pdb="MG MG A 404 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 B 402 " pdb="MG MG B 403 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 C 402 " pdb="MG MG C 403 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 E 402 " pdb="MG MG E 403 " model vdw 1.996 2.170 nonbonded pdb=" O3 PO4 D 402 " pdb="MG MG D 403 " model vdw 1.997 2.170 ... (remaining 128419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 375 or resid 401 through 402)) } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.990 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.480 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.050 1.174 15240 Z= 3.282 Angle : 3.118 70.616 20690 Z= 1.359 Chirality : 0.221 4.177 2280 Planarity : 0.017 0.145 2630 Dihedral : 18.577 177.601 5665 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 2.46 % Allowed : 5.52 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.19), residues: 1830 helix: -1.54 (0.16), residues: 725 sheet: -0.78 (0.31), residues: 225 loop : -0.69 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.006 TRP D 340 HIS 0.004 0.001 HIS C 88 PHE 0.011 0.003 PHE B 90 TYR 0.029 0.006 TYR A 294 ARG 0.005 0.001 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 631 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 THR cc_start: 0.8897 (m) cc_final: 0.8642 (p) REVERT: A 291 LYS cc_start: 0.8911 (tttt) cc_final: 0.7833 (mptt) REVERT: A 349 LEU cc_start: 0.8276 (tp) cc_final: 0.7951 (mt) REVERT: B 66 THR cc_start: 0.9254 (m) cc_final: 0.8938 (p) REVERT: B 191 LYS cc_start: 0.8858 (tttt) cc_final: 0.8313 (ttpt) REVERT: B 215 LYS cc_start: 0.8369 (mttt) cc_final: 0.7914 (mtpt) REVERT: B 222 ASP cc_start: 0.7998 (t0) cc_final: 0.7723 (m-30) REVERT: B 239 SER cc_start: 0.8846 (t) cc_final: 0.8462 (p) REVERT: B 290 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8435 (mtt180) REVERT: B 291 LYS cc_start: 0.8685 (tttt) cc_final: 0.7909 (mttp) REVERT: B 314 GLN cc_start: 0.7470 (tp40) cc_final: 0.7167 (tp40) REVERT: B 340 TRP cc_start: 0.8261 (t60) cc_final: 0.7674 (t60) REVERT: C 78 ASN cc_start: 0.8432 (t0) cc_final: 0.8172 (t0) REVERT: C 87 HIS cc_start: 0.7909 (t70) cc_final: 0.7528 (t-170) REVERT: D 56 ASP cc_start: 0.7754 (m-30) cc_final: 0.7127 (t0) REVERT: D 78 ASN cc_start: 0.8371 (t0) cc_final: 0.7699 (t0) REVERT: D 214 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7883 (mt-10) REVERT: D 244 ASP cc_start: 0.7594 (p0) cc_final: 0.7375 (p0) REVERT: D 260 THR cc_start: 0.9256 (p) cc_final: 0.8195 (m) REVERT: D 283 MET cc_start: 0.8381 (mmp) cc_final: 0.7758 (ttm) REVERT: D 355 MET cc_start: 0.7844 (mmm) cc_final: 0.7405 (mmt) REVERT: D 358 THR cc_start: 0.8741 (m) cc_final: 0.8466 (p) REVERT: E 41 GLN cc_start: 0.7990 (mt0) cc_final: 0.7598 (mm-40) REVERT: E 43 VAL cc_start: 0.6549 (t) cc_final: 0.6222 (t) REVERT: E 61 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8142 (mmpt) REVERT: E 78 ASN cc_start: 0.8054 (t0) cc_final: 0.6946 (t0) REVERT: E 81 ASP cc_start: 0.8203 (m-30) cc_final: 0.7722 (m-30) REVERT: E 82 MET cc_start: 0.7750 (tpt) cc_final: 0.7423 (tpt) REVERT: E 84 LYS cc_start: 0.8400 (tptt) cc_final: 0.8164 (tttt) REVERT: E 115 ASN cc_start: 0.8737 (t0) cc_final: 0.8527 (t0) REVERT: E 276 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8678 (mt-10) REVERT: E 284 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7526 (tmtt) REVERT: E 304 THR cc_start: 0.8582 (p) cc_final: 0.8266 (m) REVERT: E 336 LYS cc_start: 0.8173 (ptmt) cc_final: 0.7713 (ttpt) outliers start: 0 outliers final: 0 residues processed: 631 average time/residue: 0.3032 time to fit residues: 268.4620 Evaluate side-chains 312 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 115 ASN C 246 GLN D 87 HIS D 115 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN D 354 GLN E 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15240 Z= 0.237 Angle : 1.591 33.870 20690 Z= 0.596 Chirality : 0.049 0.310 2280 Planarity : 0.008 0.065 2630 Dihedral : 21.100 176.686 2185 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.43 % Favored : 95.30 % Rotamer: Outliers : 2.11 % Allowed : 11.25 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1830 helix: -0.23 (0.17), residues: 785 sheet: -0.35 (0.28), residues: 295 loop : -0.38 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 340 HIS 0.010 0.001 HIS B 275 PHE 0.032 0.002 PHE C 352 TYR 0.014 0.001 TYR B 91 ARG 0.007 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 397 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.8343 (m-10) cc_final: 0.8140 (m-10) REVERT: A 206 ARG cc_start: 0.8600 (ttp80) cc_final: 0.8362 (ttm170) REVERT: A 214 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 249 THR cc_start: 0.8917 (m) cc_final: 0.8344 (p) REVERT: A 291 LYS cc_start: 0.8909 (tttt) cc_final: 0.7862 (mptt) REVERT: A 314 GLN cc_start: 0.8117 (tt0) cc_final: 0.7739 (mt0) REVERT: A 340 TRP cc_start: 0.8893 (t60) cc_final: 0.8226 (t60) REVERT: B 66 THR cc_start: 0.9048 (m) cc_final: 0.8716 (t) REVERT: B 191 LYS cc_start: 0.8889 (tttt) cc_final: 0.8395 (ttmt) REVERT: B 291 LYS cc_start: 0.8568 (tttt) cc_final: 0.7664 (mttt) REVERT: B 305 MET cc_start: 0.8003 (mtp) cc_final: 0.7802 (mtp) REVERT: B 314 GLN cc_start: 0.7518 (tp40) cc_final: 0.7124 (tp40) REVERT: B 337 TYR cc_start: 0.7371 (m-10) cc_final: 0.7128 (m-10) REVERT: B 349 LEU cc_start: 0.8415 (tp) cc_final: 0.8192 (mp) REVERT: C 87 HIS cc_start: 0.7947 (t70) cc_final: 0.7350 (t-90) REVERT: D 56 ASP cc_start: 0.7729 (m-30) cc_final: 0.7412 (t0) REVERT: D 59 GLN cc_start: 0.8921 (mm110) cc_final: 0.8660 (mm110) REVERT: D 191 LYS cc_start: 0.8951 (tttt) cc_final: 0.8579 (mtpp) REVERT: D 283 MET cc_start: 0.8196 (mmp) cc_final: 0.7542 (ttm) REVERT: D 360 GLN cc_start: 0.8088 (pp30) cc_final: 0.6867 (pp30) REVERT: E 44 MET cc_start: 0.3813 (tpp) cc_final: 0.3575 (tpt) REVERT: E 61 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8200 (mmpt) REVERT: E 84 LYS cc_start: 0.8409 (tptt) cc_final: 0.7859 (tptt) outliers start: 33 outliers final: 20 residues processed: 419 average time/residue: 0.2575 time to fit residues: 162.3207 Evaluate side-chains 330 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 310 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 115 ASN C 128 ASN D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 354 GLN E 101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 15240 Z= 0.346 Angle : 1.573 32.365 20690 Z= 0.587 Chirality : 0.048 0.249 2280 Planarity : 0.006 0.061 2630 Dihedral : 19.538 154.664 2185 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.75 % Favored : 94.97 % Rotamer: Outliers : 3.26 % Allowed : 13.16 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1830 helix: -0.01 (0.18), residues: 805 sheet: -0.45 (0.28), residues: 305 loop : -0.03 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 79 HIS 0.007 0.001 HIS A 275 PHE 0.017 0.002 PHE C 255 TYR 0.024 0.002 TYR A 133 ARG 0.004 0.001 ARG B 335 *********************** 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 350 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 299 time to evaluate : 1.692 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7906 (mt-10) REVERT: A 120 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9086 (p) REVERT: A 214 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 226 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 249 THR cc_start: 0.8909 (m) cc_final: 0.8540 (p) REVERT: A 291 LYS cc_start: 0.8963 (tttt) cc_final: 0.7846 (mptt) REVERT: A 314 GLN cc_start: 0.8214 (tt0) cc_final: 0.7780 (mt0) REVERT: A 372 ARG cc_start: 0.7404 (mmt180) cc_final: 0.7109 (mmt180) REVERT: B 66 THR cc_start: 0.9050 (m) cc_final: 0.8764 (t) REVERT: B 123 MET cc_start: 0.8753 (mmt) cc_final: 0.8405 (mmt) REVERT: B 291 LYS cc_start: 0.8567 (tttt) cc_final: 0.7583 (mttt) REVERT: C 87 HIS cc_start: 0.8037 (t70) cc_final: 0.7520 (t-90) REVERT: C 325 MET cc_start: 0.8757 (mmm) cc_final: 0.8532 (mmm) REVERT: D 56 ASP cc_start: 0.7847 (m-30) cc_final: 0.7421 (t0) REVERT: D 191 LYS cc_start: 0.8946 (tttt) cc_final: 0.8698 (mtpp) REVERT: D 283 MET cc_start: 0.8417 (mmp) cc_final: 0.7657 (ttm) REVERT: D 346 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8790 (tp) REVERT: D 355 MET cc_start: 0.6977 (mtm) cc_final: 0.6450 (mmt) REVERT: E 28 ARG cc_start: 0.6568 (mtm180) cc_final: 0.6305 (mtm180) REVERT: E 61 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8490 (mmpt) REVERT: E 84 LYS cc_start: 0.8170 (tptt) cc_final: 0.7737 (tptt) REVERT: E 336 LYS cc_start: 0.8188 (pttm) cc_final: 0.7510 (ttmt) outliers start: 51 outliers final: 33 residues processed: 334 average time/residue: 0.2323 time to fit residues: 117.7438 Evaluate side-chains 286 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 317 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 113 optimal weight: 0.0970 chunk 168 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15240 Z= 0.161 Angle : 1.518 32.440 20690 Z= 0.549 Chirality : 0.044 0.165 2280 Planarity : 0.005 0.049 2630 Dihedral : 18.904 154.069 2185 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 2.62 % Allowed : 15.08 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1830 helix: 0.14 (0.18), residues: 810 sheet: -0.33 (0.28), residues: 305 loop : 0.16 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 79 HIS 0.016 0.001 HIS E 101 PHE 0.022 0.001 PHE E 352 TYR 0.016 0.001 TYR A 133 ARG 0.003 0.000 ARG C 116 *********************** 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 357 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 316 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 214 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7225 (mt-10) REVERT: A 226 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 249 THR cc_start: 0.8946 (m) cc_final: 0.8648 (p) REVERT: A 291 LYS cc_start: 0.8889 (tttt) cc_final: 0.7819 (mptt) REVERT: A 372 ARG cc_start: 0.7386 (mmt180) cc_final: 0.7119 (mmt180) REVERT: B 154 ASP cc_start: 0.8209 (t0) cc_final: 0.7895 (m-30) REVERT: B 191 LYS cc_start: 0.8928 (tttt) cc_final: 0.8355 (ttmt) REVERT: B 291 LYS cc_start: 0.8553 (tttt) cc_final: 0.7642 (mttt) REVERT: B 314 GLN cc_start: 0.7632 (tt0) cc_final: 0.7408 (tt0) REVERT: C 44 MET cc_start: 0.6465 (mtp) cc_final: 0.6244 (mtp) REVERT: C 87 HIS cc_start: 0.7950 (t70) cc_final: 0.7402 (t-90) REVERT: C 169 TYR cc_start: 0.7904 (m-80) cc_final: 0.7593 (m-80) REVERT: C 191 LYS cc_start: 0.8933 (tttt) cc_final: 0.8732 (tttp) REVERT: C 325 MET cc_start: 0.8723 (mmm) cc_final: 0.8492 (mmm) REVERT: D 56 ASP cc_start: 0.7659 (m-30) cc_final: 0.7268 (t0) REVERT: D 191 LYS cc_start: 0.8927 (tttt) cc_final: 0.8690 (mtpp) REVERT: D 201 VAL cc_start: 0.8866 (m) cc_final: 0.8593 (p) REVERT: D 283 MET cc_start: 0.8343 (mmp) cc_final: 0.7412 (ttm) REVERT: D 355 MET cc_start: 0.6960 (mtm) cc_final: 0.6111 (mmt) REVERT: E 8 LEU cc_start: 0.8073 (tp) cc_final: 0.7825 (tt) REVERT: E 61 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8402 (mmpt) REVERT: E 79 TRP cc_start: 0.8427 (m100) cc_final: 0.8041 (m100) REVERT: E 84 LYS cc_start: 0.8204 (tptt) cc_final: 0.7735 (tptt) REVERT: E 132 MET cc_start: 0.7751 (ppp) cc_final: 0.7475 (ppp) REVERT: E 244 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5436 (p0) REVERT: E 325 MET cc_start: 0.7226 (mmp) cc_final: 0.7007 (mmm) REVERT: E 360 GLN cc_start: 0.8680 (pp30) cc_final: 0.8455 (pp30) outliers start: 41 outliers final: 27 residues processed: 338 average time/residue: 0.2359 time to fit residues: 121.1666 Evaluate side-chains 297 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 269 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 152 optimal weight: 0.4980 chunk 123 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5532 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= 0.183 Angle : 1.516 32.297 20690 Z= 0.548 Chirality : 0.044 0.155 2280 Planarity : 0.005 0.050 2630 Dihedral : 18.760 158.723 2185 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.30 % Rotamer: Outliers : 2.94 % Allowed : 15.59 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1830 helix: 0.14 (0.18), residues: 810 sheet: -0.34 (0.28), residues: 310 loop : 0.30 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.004 0.001 HIS E 101 PHE 0.014 0.001 PHE E 352 TYR 0.014 0.001 TYR A 133 ARG 0.007 0.000 ARG A 28 *********************** 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 327 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 281 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8109 (p0) cc_final: 0.7865 (p0) REVERT: A 119 MET cc_start: 0.8856 (ttp) cc_final: 0.8607 (ttt) REVERT: A 214 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 226 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 249 THR cc_start: 0.8980 (m) cc_final: 0.8670 (p) REVERT: A 291 LYS cc_start: 0.8942 (tttt) cc_final: 0.7780 (mptt) REVERT: B 154 ASP cc_start: 0.8245 (t0) cc_final: 0.7938 (m-30) REVERT: B 191 LYS cc_start: 0.8938 (tttt) cc_final: 0.8367 (ttmt) REVERT: B 291 LYS cc_start: 0.8466 (tttt) cc_final: 0.7555 (mttt) REVERT: B 314 GLN cc_start: 0.7677 (tt0) cc_final: 0.7465 (tt0) REVERT: C 44 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6162 (mtp) REVERT: C 87 HIS cc_start: 0.7908 (t70) cc_final: 0.7351 (t-90) REVERT: C 169 TYR cc_start: 0.7886 (m-80) cc_final: 0.7578 (m-80) REVERT: C 191 LYS cc_start: 0.8971 (tttt) cc_final: 0.8707 (tttp) REVERT: C 270 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6950 (tm-30) REVERT: C 313 MET cc_start: 0.8992 (tpt) cc_final: 0.8509 (tpt) REVERT: D 56 ASP cc_start: 0.7749 (m-30) cc_final: 0.7323 (t0) REVERT: D 191 LYS cc_start: 0.8919 (tttt) cc_final: 0.8695 (mtpp) REVERT: D 283 MET cc_start: 0.8376 (mmp) cc_final: 0.7439 (ttm) REVERT: E 8 LEU cc_start: 0.8283 (tp) cc_final: 0.8008 (tt) REVERT: E 84 LYS cc_start: 0.8249 (tptt) cc_final: 0.7752 (tptt) REVERT: E 336 LYS cc_start: 0.7943 (pttm) cc_final: 0.7629 (mtpt) outliers start: 46 outliers final: 35 residues processed: 307 average time/residue: 0.2434 time to fit residues: 114.3047 Evaluate side-chains 297 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5556 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= 0.183 Angle : 1.516 32.297 20690 Z= 0.548 Chirality : 0.044 0.155 2280 Planarity : 0.005 0.050 2630 Dihedral : 18.760 158.723 2185 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.30 % Rotamer: Outliers : 2.36 % Allowed : 16.61 % Favored : 81.02 % 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: 0.01 (0.20), residues: 1830 helix: 0.14 (0.18), residues: 810 sheet: -0.34 (0.28), residues: 310 loop : 0.30 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.004 0.001 HIS E 101 PHE 0.014 0.001 PHE E 352 TYR 0.014 0.001 TYR A 133 ARG 0.007 0.000 ARG A 28 *********************** 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 299 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 262 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8123 (p0) cc_final: 0.7865 (p0) REVERT: A 119 MET cc_start: 0.8867 (ttp) cc_final: 0.8607 (ttt) REVERT: A 214 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 226 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 249 THR cc_start: 0.8981 (m) cc_final: 0.8670 (p) REVERT: A 291 LYS cc_start: 0.8945 (tttt) cc_final: 0.7779 (mptt) REVERT: B 154 ASP cc_start: 0.8246 (t0) cc_final: 0.7937 (m-30) REVERT: B 191 LYS cc_start: 0.8940 (tttt) cc_final: 0.8367 (ttmt) REVERT: B 291 LYS cc_start: 0.8464 (tttt) cc_final: 0.7555 (mttt) REVERT: B 314 GLN cc_start: 0.7674 (tt0) cc_final: 0.7465 (tt0) REVERT: C 44 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6164 (mtp) REVERT: C 87 HIS cc_start: 0.7891 (t70) cc_final: 0.7351 (t-90) REVERT: C 169 TYR cc_start: 0.7888 (m-80) cc_final: 0.7578 (m-80) REVERT: C 191 LYS cc_start: 0.8968 (tttt) cc_final: 0.8707 (tttp) REVERT: C 270 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6950 (tm-30) REVERT: C 313 MET cc_start: 0.8991 (tpt) cc_final: 0.8509 (tpt) REVERT: D 56 ASP cc_start: 0.7741 (m-30) cc_final: 0.7323 (t0) REVERT: D 191 LYS cc_start: 0.8913 (tttt) cc_final: 0.8694 (mtpp) REVERT: D 283 MET cc_start: 0.8377 (mmp) cc_final: 0.7439 (ttm) REVERT: E 8 LEU cc_start: 0.8283 (tp) cc_final: 0.8008 (tt) REVERT: E 84 LYS cc_start: 0.8258 (tptt) cc_final: 0.7752 (tptt) REVERT: E 336 LYS cc_start: 0.7958 (pttm) cc_final: 0.7629 (mtpt) outliers start: 37 outliers final: 35 residues processed: 283 average time/residue: 0.2310 time to fit residues: 100.9689 Evaluate side-chains 297 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 353 GLN B 92 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15240 Z= 0.296 Angle : 1.537 32.313 20690 Z= 0.564 Chirality : 0.046 0.217 2280 Planarity : 0.005 0.044 2630 Dihedral : 19.012 166.749 2185 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.86 % Rotamer: Outliers : 3.83 % Allowed : 15.08 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1830 helix: 0.21 (0.19), residues: 755 sheet: -0.23 (0.29), residues: 295 loop : 0.29 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 79 HIS 0.005 0.001 HIS A 101 PHE 0.021 0.002 PHE E 352 TYR 0.014 0.001 TYR A 133 ARG 0.007 0.001 ARG E 28 *********************** 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 334 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 274 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7327 (mt-10) REVERT: A 226 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8041 (mm-30) REVERT: A 249 THR cc_start: 0.9005 (m) cc_final: 0.8665 (p) REVERT: A 291 LYS cc_start: 0.8963 (tttt) cc_final: 0.7575 (mmtt) REVERT: A 299 MET cc_start: 0.8108 (mtt) cc_final: 0.7902 (mtp) REVERT: A 340 TRP cc_start: 0.8962 (t60) cc_final: 0.8039 (t60) REVERT: A 344 SER cc_start: 0.8924 (m) cc_final: 0.8503 (p) REVERT: B 154 ASP cc_start: 0.8289 (t0) cc_final: 0.8003 (m-30) REVERT: B 291 LYS cc_start: 0.8659 (tttt) cc_final: 0.7783 (mptt) REVERT: C 44 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.6026 (mtp) REVERT: C 87 HIS cc_start: 0.7908 (t70) cc_final: 0.7345 (t-90) REVERT: C 191 LYS cc_start: 0.9061 (tttt) cc_final: 0.8802 (tttp) REVERT: C 270 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7167 (tm-30) REVERT: D 56 ASP cc_start: 0.7811 (m-30) cc_final: 0.7406 (t0) REVERT: D 89 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.8033 (m) REVERT: D 191 LYS cc_start: 0.8908 (tttt) cc_final: 0.8681 (mtpp) REVERT: D 283 MET cc_start: 0.8416 (mmp) cc_final: 0.7526 (ttm) REVERT: D 297 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8524 (m-40) REVERT: D 325 MET cc_start: 0.8451 (mmm) cc_final: 0.8055 (mmp) REVERT: E 41 GLN cc_start: 0.7637 (mp10) cc_final: 0.7043 (tt0) REVERT: E 84 LYS cc_start: 0.8333 (tptt) cc_final: 0.7790 (tptt) REVERT: E 124 PHE cc_start: 0.7774 (m-10) cc_final: 0.7376 (m-80) REVERT: E 244 ASP cc_start: 0.6191 (OUTLIER) cc_final: 0.5652 (p0) REVERT: E 290 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.7859 (mtm180) outliers start: 60 outliers final: 40 residues processed: 306 average time/residue: 0.2471 time to fit residues: 113.7201 Evaluate side-chains 304 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 259 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 chunk 121 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN B 92 ASN C 115 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15240 Z= 0.193 Angle : 1.518 32.287 20690 Z= 0.551 Chirality : 0.045 0.221 2280 Planarity : 0.005 0.044 2630 Dihedral : 18.859 169.677 2185 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 3.26 % Allowed : 16.10 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1830 helix: 0.24 (0.19), residues: 755 sheet: -0.69 (0.29), residues: 275 loop : 0.49 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 79 HIS 0.004 0.001 HIS D 87 PHE 0.043 0.001 PHE C 352 TYR 0.013 0.001 TYR A 133 ARG 0.006 0.000 ARG A 28 *********************** 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 334 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 283 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7325 (mt-10) REVERT: A 249 THR cc_start: 0.8985 (m) cc_final: 0.8695 (p) REVERT: A 291 LYS cc_start: 0.8904 (tttt) cc_final: 0.7737 (mptt) REVERT: A 299 MET cc_start: 0.8178 (mtt) cc_final: 0.7922 (mtp) REVERT: B 154 ASP cc_start: 0.8272 (t0) cc_final: 0.8060 (m-30) REVERT: B 191 LYS cc_start: 0.8915 (tttt) cc_final: 0.8358 (ttmt) REVERT: B 291 LYS cc_start: 0.8682 (tttt) cc_final: 0.7780 (mptt) REVERT: B 314 GLN cc_start: 0.7661 (tt0) cc_final: 0.7438 (tt0) REVERT: B 336 LYS cc_start: 0.8064 (ptmt) cc_final: 0.7691 (ptmt) REVERT: C 59 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8198 (mm110) REVERT: C 87 HIS cc_start: 0.7873 (t70) cc_final: 0.7322 (t-90) REVERT: C 169 TYR cc_start: 0.8081 (m-80) cc_final: 0.7618 (m-80) REVERT: C 191 LYS cc_start: 0.9014 (tttt) cc_final: 0.8784 (tttp) REVERT: D 56 ASP cc_start: 0.7615 (m-30) cc_final: 0.7284 (t0) REVERT: D 191 LYS cc_start: 0.8893 (tttt) cc_final: 0.8689 (mtpp) REVERT: D 283 MET cc_start: 0.8416 (mmp) cc_final: 0.7532 (ttm) REVERT: D 297 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8290 (m-40) REVERT: E 41 GLN cc_start: 0.7986 (mp10) cc_final: 0.7381 (tt0) REVERT: E 84 LYS cc_start: 0.8264 (tptt) cc_final: 0.7961 (tttp) REVERT: E 124 PHE cc_start: 0.7732 (m-10) cc_final: 0.7339 (m-80) REVERT: E 336 LYS cc_start: 0.8341 (pttm) cc_final: 0.7585 (mtmt) outliers start: 51 outliers final: 40 residues processed: 311 average time/residue: 0.2368 time to fit residues: 111.3718 Evaluate side-chains 303 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 262 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 41 GLN B 92 ASN C 115 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN E 101 HIS ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15240 Z= 0.312 Angle : 1.549 32.311 20690 Z= 0.572 Chirality : 0.047 0.205 2280 Planarity : 0.005 0.045 2630 Dihedral : 19.140 174.289 2185 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.19 % Favored : 94.59 % Rotamer: Outliers : 3.07 % Allowed : 16.42 % Favored : 80.51 % 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: -0.02 (0.20), residues: 1830 helix: 0.14 (0.19), residues: 755 sheet: -0.65 (0.30), residues: 270 loop : 0.32 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 79 HIS 0.005 0.001 HIS A 101 PHE 0.033 0.002 PHE C 352 TYR 0.014 0.001 TYR E 166 ARG 0.005 0.001 ARG A 28 *********************** 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 315 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 267 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8367 (pm20) cc_final: 0.8053 (pm20) REVERT: A 249 THR cc_start: 0.8947 (m) cc_final: 0.8624 (p) REVERT: A 291 LYS cc_start: 0.8980 (tttt) cc_final: 0.7820 (mptt) REVERT: A 299 MET cc_start: 0.8048 (mtt) cc_final: 0.7821 (mtp) REVERT: B 154 ASP cc_start: 0.8333 (t0) cc_final: 0.8089 (m-30) REVERT: B 290 ARG cc_start: 0.8916 (mtm-85) cc_final: 0.8621 (mtt180) REVERT: B 291 LYS cc_start: 0.8732 (tttt) cc_final: 0.7889 (mptt) REVERT: B 336 LYS cc_start: 0.8128 (ptmt) cc_final: 0.7770 (ptmt) REVERT: C 44 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.6012 (mmt) REVERT: C 87 HIS cc_start: 0.7893 (t70) cc_final: 0.7331 (t-90) REVERT: C 191 LYS cc_start: 0.9131 (tttt) cc_final: 0.8899 (tttp) REVERT: C 284 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7662 (mmtp) REVERT: D 191 LYS cc_start: 0.8922 (tttt) cc_final: 0.8692 (mtpp) REVERT: D 283 MET cc_start: 0.8376 (mmp) cc_final: 0.7554 (ttm) REVERT: D 297 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8385 (m-40) REVERT: E 21 PHE cc_start: 0.7641 (m-80) cc_final: 0.7343 (m-80) REVERT: E 41 GLN cc_start: 0.7876 (mp10) cc_final: 0.7344 (tt0) REVERT: E 84 LYS cc_start: 0.8268 (tptt) cc_final: 0.8000 (tttp) REVERT: E 124 PHE cc_start: 0.7677 (m-10) cc_final: 0.7406 (m-10) REVERT: E 290 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7943 (mtm180) outliers start: 48 outliers final: 41 residues processed: 295 average time/residue: 0.2484 time to fit residues: 110.5343 Evaluate side-chains 301 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 257 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.2980 chunk 107 optimal weight: 0.0070 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 115 ASN D 297 ASN ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15240 Z= 0.162 Angle : 1.521 32.202 20690 Z= 0.552 Chirality : 0.044 0.191 2280 Planarity : 0.005 0.046 2630 Dihedral : 18.829 177.712 2185 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.64 % Favored : 95.14 % Rotamer: Outliers : 1.98 % Allowed : 18.02 % Favored : 80.00 % 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: 0.18 (0.20), residues: 1830 helix: 0.26 (0.19), residues: 755 sheet: -0.70 (0.29), residues: 275 loop : 0.57 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 79 HIS 0.012 0.001 HIS E 101 PHE 0.032 0.001 PHE C 352 TYR 0.030 0.001 TYR B 362 ARG 0.005 0.000 ARG A 28 ********************** 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 309 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 278 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8300 (pm20) cc_final: 0.8094 (pm20) REVERT: A 291 LYS cc_start: 0.8924 (tttt) cc_final: 0.7784 (mptt) REVERT: A 299 MET cc_start: 0.8107 (mtt) cc_final: 0.7854 (mtp) REVERT: B 65 LEU cc_start: 0.8208 (mt) cc_final: 0.7969 (mt) REVERT: B 154 ASP cc_start: 0.8259 (t0) cc_final: 0.8056 (m-30) REVERT: B 191 LYS cc_start: 0.8895 (tttt) cc_final: 0.8345 (ttmt) REVERT: B 290 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8545 (mtt180) REVERT: B 291 LYS cc_start: 0.8706 (tttt) cc_final: 0.7809 (mptt) REVERT: B 340 TRP cc_start: 0.9001 (t60) cc_final: 0.8239 (t60) REVERT: C 87 HIS cc_start: 0.7858 (t70) cc_final: 0.7323 (t-90) REVERT: C 132 MET cc_start: 0.8418 (ppp) cc_final: 0.8170 (ppp) REVERT: D 283 MET cc_start: 0.8308 (mmp) cc_final: 0.7503 (ttm) REVERT: D 297 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8132 (m-40) REVERT: E 41 GLN cc_start: 0.7793 (mp10) cc_final: 0.7267 (tt0) REVERT: E 84 LYS cc_start: 0.8256 (tptt) cc_final: 0.7957 (tttp) REVERT: E 124 PHE cc_start: 0.7823 (m-10) cc_final: 0.7483 (m-80) REVERT: E 336 LYS cc_start: 0.8348 (pttm) cc_final: 0.7613 (mtmt) outliers start: 31 outliers final: 26 residues processed: 299 average time/residue: 0.2513 time to fit residues: 112.9788 Evaluate side-chains 282 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 255 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN B 92 ASN C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN E 101 HIS ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104032 restraints weight = 27094.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106971 restraints weight = 13664.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108911 restraints weight = 8347.440| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6440 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= 0.198 Angle : 1.523 32.221 20690 Z= 0.554 Chirality : 0.045 0.201 2280 Planarity : 0.005 0.045 2630 Dihedral : 18.863 179.830 2185 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.86 % Favored : 94.92 % Rotamer: Outliers : 2.11 % Allowed : 18.08 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1830 helix: 0.26 (0.19), residues: 755 sheet: -0.63 (0.30), residues: 275 loop : 0.58 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 79 HIS 0.007 0.001 HIS A 275 PHE 0.034 0.001 PHE C 352 TYR 0.012 0.001 TYR A 198 ARG 0.005 0.000 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.59 seconds wall clock time: 57 minutes 30.17 seconds (3450.17 seconds total)