Starting phenix.real_space_refine on Sat Mar 16 15:33:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/03_2024/6t23_10365_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/03_2024/6t23_10365.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/03_2024/6t23_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_10365/03_2024/6t23_10365_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/03_2024/6t23_10365_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/03_2024/6t23_10365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/03_2024/6t23_10365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/03_2024/6t23_10365_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t23_10365/03_2024/6t23_10365_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 0.04s 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: 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: 8.72, per 1000 atoms: 0.58 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: 5.59 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: 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: 3.09 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: 4.63 Time building geometry restraints manager: 6.10 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: 8916 34.33 - 68.67: 109 68.67 - 103.00: 30 103.00 - 137.33: 25 137.33 - 171.67: 15 Dihedral angle restraints: 9095 sinusoidal: 3735 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 9092 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: 1.160 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: 4.230 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 42.640 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.080 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.230 ------------------------------------------------------------------------------- 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 : 16.870 171.667 5665 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 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.010 TRP E 340 HIS 0.010 0.004 HIS B 173 PHE 0.025 0.005 PHE A 200 TYR 0.054 0.009 TYR A 279 ARG 0.006 0.001 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8479 (mmm) cc_final: 0.8096 (mmt) REVERT: B 283 MET cc_start: 0.8209 (mmm) cc_final: 0.7967 (mmp) REVERT: C 206 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7448 (ttm-80) REVERT: D 119 MET cc_start: 0.8643 (ttp) cc_final: 0.8413 (ttm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.3039 time to fit residues: 157.4392 Evaluate side-chains 169 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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: 0.9980 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 297 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15240 Z= 0.205 Angle : 1.529 32.846 20690 Z= 0.555 Chirality : 0.045 0.170 2280 Planarity : 0.004 0.027 2630 Dihedral : 21.104 179.706 2185 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.28 % Allowed : 6.45 % Favored : 92.27 % 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: 1.60 (0.19), residues: 1830 helix: 0.68 (0.18), residues: 740 sheet: 1.27 (0.30), residues: 260 loop : 1.65 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.004 0.001 HIS D 101 PHE 0.011 0.002 PHE E 255 TYR 0.012 0.001 TYR D 294 ARG 0.005 0.000 ARG C 39 *********************** 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 242 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 1.843 Fit side-chains REVERT: A 47 MET cc_start: 0.2570 (mmt) cc_final: 0.2099 (mmt) REVERT: B 178 LEU cc_start: 0.8290 (mp) cc_final: 0.8076 (mp) REVERT: C 82 MET cc_start: 0.8743 (tpt) cc_final: 0.8240 (tpt) REVERT: C 206 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.7165 (ttm-80) REVERT: C 305 MET cc_start: 0.8539 (mmm) cc_final: 0.8318 (mmm) REVERT: C 325 MET cc_start: 0.8328 (tpt) cc_final: 0.8097 (mmp) REVERT: C 354 GLN cc_start: 0.8110 (pp30) cc_final: 0.7881 (pp30) REVERT: D 162 ASN cc_start: 0.7760 (m-40) cc_final: 0.7554 (m110) REVERT: D 336 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8190 (tttt) REVERT: E 44 MET cc_start: 0.4168 (tpp) cc_final: 0.3839 (tpp) outliers start: 20 outliers final: 8 residues processed: 236 average time/residue: 0.2972 time to fit residues: 101.5851 Evaluate side-chains 152 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 363 ASP 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: 5.9990 chunk 46 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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** C 40 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS D 137 GLN D 353 GLN E 101 HIS E 173 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 15240 Z= 0.566 Angle : 1.573 32.727 20690 Z= 0.589 Chirality : 0.053 0.326 2280 Planarity : 0.005 0.039 2630 Dihedral : 19.104 176.781 2185 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.30 % Allowed : 8.75 % Favored : 88.95 % 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: 1.00 (0.19), residues: 1830 helix: 0.47 (0.19), residues: 730 sheet: 0.01 (0.28), residues: 310 loop : 1.46 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 340 HIS 0.007 0.002 HIS A 40 PHE 0.016 0.002 PHE B 255 TYR 0.020 0.002 TYR E 337 ARG 0.006 0.001 ARG D 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 174 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.570 Fit side-chains REVERT: A 44 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5602 (ttp) REVERT: A 82 MET cc_start: 0.8338 (tpt) cc_final: 0.8067 (tpt) REVERT: A 325 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7620 (mmt) REVERT: E 44 MET cc_start: 0.4132 (tpp) cc_final: 0.3663 (tpp) outliers start: 36 outliers final: 21 residues processed: 163 average time/residue: 0.2525 time to fit residues: 61.5425 Evaluate side-chains 140 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 304 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8281 moved from start: 0.4217 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= 0.171 Angle : 1.488 32.227 20690 Z= 0.529 Chirality : 0.044 0.144 2280 Planarity : 0.004 0.039 2630 Dihedral : 17.693 132.885 2185 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.96 % Allowed : 10.10 % Favored : 88.95 % 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: 1.50 (0.19), residues: 1830 helix: 0.93 (0.19), residues: 730 sheet: 0.58 (0.28), residues: 310 loop : 1.54 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE B 255 TYR 0.009 0.001 TYR D 294 ARG 0.003 0.000 ARG C 39 *********************** 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 157 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.914 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8222 (tpt) cc_final: 0.7965 (tpt) REVERT: A 325 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7303 (mmt) REVERT: D 82 MET cc_start: 0.8457 (tpt) cc_final: 0.8176 (mmm) REVERT: D 113 LYS cc_start: 0.8623 (mttt) cc_final: 0.8334 (mmtt) outliers start: 15 outliers final: 11 residues processed: 153 average time/residue: 0.2628 time to fit residues: 60.1383 Evaluate side-chains 135 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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: 0.8363 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15240 Z= 0.478 Angle : 1.534 32.363 20690 Z= 0.561 Chirality : 0.050 0.235 2280 Planarity : 0.005 0.042 2630 Dihedral : 18.338 142.419 2185 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.79 % Allowed : 10.22 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 1830 helix: 0.63 (0.19), residues: 730 sheet: 0.08 (0.27), residues: 340 loop : 1.35 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.008 0.002 HIS D 101 PHE 0.013 0.002 PHE B 255 TYR 0.015 0.001 TYR E 337 ARG 0.005 0.001 ARG C 177 *********************** 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 153 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.686 Fit side-chains REVERT: A 82 MET cc_start: 0.8257 (tpt) cc_final: 0.8007 (tpt) REVERT: A 325 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7476 (mmt) REVERT: B 314 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.6947 (tp40) REVERT: E 314 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7900 (tt0) outliers start: 28 outliers final: 18 residues processed: 146 average time/residue: 0.2704 time to fit residues: 58.8950 Evaluate side-chains 139 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 104 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN C 162 ASN D 101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4445 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= 0.203 Angle : 1.487 32.231 20690 Z= 0.528 Chirality : 0.044 0.139 2280 Planarity : 0.004 0.040 2630 Dihedral : 17.722 137.394 2185 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.53 % Allowed : 11.12 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1830 helix: 0.88 (0.20), residues: 730 sheet: 0.38 (0.28), residues: 310 loop : 1.38 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE B 255 TYR 0.008 0.001 TYR D 294 ARG 0.005 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.755 Fit side-chains REVERT: A 82 MET cc_start: 0.8177 (tpt) cc_final: 0.7911 (tpt) REVERT: A 325 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7405 (mmt) REVERT: B 314 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.6956 (tp40) REVERT: C 47 MET cc_start: 0.3610 (OUTLIER) cc_final: 0.2629 (mtt) REVERT: D 82 MET cc_start: 0.8456 (tpt) cc_final: 0.8216 (mmm) REVERT: E 244 ASP cc_start: 0.5234 (OUTLIER) cc_final: 0.4836 (t0) outliers start: 24 outliers final: 19 residues processed: 148 average time/residue: 0.2660 time to fit residues: 59.0541 Evaluate side-chains 145 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15240 Z= 0.164 Angle : 1.480 32.221 20690 Z= 0.524 Chirality : 0.043 0.132 2280 Planarity : 0.004 0.039 2630 Dihedral : 17.515 137.732 2185 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.47 % Allowed : 11.25 % Favored : 87.28 % 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: 1.47 (0.20), residues: 1830 helix: 1.02 (0.20), residues: 730 sheet: 0.49 (0.28), residues: 310 loop : 1.42 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 356 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE B 255 TYR 0.008 0.001 TYR D 294 ARG 0.006 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.655 Fit side-chains REVERT: A 82 MET cc_start: 0.8152 (tpt) cc_final: 0.7898 (tpt) REVERT: A 313 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7336 (ttt) REVERT: A 325 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7391 (mmt) REVERT: B 314 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6917 (tp40) REVERT: C 47 MET cc_start: 0.3075 (OUTLIER) cc_final: 0.2610 (mtt) REVERT: E 244 ASP cc_start: 0.5211 (OUTLIER) cc_final: 0.4839 (t0) outliers start: 23 outliers final: 15 residues processed: 145 average time/residue: 0.2621 time to fit residues: 57.2662 Evaluate side-chains 145 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.0030 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15240 Z= 0.236 Angle : 1.486 32.256 20690 Z= 0.527 Chirality : 0.044 0.133 2280 Planarity : 0.004 0.038 2630 Dihedral : 17.520 137.730 2185 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.53 % Allowed : 11.37 % Favored : 87.09 % 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: 1.46 (0.20), residues: 1830 helix: 1.01 (0.20), residues: 730 sheet: 0.50 (0.28), residues: 310 loop : 1.41 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE B 255 TYR 0.006 0.001 TYR C 143 ARG 0.004 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.798 Fit side-chains REVERT: A 82 MET cc_start: 0.8161 (tpt) cc_final: 0.7903 (tpt) REVERT: A 325 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7410 (mmt) REVERT: B 314 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6957 (tp40) REVERT: E 244 ASP cc_start: 0.5224 (OUTLIER) cc_final: 0.4852 (t0) REVERT: E 355 MET cc_start: 0.7424 (mmt) cc_final: 0.7133 (mmt) outliers start: 24 outliers final: 18 residues processed: 141 average time/residue: 0.2554 time to fit residues: 54.1336 Evaluate side-chains 144 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15240 Z= 0.236 Angle : 1.486 32.256 20690 Z= 0.527 Chirality : 0.044 0.133 2280 Planarity : 0.004 0.038 2630 Dihedral : 17.521 137.730 2185 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.34 % Allowed : 11.57 % Favored : 87.09 % 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: 1.46 (0.20), residues: 1830 helix: 1.01 (0.20), residues: 730 sheet: 0.50 (0.28), residues: 310 loop : 1.41 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE B 255 TYR 0.006 0.001 TYR C 143 ARG 0.004 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.891 Fit side-chains REVERT: A 82 MET cc_start: 0.8162 (tpt) cc_final: 0.7903 (tpt) REVERT: A 325 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7410 (mmt) REVERT: B 314 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6957 (tp40) REVERT: E 244 ASP cc_start: 0.5223 (OUTLIER) cc_final: 0.4852 (t0) REVERT: E 355 MET cc_start: 0.7378 (mmt) cc_final: 0.7133 (mmt) outliers start: 21 outliers final: 18 residues processed: 139 average time/residue: 0.2691 time to fit residues: 56.1802 Evaluate side-chains 144 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15240 Z= 0.236 Angle : 1.486 32.256 20690 Z= 0.527 Chirality : 0.044 0.133 2280 Planarity : 0.004 0.038 2630 Dihedral : 17.523 137.730 2185 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.34 % Allowed : 11.57 % Favored : 87.09 % 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: 1.46 (0.20), residues: 1830 helix: 1.01 (0.20), residues: 730 sheet: 0.50 (0.28), residues: 310 loop : 1.41 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE B 255 TYR 0.006 0.001 TYR C 143 ARG 0.004 0.000 ARG E 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.641 Fit side-chains REVERT: A 82 MET cc_start: 0.8162 (tpt) cc_final: 0.7903 (tpt) REVERT: A 325 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7410 (mmt) REVERT: B 314 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6957 (tp40) REVERT: E 244 ASP cc_start: 0.5223 (OUTLIER) cc_final: 0.4852 (t0) REVERT: E 355 MET cc_start: 0.7378 (mmt) cc_final: 0.7133 (mmt) outliers start: 21 outliers final: 18 residues processed: 139 average time/residue: 0.2753 time to fit residues: 57.2490 Evaluate side-chains 144 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.091035 restraints weight = 21193.785| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.77 r_work: 0.2905 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 15240 Z= 0.247 Angle : 1.486 32.251 20690 Z= 0.527 Chirality : 0.044 0.132 2280 Planarity : 0.004 0.038 2630 Dihedral : 17.551 137.723 2185 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.34 % Allowed : 11.63 % Favored : 87.03 % 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: 1.46 (0.20), residues: 1830 helix: 1.02 (0.20), residues: 730 sheet: 0.50 (0.28), residues: 310 loop : 1.41 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE B 255 TYR 0.006 0.001 TYR C 143 ARG 0.003 0.000 ARG E 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2872.15 seconds wall clock time: 53 minutes 3.92 seconds (3183.92 seconds total)