Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 12:30:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/04_2023/6t23_10365_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "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-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.17, per 1000 atoms: 0.55 Number of scatterers: 14910 At special positions: 0 Unit cell: (96.6, 92.4, 193.2, 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: 6.13 Conformation dependent library (CDL) restraints added in 2.3 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: 110 helices and 20 sheets defined 44.5% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 123 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: 3.880A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.767A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.551A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.514A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 347 removed outlier: 5.376A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 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 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 123 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: 3.881A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.767A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.551A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.513A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 347 removed outlier: 5.376A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 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 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 123 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: 3.880A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.767A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.551A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.514A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 347 removed outlier: 5.376A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 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 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 123 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: 3.880A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.767A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.552A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.514A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 5.376A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 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 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 123 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: 3.881A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 removed outlier: 3.767A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.551A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.514A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 347 removed outlier: 5.376A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 355 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.778A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.889A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.777A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 5.889A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.777A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 5.889A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.777A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 5.889A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.777A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 5.889A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.924A 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 241 525 hydrogen bonds defined for protein. 1275 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: 5.65 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2490 1.30 - 1.43: 3931 1.43 - 1.56: 8550 1.56 - 1.70: 84 1.70 - 1.83: 185 Bond restraints: 15240 Sorted by residual: bond pdb=" C07 9ZK E 379 " pdb=" C08 9ZK E 379 " ideal model delta sigma weight residual 2.679 1.524 1.155 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C07 9ZK B 379 " pdb=" C08 9ZK B 379 " ideal model delta sigma weight residual 2.679 1.525 1.154 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C07 9ZK D 379 " pdb=" C08 9ZK D 379 " ideal model delta sigma weight residual 2.679 1.525 1.154 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C07 9ZK C 379 " pdb=" C08 9ZK C 379 " ideal model delta sigma weight residual 2.679 1.525 1.154 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C07 9ZK A 379 " pdb=" C08 9ZK A 379 " ideal model delta sigma weight residual 2.679 1.526 1.153 2.00e-02 2.50e+03 3.32e+03 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.28: 469 105.28 - 112.90: 7464 112.90 - 120.52: 7561 120.52 - 128.14: 5068 128.14 - 135.76: 128 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C41 9ZK A 379 " pdb=" C42 9ZK A 379 " pdb=" O43 9ZK A 379 " ideal model delta sigma weight residual 59.79 119.05 -59.26 3.00e+00 1.11e-01 3.90e+02 angle pdb=" C41 9ZK C 379 " pdb=" C42 9ZK C 379 " pdb=" O43 9ZK C 379 " ideal model delta sigma weight residual 59.79 119.03 -59.24 3.00e+00 1.11e-01 3.90e+02 angle pdb=" C41 9ZK D 379 " pdb=" C42 9ZK D 379 " pdb=" O43 9ZK D 379 " ideal model delta sigma weight residual 59.79 119.00 -59.21 3.00e+00 1.11e-01 3.90e+02 angle pdb=" C41 9ZK E 379 " pdb=" C42 9ZK E 379 " pdb=" O43 9ZK E 379 " ideal model delta sigma weight residual 59.79 118.99 -59.20 3.00e+00 1.11e-01 3.89e+02 angle pdb=" C41 9ZK B 379 " pdb=" C42 9ZK B 379 " pdb=" O43 9ZK B 379 " ideal model delta sigma weight residual 59.79 118.98 -59.19 3.00e+00 1.11e-01 3.89e+02 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 8901 34.33 - 68.67: 104 68.67 - 103.00: 15 103.00 - 137.33: 10 137.33 - 171.67: 10 Dihedral angle restraints: 9040 sinusoidal: 3680 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP D 376 " pdb=" O3A ADP D 376 " pdb=" PB ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.79 -149.79 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP C 376 " pdb=" O3A ADP C 376 " pdb=" PB ADP C 376 " pdb=" PA ADP C 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.77 -149.78 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP E 376 " pdb=" O3A ADP E 376 " pdb=" PB ADP E 376 " pdb=" PA ADP E 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.77 -149.78 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 9037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.846: 2270 0.846 - 1.692: 0 1.692 - 2.538: 5 2.538 - 3.384: 0 3.384 - 4.230: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C16 9ZK D 379 " pdb=" C17 9ZK D 379 " pdb=" C22 9ZK D 379 " pdb=" N15 9ZK D 379 " both_signs ideal model delta sigma weight residual False 1.76 -2.47 4.23 2.00e-01 2.50e+01 4.47e+02 chirality pdb=" C16 9ZK A 379 " pdb=" C17 9ZK A 379 " pdb=" C22 9ZK A 379 " pdb=" N15 9ZK A 379 " both_signs ideal model delta sigma weight residual False 1.76 -2.47 4.23 2.00e-01 2.50e+01 4.47e+02 chirality pdb=" C16 9ZK B 379 " pdb=" C17 9ZK B 379 " pdb=" C22 9ZK B 379 " pdb=" N15 9ZK B 379 " both_signs ideal model delta sigma weight residual False 1.76 -2.46 4.23 2.00e-01 2.50e+01 4.47e+02 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 375 " -0.031 2.00e-02 2.50e+03 6.31e-02 3.98e+01 pdb=" C PHE A 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE A 375 " -0.040 2.00e-02 2.50e+03 pdb=" OXT PHE A 375 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 375 " 0.031 2.00e-02 2.50e+03 6.30e-02 3.97e+01 pdb=" C PHE D 375 " -0.109 2.00e-02 2.50e+03 pdb=" O PHE D 375 " 0.040 2.00e-02 2.50e+03 pdb=" OXT PHE D 375 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.96e+01 pdb=" C PHE C 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE C 375 " -0.040 2.00e-02 2.50e+03 pdb=" OXT PHE C 375 " -0.038 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 899 2.69 - 3.24: 14942 3.24 - 3.80: 24507 3.80 - 4.35: 34314 4.35 - 4.90: 54119 Nonbonded interactions: 128781 Sorted by model distance: nonbonded pdb=" O3 PO4 B 377 " pdb="MG MG B 378 " model vdw 2.141 2.170 nonbonded pdb=" O3 PO4 A 377 " pdb="MG MG A 378 " model vdw 2.141 2.170 nonbonded pdb=" O3 PO4 C 377 " pdb="MG MG C 378 " model vdw 2.141 2.170 nonbonded pdb=" O3 PO4 D 377 " pdb="MG MG D 378 " model vdw 2.141 2.170 nonbonded pdb=" O3 PO4 E 377 " pdb="MG MG E 378 " model vdw 2.142 2.170 ... (remaining 128776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 375) selection = (chain 'B' and resid 5 through 375) selection = (chain 'C' and resid 5 through 375) selection = (chain 'D' and resid 5 through 375) selection = (chain 'E' and resid 5 through 375) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.850 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.430 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.130 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:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 1.155 15240 Z= 3.224 Angle : 3.170 59.262 20690 Z= 1.460 Chirality : 0.233 4.230 2280 Planarity : 0.009 0.063 2630 Dihedral : 14.191 171.667 5610 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1830 helix: -0.33 (0.18), residues: 735 sheet: 0.19 (0.28), residues: 290 loop : 2.16 (0.24), residues: 805 *********************** 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 369 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.849 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.3076 time to fit residues: 159.7764 Evaluate side-chains 168 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5365 ------------------------------------------------------------------------------- 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: 0.9990 chunk 140 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 137 GLN A 297 ASN C 12 ASN C 173 HIS D 12 ASN D 41 GLN D 101 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15240 Z= 0.198 Angle : 1.531 33.930 20690 Z= 0.553 Chirality : 0.046 0.211 2280 Planarity : 0.004 0.026 2630 Dihedral : 17.364 179.834 2130 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer Outliers : 1.34 % 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: 1.57 (0.19), residues: 1830 helix: 0.64 (0.18), residues: 740 sheet: 1.28 (0.30), residues: 260 loop : 1.65 (0.22), residues: 830 *********************** 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 245 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 1.943 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 238 average time/residue: 0.2872 time to fit residues: 99.4180 Evaluate side-chains 153 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.846 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1396 time to fit residues: 4.5052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 59 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS D 137 GLN D 162 ASN E 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 15240 Z= 0.357 Angle : 1.530 32.468 20690 Z= 0.558 Chirality : 0.048 0.265 2280 Planarity : 0.004 0.035 2630 Dihedral : 14.393 155.589 2130 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 1.34 % 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: 1.53 (0.19), residues: 1830 helix: 0.82 (0.19), residues: 730 sheet: 1.09 (0.30), residues: 260 loop : 1.45 (0.22), residues: 840 *********************** 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 167 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 1.929 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 158 average time/residue: 0.3074 time to fit residues: 71.5452 Evaluate side-chains 132 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1539 time to fit residues: 5.5304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 168 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 15240 Z= 0.302 Angle : 1.510 32.320 20690 Z= 0.543 Chirality : 0.046 0.179 2280 Planarity : 0.004 0.044 2630 Dihedral : 14.031 146.904 2130 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 1830 helix: 0.87 (0.19), residues: 730 sheet: 0.95 (0.30), residues: 260 loop : 1.37 (0.21), residues: 840 *********************** 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 139 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.989 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 135 average time/residue: 0.2837 time to fit residues: 57.2253 Evaluate side-chains 126 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1463 time to fit residues: 3.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 15240 Z= 0.436 Angle : 1.527 34.346 20690 Z= 0.556 Chirality : 0.048 0.223 2280 Planarity : 0.005 0.054 2630 Dihedral : 13.975 148.162 2130 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.89 % 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: 1.27 (0.19), residues: 1830 helix: 0.77 (0.19), residues: 730 sheet: 0.74 (0.30), residues: 260 loop : 1.21 (0.21), residues: 840 *********************** 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 138 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.877 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 132 average time/residue: 0.2691 time to fit residues: 53.7320 Evaluate side-chains 121 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2495 time to fit residues: 4.3400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.0980 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 15240 Z= 0.436 Angle : 1.527 34.346 20690 Z= 0.556 Chirality : 0.048 0.223 2280 Planarity : 0.005 0.054 2630 Dihedral : 13.975 148.162 2130 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 1830 helix: 0.77 (0.19), residues: 730 sheet: 0.74 (0.30), residues: 260 loop : 1.21 (0.21), residues: 840 *********************** 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 117 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.851 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3066 time to fit residues: 54.4479 Evaluate side-chains 116 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 15240 Z= 0.180 Angle : 1.498 32.225 20690 Z= 0.535 Chirality : 0.044 0.134 2280 Planarity : 0.004 0.037 2630 Dihedral : 13.633 139.796 2130 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.45 % 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: 1.37 (0.20), residues: 1830 helix: 0.95 (0.20), residues: 730 sheet: 0.10 (0.30), residues: 280 loop : 1.46 (0.22), residues: 820 *********************** 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 132 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.841 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 128 average time/residue: 0.2994 time to fit residues: 57.1028 Evaluate side-chains 123 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2481 time to fit residues: 4.2599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.0040 chunk 106 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 15240 Z= 0.182 Angle : 1.497 32.224 20690 Z= 0.534 Chirality : 0.044 0.133 2280 Planarity : 0.004 0.037 2630 Dihedral : 13.655 139.792 2130 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.06 % 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: 1.37 (0.20), residues: 1830 helix: 0.95 (0.20), residues: 730 sheet: 0.10 (0.30), residues: 280 loop : 1.46 (0.22), residues: 820 *********************** 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 119 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.950 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.3010 time to fit residues: 53.2510 Evaluate side-chains 119 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1682 time to fit residues: 2.7537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 15240 Z= 0.469 Angle : 1.527 33.370 20690 Z= 0.555 Chirality : 0.049 0.201 2280 Planarity : 0.005 0.047 2630 Dihedral : 13.596 141.485 2130 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1830 helix: 0.78 (0.19), residues: 730 sheet: 0.34 (0.28), residues: 310 loop : 1.30 (0.22), residues: 790 *********************** 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 122 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.838 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 120 average time/residue: 0.3032 time to fit residues: 54.4354 Evaluate side-chains 119 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3147 time to fit residues: 3.6496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 15240 Z= 0.469 Angle : 1.527 33.370 20690 Z= 0.555 Chirality : 0.049 0.201 2280 Planarity : 0.005 0.047 2630 Dihedral : 13.596 141.485 2130 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1830 helix: 0.78 (0.19), residues: 730 sheet: 0.34 (0.28), residues: 310 loop : 1.30 (0.22), residues: 790 ********************** 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 117 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.878 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2992 time to fit residues: 52.2321 Evaluate side-chains 116 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 135 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.090369 restraints weight = 21136.119| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.72 r_work: 0.2902 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4207 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= 0.174 Angle : 1.497 32.249 20690 Z= 0.534 Chirality : 0.044 0.162 2280 Planarity : 0.004 0.038 2630 Dihedral : 13.364 135.560 2130 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 1830 helix: 0.95 (0.20), residues: 730 sheet: 0.09 (0.30), residues: 280 loop : 1.37 (0.21), residues: 820 =============================================================================== Job complete usr+sys time: 2756.56 seconds wall clock time: 51 minutes 32.21 seconds (3092.21 seconds total)