Starting phenix.real_space_refine on Fri Feb 16 04:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooe_3838/02_2024/5ooe_3838_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooe_3838/02_2024/5ooe_3838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooe_3838/02_2024/5ooe_3838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooe_3838/02_2024/5ooe_3838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooe_3838/02_2024/5ooe_3838_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooe_3838/02_2024/5ooe_3838_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 95 5.16 5 C 9020 2.51 5 N 2405 2.21 5 O 2770 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 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 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 TYR 362": "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 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 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 TYR 362": "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 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 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 TYR 362": "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 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 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 TYR 362": "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 ASP 154": "OD1" <-> "OD2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 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 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14310 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.20, per 1000 atoms: 0.57 Number of scatterers: 14310 At special positions: 0 Unit cell: (99.18, 91.2, 193.8, 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 95 16.00 P 15 15.00 Mg 5 11.99 O 2770 8.00 N 2405 7.00 C 9020 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: 5.93 Conformation dependent library (CDL) restraints added in 2.8 seconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 20 sheets defined 44.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.336A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 252 through 261 removed outlier: 5.047A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.272A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.561A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.963A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 370 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 195 removed outlier: 4.336A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 252 through 261 removed outlier: 5.047A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.272A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.562A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.963A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.336A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 252 through 261 removed outlier: 5.047A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.272A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.561A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.963A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 370 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.336A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 252 through 261 removed outlier: 5.047A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.272A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.562A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 4.963A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 370 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.336A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 231 Processing helix chain 'E' and resid 252 through 261 removed outlier: 5.048A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.271A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.562A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 removed outlier: 4.964A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 370 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.551A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.013A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.015A 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: 6.552A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.014A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.016A 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: 6.552A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.014A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.016A 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: 6.552A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.014A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.016A 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: 6.553A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.013A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.016A 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 241 540 hydrogen bonds defined for protein. 1290 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: 4.44 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3628 1.32 - 1.44: 3102 1.44 - 1.56: 7690 1.56 - 1.68: 30 1.68 - 1.81: 170 Bond restraints: 14620 Sorted by residual: bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 14615 not shown) Histogram of bond angle deviations from ideal: 94.36 - 102.37: 82 102.37 - 110.38: 4564 110.38 - 118.39: 7154 118.39 - 126.39: 7881 126.39 - 134.40: 179 Bond angle restraints: 19860 Sorted by residual: angle pdb=" C GLN E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta sigma weight residual 119.84 128.62 -8.78 1.25e+00 6.40e-01 4.93e+01 angle pdb=" C GLN A 263 " pdb=" N PRO A 264 " pdb=" CA PRO A 264 " ideal model delta sigma weight residual 119.84 128.61 -8.77 1.25e+00 6.40e-01 4.92e+01 angle pdb=" C GLN B 263 " pdb=" N PRO B 264 " pdb=" CA PRO B 264 " ideal model delta sigma weight residual 119.84 128.59 -8.75 1.25e+00 6.40e-01 4.90e+01 angle pdb=" C GLN C 263 " pdb=" N PRO C 264 " pdb=" CA PRO C 264 " ideal model delta sigma weight residual 119.84 128.56 -8.72 1.25e+00 6.40e-01 4.87e+01 angle pdb=" C GLN D 263 " pdb=" N PRO D 264 " pdb=" CA PRO D 264 " ideal model delta sigma weight residual 119.84 128.55 -8.71 1.25e+00 6.40e-01 4.85e+01 ... (remaining 19855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 8425 18.22 - 36.44: 280 36.44 - 54.66: 80 54.66 - 72.87: 55 72.87 - 91.09: 40 Dihedral angle restraints: 8880 sinusoidal: 3640 harmonic: 5240 Sorted by residual: dihedral pdb=" C5' ANP A 401 " pdb=" C3' ANP A 401 " pdb=" C4' ANP A 401 " pdb=" O3' ANP A 401 " ideal model delta sinusoidal sigma weight residual -74.79 -165.88 91.09 1 3.00e+01 1.11e-03 1.09e+01 dihedral pdb=" C5' ANP E 401 " pdb=" C3' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " ideal model delta sinusoidal sigma weight residual -74.79 -165.88 91.09 1 3.00e+01 1.11e-03 1.09e+01 dihedral pdb=" C5' ANP B 401 " pdb=" C3' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " ideal model delta sinusoidal sigma weight residual -74.79 -165.86 91.07 1 3.00e+01 1.11e-03 1.09e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1712 0.085 - 0.169: 468 0.169 - 0.254: 30 0.254 - 0.339: 0 0.339 - 0.423: 5 Chirality restraints: 2215 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" C3' ANP E 401 " pdb=" C2' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C3' ANP A 401 " pdb=" C2' ANP A 401 " pdb=" C4' ANP A 401 " pdb=" O3' ANP A 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 2212 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP D 401 " 0.404 2.00e-02 2.50e+03 1.59e-01 6.95e+02 pdb=" C2 ANP D 401 " -0.042 2.00e-02 2.50e+03 pdb=" C4 ANP D 401 " -0.118 2.00e-02 2.50e+03 pdb=" C5 ANP D 401 " -0.030 2.00e-02 2.50e+03 pdb=" C6 ANP D 401 " 0.059 2.00e-02 2.50e+03 pdb=" C8 ANP D 401 " -0.132 2.00e-02 2.50e+03 pdb=" N1 ANP D 401 " 0.047 2.00e-02 2.50e+03 pdb=" N3 ANP D 401 " -0.120 2.00e-02 2.50e+03 pdb=" N6 ANP D 401 " 0.160 2.00e-02 2.50e+03 pdb=" N7 ANP D 401 " -0.047 2.00e-02 2.50e+03 pdb=" N9 ANP D 401 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP E 401 " 0.404 2.00e-02 2.50e+03 1.59e-01 6.95e+02 pdb=" C2 ANP E 401 " -0.042 2.00e-02 2.50e+03 pdb=" C4 ANP E 401 " -0.118 2.00e-02 2.50e+03 pdb=" C5 ANP E 401 " -0.030 2.00e-02 2.50e+03 pdb=" C6 ANP E 401 " 0.059 2.00e-02 2.50e+03 pdb=" C8 ANP E 401 " -0.132 2.00e-02 2.50e+03 pdb=" N1 ANP E 401 " 0.048 2.00e-02 2.50e+03 pdb=" N3 ANP E 401 " -0.120 2.00e-02 2.50e+03 pdb=" N6 ANP E 401 " 0.160 2.00e-02 2.50e+03 pdb=" N7 ANP E 401 " -0.047 2.00e-02 2.50e+03 pdb=" N9 ANP E 401 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP A 401 " 0.404 2.00e-02 2.50e+03 1.59e-01 6.95e+02 pdb=" C2 ANP A 401 " -0.042 2.00e-02 2.50e+03 pdb=" C4 ANP A 401 " -0.118 2.00e-02 2.50e+03 pdb=" C5 ANP A 401 " -0.030 2.00e-02 2.50e+03 pdb=" C6 ANP A 401 " 0.059 2.00e-02 2.50e+03 pdb=" C8 ANP A 401 " -0.132 2.00e-02 2.50e+03 pdb=" N1 ANP A 401 " 0.047 2.00e-02 2.50e+03 pdb=" N3 ANP A 401 " -0.120 2.00e-02 2.50e+03 pdb=" N6 ANP A 401 " 0.160 2.00e-02 2.50e+03 pdb=" N7 ANP A 401 " -0.048 2.00e-02 2.50e+03 pdb=" N9 ANP A 401 " -0.181 2.00e-02 2.50e+03 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 62 2.53 - 3.12: 12663 3.12 - 3.72: 21900 3.72 - 4.31: 35198 4.31 - 4.90: 53207 Nonbonded interactions: 123030 Sorted by model distance: nonbonded pdb=" O1G ANP A 401 " pdb="MG MG A 402 " model vdw 1.939 2.170 nonbonded pdb=" O1G ANP E 401 " pdb="MG MG E 402 " model vdw 1.939 2.170 nonbonded pdb=" O1G ANP D 401 " pdb="MG MG D 402 " model vdw 1.940 2.170 nonbonded pdb=" O1G ANP C 401 " pdb="MG MG C 402 " model vdw 1.940 2.170 nonbonded pdb=" O1G ANP B 401 " pdb="MG MG B 402 " model vdw 1.940 2.170 ... (remaining 123025 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 4.710 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 41.060 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.016 0.177 14620 Z= 1.065 Angle : 1.635 16.965 19860 Z= 1.009 Chirality : 0.075 0.423 2215 Planarity : 0.019 0.159 2525 Dihedral : 13.638 91.091 5520 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 1.97 % Allowed : 4.79 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1775 helix: -1.35 (0.16), residues: 745 sheet: -0.63 (0.29), residues: 285 loop : -0.29 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.006 TRP B 340 HIS 0.006 0.002 HIS E 88 PHE 0.009 0.003 PHE E 352 TYR 0.032 0.006 TYR B 166 ARG 0.006 0.001 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8025 (p0) cc_final: 0.7802 (p0) REVERT: A 62 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8177 (ttm170) REVERT: A 176 MET cc_start: 0.8621 (mmm) cc_final: 0.8421 (mmt) REVERT: A 191 LYS cc_start: 0.8780 (tttt) cc_final: 0.8204 (ttmm) REVERT: A 270 GLU cc_start: 0.5935 (pt0) cc_final: 0.5432 (mm-30) REVERT: A 355 MET cc_start: 0.8348 (mmm) cc_final: 0.7657 (mtt) REVERT: B 16 LEU cc_start: 0.9174 (mt) cc_final: 0.8901 (mp) REVERT: B 78 ASN cc_start: 0.8779 (t0) cc_final: 0.8306 (t0) REVERT: B 270 GLU cc_start: 0.7243 (pt0) cc_final: 0.6894 (tt0) REVERT: B 283 MET cc_start: 0.8595 (mmp) cc_final: 0.8333 (mmt) REVERT: B 291 LYS cc_start: 0.9014 (tmmt) cc_final: 0.8237 (mptt) REVERT: B 315 LYS cc_start: 0.8834 (tttm) cc_final: 0.8628 (tttm) REVERT: C 148 THR cc_start: 0.8416 (p) cc_final: 0.8184 (t) REVERT: C 283 MET cc_start: 0.8602 (mmp) cc_final: 0.8400 (mmm) REVERT: E 134 VAL cc_start: 0.8876 (t) cc_final: 0.8581 (m) REVERT: E 276 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8006 (mp0) REVERT: E 367 PRO cc_start: 0.8851 (Cg_exo) cc_final: 0.7940 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.2923 time to fit residues: 191.0239 Evaluate side-chains 210 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.0070 chunk 72 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS B 173 HIS B 371 HIS C 161 HIS C 371 HIS D 161 HIS E 161 HIS E 246 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14620 Z= 0.194 Angle : 0.544 6.875 19860 Z= 0.296 Chirality : 0.046 0.165 2215 Planarity : 0.008 0.079 2525 Dihedral : 9.042 72.416 2130 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.83 % Allowed : 10.13 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1775 helix: -0.27 (0.17), residues: 760 sheet: -0.07 (0.30), residues: 270 loop : 0.36 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 340 HIS 0.005 0.001 HIS C 88 PHE 0.012 0.001 PHE D 124 TYR 0.009 0.001 TYR D 294 ARG 0.005 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 319 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9193 (mm) cc_final: 0.8974 (pt) REVERT: A 191 LYS cc_start: 0.8487 (tttt) cc_final: 0.7873 (ttmm) REVERT: A 270 GLU cc_start: 0.6079 (pt0) cc_final: 0.5480 (mm-30) REVERT: A 355 MET cc_start: 0.8280 (mmm) cc_final: 0.7703 (mtt) REVERT: B 82 MET cc_start: 0.8724 (tpt) cc_final: 0.8353 (tpt) REVERT: B 149 THR cc_start: 0.8907 (m) cc_final: 0.8633 (p) REVERT: B 283 MET cc_start: 0.8405 (mmp) cc_final: 0.8169 (mmt) REVERT: B 291 LYS cc_start: 0.8993 (tmmt) cc_final: 0.8340 (mptt) REVERT: C 64 ILE cc_start: 0.9392 (mm) cc_final: 0.9169 (pt) REVERT: C 248 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8801 (pt) REVERT: C 355 MET cc_start: 0.8367 (mmm) cc_final: 0.8145 (mtt) REVERT: E 227 MET cc_start: 0.8375 (mmm) cc_final: 0.8115 (mmm) REVERT: E 249 THR cc_start: 0.8537 (m) cc_final: 0.8103 (p) outliers start: 28 outliers final: 15 residues processed: 338 average time/residue: 0.2238 time to fit residues: 115.5183 Evaluate side-chains 247 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN B 371 HIS C 371 HIS D 59 GLN D 101 HIS ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14620 Z= 0.237 Angle : 0.520 6.185 19860 Z= 0.273 Chirality : 0.045 0.155 2215 Planarity : 0.006 0.047 2525 Dihedral : 8.110 71.474 2130 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.14 % Allowed : 12.48 % Favored : 84.38 % 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: 0.69 (0.20), residues: 1775 helix: 0.37 (0.19), residues: 730 sheet: 0.11 (0.31), residues: 270 loop : 0.97 (0.25), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.008 0.002 HIS C 88 PHE 0.012 0.001 PHE E 124 TYR 0.020 0.001 TYR E 133 ARG 0.002 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 276 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8638 (tttt) cc_final: 0.8038 (ttmm) REVERT: A 305 MET cc_start: 0.9031 (mmm) cc_final: 0.8634 (mpp) REVERT: A 355 MET cc_start: 0.8342 (mmm) cc_final: 0.7936 (mtt) REVERT: B 149 THR cc_start: 0.8890 (m) cc_final: 0.8594 (p) REVERT: B 283 MET cc_start: 0.8348 (mmp) cc_final: 0.8137 (mmt) REVERT: B 291 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8388 (mptt) REVERT: C 24 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: C 72 GLU cc_start: 0.8384 (pm20) cc_final: 0.8058 (pm20) REVERT: C 248 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8682 (pt) REVERT: C 259 GLU cc_start: 0.8489 (tp30) cc_final: 0.8254 (tp30) REVERT: C 305 MET cc_start: 0.8939 (mmm) cc_final: 0.8253 (mpp) REVERT: D 148 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8189 (t) REVERT: E 249 THR cc_start: 0.8743 (m) cc_final: 0.8398 (p) REVERT: E 325 MET cc_start: 0.8416 (tpp) cc_final: 0.7866 (tpp) outliers start: 48 outliers final: 34 residues processed: 312 average time/residue: 0.2166 time to fit residues: 105.8505 Evaluate side-chains 255 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS C 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 14620 Z= 0.376 Angle : 0.582 5.473 19860 Z= 0.302 Chirality : 0.047 0.153 2215 Planarity : 0.005 0.044 2525 Dihedral : 8.213 70.285 2130 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.05 % Allowed : 13.99 % Favored : 81.96 % 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: 0.47 (0.20), residues: 1775 helix: 0.29 (0.19), residues: 730 sheet: 0.07 (0.32), residues: 270 loop : 0.69 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 79 HIS 0.020 0.002 HIS C 371 PHE 0.012 0.002 PHE E 124 TYR 0.021 0.001 TYR E 133 ARG 0.005 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 222 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8673 (tttt) cc_final: 0.8081 (ttmm) REVERT: A 325 MET cc_start: 0.8016 (tpp) cc_final: 0.7695 (tpp) REVERT: A 355 MET cc_start: 0.8320 (mmm) cc_final: 0.7902 (mtt) REVERT: B 76 ILE cc_start: 0.8943 (mp) cc_final: 0.8583 (mp) REVERT: B 82 MET cc_start: 0.8857 (tpt) cc_final: 0.8634 (tpt) REVERT: B 291 LYS cc_start: 0.8936 (tmmt) cc_final: 0.8353 (mptt) REVERT: C 24 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: C 72 GLU cc_start: 0.8343 (pm20) cc_final: 0.8074 (pm20) REVERT: C 82 MET cc_start: 0.8798 (tpt) cc_final: 0.8196 (tpt) REVERT: C 305 MET cc_start: 0.8964 (mmm) cc_final: 0.8273 (mpp) REVERT: C 371 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6808 (m90) REVERT: D 148 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8410 (t) REVERT: D 325 MET cc_start: 0.8613 (mmm) cc_final: 0.8018 (mmm) REVERT: D 353 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7868 (mm110) REVERT: E 12 ASN cc_start: 0.8250 (p0) cc_final: 0.8038 (p0) REVERT: E 249 THR cc_start: 0.8959 (m) cc_final: 0.8626 (p) outliers start: 62 outliers final: 44 residues processed: 267 average time/residue: 0.2113 time to fit residues: 88.5572 Evaluate side-chains 244 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN A 173 HIS C 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 14620 Z= 0.240 Angle : 0.506 8.397 19860 Z= 0.259 Chirality : 0.044 0.152 2215 Planarity : 0.005 0.040 2525 Dihedral : 7.886 70.512 2130 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.92 % Allowed : 15.03 % Favored : 81.05 % 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: 0.65 (0.20), residues: 1775 helix: 0.49 (0.19), residues: 750 sheet: 0.05 (0.31), residues: 270 loop : 0.79 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.013 0.001 HIS C 371 PHE 0.009 0.001 PHE E 124 TYR 0.017 0.001 TYR E 133 ARG 0.002 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 219 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8606 (tttt) cc_final: 0.7951 (ttmm) REVERT: A 283 MET cc_start: 0.8378 (mmm) cc_final: 0.8171 (mmm) REVERT: A 325 MET cc_start: 0.7867 (tpp) cc_final: 0.7564 (tpp) REVERT: A 355 MET cc_start: 0.8238 (mmm) cc_final: 0.7908 (mtt) REVERT: B 76 ILE cc_start: 0.8930 (mp) cc_final: 0.8541 (mp) REVERT: B 82 MET cc_start: 0.8829 (tpt) cc_final: 0.8534 (tpt) REVERT: B 291 LYS cc_start: 0.8875 (tmmt) cc_final: 0.8154 (mptt) REVERT: B 313 MET cc_start: 0.8531 (tpp) cc_final: 0.8001 (tpt) REVERT: C 24 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: C 72 GLU cc_start: 0.8340 (pm20) cc_final: 0.8108 (pm20) REVERT: C 82 MET cc_start: 0.8644 (tpt) cc_final: 0.8172 (tpt) REVERT: C 283 MET cc_start: 0.8505 (mmm) cc_final: 0.8265 (mmm) REVERT: C 305 MET cc_start: 0.8894 (mmm) cc_final: 0.8218 (mpp) REVERT: D 82 MET cc_start: 0.8906 (mmm) cc_final: 0.8303 (tpt) REVERT: D 148 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8463 (t) REVERT: D 325 MET cc_start: 0.8581 (mmm) cc_final: 0.7954 (mmm) REVERT: E 12 ASN cc_start: 0.8246 (p0) cc_final: 0.7970 (p0) REVERT: E 249 THR cc_start: 0.8953 (m) cc_final: 0.8644 (p) outliers start: 60 outliers final: 41 residues processed: 264 average time/residue: 0.2063 time to fit residues: 86.3349 Evaluate side-chains 243 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 14620 Z= 0.263 Angle : 0.513 7.531 19860 Z= 0.262 Chirality : 0.044 0.149 2215 Planarity : 0.005 0.039 2525 Dihedral : 7.833 71.257 2130 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.66 % Allowed : 15.36 % Favored : 80.98 % 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: 0.76 (0.20), residues: 1775 helix: 0.65 (0.19), residues: 720 sheet: -0.02 (0.31), residues: 270 loop : 0.82 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 79 HIS 0.006 0.001 HIS A 275 PHE 0.012 0.001 PHE A 262 TYR 0.016 0.001 TYR E 133 ARG 0.003 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 223 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.7924 (t0) cc_final: 0.7596 (t0) REVERT: A 83 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7725 (tm-30) REVERT: A 191 LYS cc_start: 0.8654 (tttt) cc_final: 0.7998 (ttmm) REVERT: A 283 MET cc_start: 0.8375 (mmm) cc_final: 0.8037 (tpp) REVERT: A 325 MET cc_start: 0.7640 (tpp) cc_final: 0.7328 (tpp) REVERT: A 355 MET cc_start: 0.8249 (mmm) cc_final: 0.7919 (mtt) REVERT: B 76 ILE cc_start: 0.8939 (mp) cc_final: 0.8555 (mp) REVERT: B 82 MET cc_start: 0.8840 (tpt) cc_final: 0.8574 (tpt) REVERT: C 24 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: C 72 GLU cc_start: 0.8340 (pm20) cc_final: 0.8100 (pm20) REVERT: C 82 MET cc_start: 0.8661 (tpt) cc_final: 0.8245 (tpt) REVERT: C 259 GLU cc_start: 0.8535 (tp30) cc_final: 0.8286 (tp30) REVERT: C 283 MET cc_start: 0.8488 (mmm) cc_final: 0.8235 (mmm) REVERT: C 305 MET cc_start: 0.8904 (mmm) cc_final: 0.8558 (tpp) REVERT: D 12 ASN cc_start: 0.8621 (t0) cc_final: 0.8331 (t0) REVERT: D 148 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8478 (t) REVERT: E 249 THR cc_start: 0.8992 (m) cc_final: 0.8728 (p) REVERT: E 325 MET cc_start: 0.8556 (mmm) cc_final: 0.8031 (tpp) outliers start: 56 outliers final: 48 residues processed: 264 average time/residue: 0.2095 time to fit residues: 87.8750 Evaluate side-chains 254 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 204 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 97 optimal weight: 0.0050 chunk 173 optimal weight: 0.2980 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 0.0060 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN B 371 HIS C 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.125 14620 Z= 0.154 Angle : 0.476 10.517 19860 Z= 0.242 Chirality : 0.042 0.149 2215 Planarity : 0.004 0.041 2525 Dihedral : 7.362 74.472 2130 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.16 % Allowed : 17.19 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1775 helix: 0.86 (0.19), residues: 720 sheet: 0.12 (0.31), residues: 270 loop : 0.98 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.005 0.001 HIS A 275 PHE 0.009 0.001 PHE A 255 TYR 0.013 0.001 TYR E 133 ARG 0.008 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 242 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7552 (mm-30) REVERT: A 132 MET cc_start: 0.8066 (ptm) cc_final: 0.7274 (ttp) REVERT: A 191 LYS cc_start: 0.8553 (tttt) cc_final: 0.7875 (ttmm) REVERT: A 330 ILE cc_start: 0.8656 (mt) cc_final: 0.8455 (mt) REVERT: B 149 THR cc_start: 0.9048 (m) cc_final: 0.8729 (p) REVERT: B 305 MET cc_start: 0.8911 (mmm) cc_final: 0.8700 (tpp) REVERT: B 313 MET cc_start: 0.8332 (tpp) cc_final: 0.7849 (tpt) REVERT: C 72 GLU cc_start: 0.8339 (pm20) cc_final: 0.8119 (pm20) REVERT: C 259 GLU cc_start: 0.8543 (tp30) cc_final: 0.8248 (tp30) REVERT: C 283 MET cc_start: 0.8391 (mmm) cc_final: 0.7942 (mmm) REVERT: C 305 MET cc_start: 0.8843 (mmm) cc_final: 0.8416 (mpp) REVERT: D 227 MET cc_start: 0.8046 (tpp) cc_final: 0.7479 (mmt) REVERT: D 353 GLN cc_start: 0.8037 (mm110) cc_final: 0.7796 (mm-40) REVERT: E 191 LYS cc_start: 0.9149 (tttt) cc_final: 0.8942 (tttp) REVERT: E 249 THR cc_start: 0.8906 (m) cc_final: 0.8612 (p) REVERT: E 305 MET cc_start: 0.9111 (mmm) cc_final: 0.8601 (tpp) REVERT: E 325 MET cc_start: 0.8477 (mmm) cc_final: 0.8001 (tpp) outliers start: 33 outliers final: 25 residues processed: 265 average time/residue: 0.2148 time to fit residues: 88.9923 Evaluate side-chains 237 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 14620 Z= 0.312 Angle : 0.554 7.747 19860 Z= 0.283 Chirality : 0.045 0.162 2215 Planarity : 0.005 0.043 2525 Dihedral : 7.683 72.133 2130 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.94 % Allowed : 16.93 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1775 helix: 0.73 (0.19), residues: 720 sheet: 0.03 (0.31), residues: 270 loop : 0.95 (0.25), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 79 HIS 0.007 0.001 HIS C 88 PHE 0.012 0.001 PHE A 262 TYR 0.018 0.001 TYR E 133 ARG 0.006 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 1.731 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7645 (mm-30) REVERT: A 191 LYS cc_start: 0.8673 (tttt) cc_final: 0.8053 (ttmm) REVERT: A 330 ILE cc_start: 0.8732 (mt) cc_final: 0.8527 (mt) REVERT: B 82 MET cc_start: 0.8866 (tpt) cc_final: 0.8647 (tpt) REVERT: B 313 MET cc_start: 0.8487 (tpp) cc_final: 0.7819 (tpt) REVERT: C 82 MET cc_start: 0.8684 (tpt) cc_final: 0.8322 (tpt) REVERT: C 259 GLU cc_start: 0.8593 (tp30) cc_final: 0.8314 (tp30) REVERT: C 283 MET cc_start: 0.8488 (mmm) cc_final: 0.8227 (mmm) REVERT: C 305 MET cc_start: 0.8918 (mmm) cc_final: 0.8581 (tpp) REVERT: E 191 LYS cc_start: 0.9147 (tttt) cc_final: 0.8938 (tttp) REVERT: E 249 THR cc_start: 0.8997 (m) cc_final: 0.8738 (p) outliers start: 45 outliers final: 39 residues processed: 236 average time/residue: 0.2117 time to fit residues: 79.5643 Evaluate side-chains 237 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS C 88 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 14620 Z= 0.323 Angle : 0.574 10.011 19860 Z= 0.290 Chirality : 0.046 0.169 2215 Planarity : 0.005 0.041 2525 Dihedral : 7.794 74.645 2130 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.40 % Allowed : 16.80 % Favored : 79.80 % 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: 0.64 (0.20), residues: 1775 helix: 0.67 (0.19), residues: 715 sheet: -0.26 (0.29), residues: 300 loop : 0.73 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 79 HIS 0.007 0.001 HIS C 88 PHE 0.011 0.001 PHE A 262 TYR 0.021 0.001 TYR A 279 ARG 0.005 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 1.695 Fit side-chains revert: symmetry clash REVERT: A 89 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 191 LYS cc_start: 0.8766 (tttt) cc_final: 0.8183 (ttmm) REVERT: B 76 ILE cc_start: 0.8916 (mp) cc_final: 0.8527 (mp) REVERT: B 82 MET cc_start: 0.8842 (tpt) cc_final: 0.8615 (tpt) REVERT: B 291 LYS cc_start: 0.8885 (tmmt) cc_final: 0.8311 (mptt) REVERT: B 313 MET cc_start: 0.8546 (tpp) cc_final: 0.7822 (tpt) REVERT: C 82 MET cc_start: 0.8684 (tpt) cc_final: 0.8241 (tpt) REVERT: C 259 GLU cc_start: 0.8597 (tp30) cc_final: 0.8174 (tp30) REVERT: C 283 MET cc_start: 0.8523 (mmm) cc_final: 0.8299 (mmm) REVERT: C 305 MET cc_start: 0.8927 (mmm) cc_final: 0.8568 (tpp) REVERT: D 325 MET cc_start: 0.7639 (mmm) cc_final: 0.7390 (ttp) REVERT: E 12 ASN cc_start: 0.8199 (p0) cc_final: 0.7985 (p0) REVERT: E 191 LYS cc_start: 0.9151 (tttt) cc_final: 0.8932 (tttp) REVERT: E 249 THR cc_start: 0.9025 (m) cc_final: 0.8779 (p) outliers start: 52 outliers final: 44 residues processed: 233 average time/residue: 0.2113 time to fit residues: 78.8861 Evaluate side-chains 235 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 190 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.0170 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14620 Z= 0.205 Angle : 0.531 9.826 19860 Z= 0.268 Chirality : 0.044 0.164 2215 Planarity : 0.004 0.037 2525 Dihedral : 7.570 76.664 2130 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.35 % Allowed : 17.97 % Favored : 79.67 % 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: 0.59 (0.20), residues: 1775 helix: 0.60 (0.19), residues: 755 sheet: -0.21 (0.30), residues: 300 loop : 0.71 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.004 0.001 HIS E 275 PHE 0.010 0.001 PHE A 262 TYR 0.022 0.001 TYR A 279 ARG 0.004 0.000 ARG A 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8742 (tttt) cc_final: 0.8111 (ttmm) REVERT: A 325 MET cc_start: 0.6964 (tpp) cc_final: 0.6713 (tpt) REVERT: B 76 ILE cc_start: 0.8864 (mp) cc_final: 0.8491 (mp) REVERT: B 82 MET cc_start: 0.8827 (tpt) cc_final: 0.8601 (tpt) REVERT: B 313 MET cc_start: 0.8468 (tpp) cc_final: 0.7712 (tpt) REVERT: C 24 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: C 259 GLU cc_start: 0.8553 (tp30) cc_final: 0.8272 (tp30) REVERT: C 305 MET cc_start: 0.8896 (mmm) cc_final: 0.8559 (tpp) REVERT: D 325 MET cc_start: 0.7519 (mmm) cc_final: 0.7284 (ttp) REVERT: D 353 GLN cc_start: 0.8068 (mm110) cc_final: 0.7825 (mm-40) REVERT: E 12 ASN cc_start: 0.8125 (p0) cc_final: 0.7896 (p0) REVERT: E 191 LYS cc_start: 0.9145 (tttt) cc_final: 0.8933 (tttp) REVERT: E 249 THR cc_start: 0.9006 (m) cc_final: 0.8768 (p) REVERT: E 305 MET cc_start: 0.9132 (mmm) cc_final: 0.8663 (tpp) REVERT: E 313 MET cc_start: 0.8182 (ttm) cc_final: 0.7821 (ttm) outliers start: 36 outliers final: 33 residues processed: 229 average time/residue: 0.2143 time to fit residues: 77.9202 Evaluate side-chains 230 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 125 optimal weight: 0.7980 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN B 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086355 restraints weight = 25802.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.089193 restraints weight = 12939.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.090955 restraints weight = 7598.853| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 14620 Z= 0.202 Angle : 0.521 9.754 19860 Z= 0.263 Chirality : 0.044 0.160 2215 Planarity : 0.004 0.037 2525 Dihedral : 7.426 76.606 2130 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.55 % Allowed : 18.30 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1775 helix: 0.84 (0.20), residues: 715 sheet: -0.21 (0.30), residues: 295 loop : 0.76 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 79 HIS 0.004 0.001 HIS E 275 PHE 0.010 0.001 PHE A 255 TYR 0.016 0.001 TYR A 279 ARG 0.003 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.28 seconds wall clock time: 51 minutes 10.82 seconds (3070.82 seconds total)