Starting phenix.real_space_refine on Sat Mar 16 15:15:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/03_2024/8oi8_16888_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/03_2024/8oi8_16888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/03_2024/8oi8_16888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/03_2024/8oi8_16888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/03_2024/8oi8_16888_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/03_2024/8oi8_16888_updated.pdb" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 95 5.16 5 C 9050 2.51 5 N 2390 2.21 5 O 3345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14895 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2834 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} 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: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2834 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} 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: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2834 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} 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: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2834 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} 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: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2834 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Time building chain proxies: 8.50, per 1000 atoms: 0.57 Number of scatterers: 14895 At special positions: 0 Unit cell: (92.435, 93.13, 193.21, 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 10 15.00 Mg 5 11.99 O 3345 8.00 N 2390 7.00 C 9050 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: 5.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 20 sheets defined 44.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.730A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.714A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.524A pdb=" N ARG C 290 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.552A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 359 through 370 Proline residue: C 367 - end of helix removed outlier: 5.266A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.729A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.714A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.525A pdb=" N ARG A 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.552A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 370 Proline residue: A 367 - end of helix removed outlier: 5.266A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.730A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.713A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.525A pdb=" N ARG B 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.553A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 370 Proline residue: B 367 - end of helix removed outlier: 5.267A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.730A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.713A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.525A pdb=" N ARG D 290 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.553A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 370 Proline residue: D 367 - end of helix removed outlier: 5.267A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.730A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.713A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.524A pdb=" N ARG E 290 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 294 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 3.553A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 359 through 370 Proline residue: E 367 - end of helix removed outlier: 5.267A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.526A pdb=" N VAL C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA C 135 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.371A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.526A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.372A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.526A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.371A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.526A pdb=" N VAL D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA D 135 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL 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: 6.371A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET 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: 6.526A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL 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: 6.371A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N MET E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 505 hydrogen bonds defined for protein. 1245 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: 4.38 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4643 1.34 - 1.46: 2873 1.46 - 1.57: 6929 1.57 - 1.69: 15 1.69 - 1.81: 170 Bond restraints: 14630 Sorted by residual: bond pdb=" CG HIC C 73 " pdb=" ND1 HIC C 73 " ideal model delta sigma weight residual 1.370 1.312 0.058 2.00e-02 2.50e+03 8.30e+00 bond pdb=" CG HIC E 73 " pdb=" ND1 HIC E 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" CG HIC B 73 " pdb=" ND1 HIC B 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.14e+00 bond pdb=" CG HIC D 73 " pdb=" ND1 HIC D 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CG HIC A 73 " pdb=" ND1 HIC A 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.05e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 99.97 - 107.21: 626 107.21 - 114.45: 8559 114.45 - 121.69: 7454 121.69 - 128.92: 3126 128.92 - 136.16: 105 Bond angle restraints: 19870 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.47 109.91 3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 ... (remaining 19865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.25: 8640 32.25 - 64.50: 110 64.50 - 96.76: 10 96.76 - 129.01: 0 129.01 - 161.26: 5 Dihedral angle restraints: 8765 sinusoidal: 3515 harmonic: 5250 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.74 161.26 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.74 161.26 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.77 161.22 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1261 0.031 - 0.062: 626 0.062 - 0.093: 189 0.093 - 0.124: 134 0.124 - 0.155: 5 Chirality restraints: 2215 Sorted by residual: chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2212 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 243 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 243 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 243 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.017 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 112 2.42 - 3.04: 8898 3.04 - 3.66: 23937 3.66 - 4.28: 40289 4.28 - 4.90: 61757 Nonbonded interactions: 134993 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 507 " model vdw 1.798 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 512 " model vdw 1.819 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 541 " model vdw 1.824 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 525 " model vdw 1.827 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 530 " model vdw 1.836 2.170 ... (remaining 134988 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 12.240 Check model and map are aligned: 0.210 Set scattering table: 0.160 Process input model: 40.620 Find NCS groups from input model: 0.950 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.004 0.058 14630 Z= 0.276 Angle : 0.583 7.113 19870 Z= 0.280 Chirality : 0.044 0.155 2215 Planarity : 0.004 0.030 2525 Dihedral : 12.070 161.259 5395 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.65 % Allowed : 2.61 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.19), residues: 1780 helix: -2.34 (0.14), residues: 755 sheet: -0.63 (0.26), residues: 325 loop : 0.86 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS E 88 PHE 0.009 0.001 PHE D 262 TYR 0.009 0.001 TYR D 143 ARG 0.003 0.001 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 244 time to evaluate : 1.805 Fit side-chains REVERT: B 121 GLN cc_start: 0.8236 (tt0) cc_final: 0.8015 (tm-30) REVERT: B 211 ASP cc_start: 0.8004 (t70) cc_final: 0.7764 (t70) REVERT: D 44 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6789 (mpt) REVERT: D 276 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7023 (mt-10) REVERT: E 44 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6044 (mpt) outliers start: 10 outliers final: 0 residues processed: 249 average time/residue: 1.5050 time to fit residues: 405.8290 Evaluate side-chains 177 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain E residue 44 MET 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: 2.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 161 HIS A 12 ASN A 78 ASN B 12 ASN B 161 HIS D 161 HIS D 225 GLN D 353 GLN E 12 ASN E 121 GLN E 225 GLN E 354 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14630 Z= 0.207 Angle : 0.586 6.979 19870 Z= 0.279 Chirality : 0.045 0.167 2215 Planarity : 0.004 0.036 2525 Dihedral : 8.917 130.011 2026 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.07 % Allowed : 6.21 % Favored : 90.72 % 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: 0.25 (0.20), residues: 1780 helix: -0.60 (0.17), residues: 760 sheet: 0.07 (0.27), residues: 330 loop : 1.56 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.004 0.001 HIS E 275 PHE 0.013 0.001 PHE C 255 TYR 0.014 0.001 TYR D 143 ARG 0.003 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 1.441 Fit side-chains REVERT: C 72 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: C 314 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 276 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: D 44 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.6913 (mpt) REVERT: D 125 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: D 180 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8785 (tp) REVERT: E 44 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.6423 (mpt) REVERT: E 64 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8569 (pp) REVERT: E 328 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8283 (tttt) outliers start: 47 outliers final: 12 residues processed: 210 average time/residue: 1.3961 time to fit residues: 320.6851 Evaluate side-chains 187 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS 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: 0.0770 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 161 HIS A 225 GLN B 12 ASN D 92 ASN E 161 HIS E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14630 Z= 0.253 Angle : 0.591 7.991 19870 Z= 0.280 Chirality : 0.046 0.176 2215 Planarity : 0.004 0.037 2525 Dihedral : 9.430 134.466 2026 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.14 % Allowed : 6.99 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1780 helix: -0.02 (0.18), residues: 760 sheet: 0.33 (0.27), residues: 330 loop : 1.80 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS A 161 PHE 0.011 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.002 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 176 time to evaluate : 1.834 Fit side-chains REVERT: C 72 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: C 314 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: A 276 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: B 95 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7507 (mtp180) REVERT: B 125 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: B 132 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7520 (tmt) REVERT: B 227 MET cc_start: 0.8762 (mmm) cc_final: 0.8410 (mmm) REVERT: B 314 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: D 44 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6754 (mpt) REVERT: D 125 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: D 180 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8779 (tp) REVERT: D 334 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7122 (pp20) REVERT: E 44 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6356 (mpt) REVERT: E 64 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8609 (pp) REVERT: E 328 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8307 (tttt) outliers start: 48 outliers final: 12 residues processed: 199 average time/residue: 1.3692 time to fit residues: 297.8222 Evaluate side-chains 196 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN B 12 ASN B 128 ASN E 92 ASN E 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14630 Z= 0.270 Angle : 0.592 7.768 19870 Z= 0.281 Chirality : 0.046 0.180 2215 Planarity : 0.004 0.037 2525 Dihedral : 9.484 131.807 2026 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.01 % Allowed : 7.32 % Favored : 89.67 % 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: 1.07 (0.20), residues: 1780 helix: 0.22 (0.19), residues: 760 sheet: 0.40 (0.27), residues: 330 loop : 1.86 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.012 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.003 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.669 Fit side-chains REVERT: C 72 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: C 314 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: A 276 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: B 95 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7492 (mtp180) REVERT: B 125 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: B 132 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7564 (tmt) REVERT: B 314 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: D 44 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.6859 (mpt) REVERT: D 125 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: D 180 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8802 (tp) REVERT: D 334 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7137 (pp20) REVERT: E 44 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6429 (mpt) REVERT: E 64 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8629 (pp) REVERT: E 132 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7657 (ttp) REVERT: E 328 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8297 (tttt) outliers start: 46 outliers final: 16 residues processed: 192 average time/residue: 1.3311 time to fit residues: 280.1750 Evaluate side-chains 199 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS 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: 0.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14630 Z= 0.241 Angle : 0.578 7.469 19870 Z= 0.273 Chirality : 0.045 0.170 2215 Planarity : 0.004 0.037 2525 Dihedral : 9.399 130.632 2026 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.27 % Allowed : 7.45 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1780 helix: 0.32 (0.19), residues: 760 sheet: 0.48 (0.27), residues: 330 loop : 1.89 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.012 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 1.785 Fit side-chains REVERT: C 72 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: C 95 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7577 (mtm-85) REVERT: C 132 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7779 (tmt) REVERT: C 314 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: A 72 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: A 276 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: B 95 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7447 (mtp180) REVERT: B 125 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: B 314 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: D 125 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: D 180 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8759 (tp) REVERT: D 286 ASP cc_start: 0.7565 (m-30) cc_final: 0.7324 (m-30) REVERT: D 334 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7124 (pp20) REVERT: E 44 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.6432 (mpt) REVERT: E 64 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8618 (pp) REVERT: E 132 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7632 (ttp) outliers start: 50 outliers final: 16 residues processed: 196 average time/residue: 1.3937 time to fit residues: 299.2914 Evaluate side-chains 202 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 324 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: 0.0370 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 92 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14630 Z= 0.221 Angle : 0.568 7.276 19870 Z= 0.268 Chirality : 0.045 0.166 2215 Planarity : 0.003 0.037 2525 Dihedral : 9.222 128.606 2023 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.94 % Allowed : 7.65 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1780 helix: 0.38 (0.19), residues: 760 sheet: 0.53 (0.27), residues: 330 loop : 1.90 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.011 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.002 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 171 time to evaluate : 1.698 Fit side-chains REVERT: C 72 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: C 95 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7605 (mtm-85) REVERT: C 314 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: A 72 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: A 276 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: B 125 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: B 132 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7501 (tmt) REVERT: B 314 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: D 125 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: D 180 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8735 (tp) REVERT: D 286 ASP cc_start: 0.7577 (m-30) cc_final: 0.7333 (m-30) REVERT: E 44 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.6412 (mpt) REVERT: E 64 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8614 (pp) REVERT: E 132 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7617 (ttp) outliers start: 45 outliers final: 13 residues processed: 192 average time/residue: 1.3951 time to fit residues: 292.7604 Evaluate side-chains 193 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 324 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: 2.9990 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 92 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14630 Z= 0.383 Angle : 0.644 8.907 19870 Z= 0.310 Chirality : 0.049 0.193 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.912 138.292 2023 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.40 % Allowed : 7.19 % Favored : 89.41 % 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: 1.14 (0.20), residues: 1780 helix: 0.34 (0.19), residues: 755 sheet: 0.37 (0.26), residues: 340 loop : 1.86 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 340 HIS 0.005 0.001 HIS B 161 PHE 0.016 0.002 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.004 0.001 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 167 time to evaluate : 1.699 Fit side-chains REVERT: C 72 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: C 95 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7581 (mtm-85) REVERT: C 132 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7809 (tmt) REVERT: C 314 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: A 64 ILE cc_start: 0.9534 (OUTLIER) cc_final: 0.8880 (pp) REVERT: A 72 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 276 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: B 125 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: B 132 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7571 (tmt) REVERT: B 314 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: D 125 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: D 286 ASP cc_start: 0.7596 (m-30) cc_final: 0.7363 (m-30) REVERT: D 334 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7154 (pp20) REVERT: E 44 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.6312 (mpt) REVERT: E 64 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8652 (pp) REVERT: E 132 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7655 (ttp) REVERT: E 179 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7151 (t0) outliers start: 52 outliers final: 20 residues processed: 192 average time/residue: 1.3902 time to fit residues: 291.7991 Evaluate side-chains 199 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 324 THR 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: 4.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 92 ASN E 128 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14630 Z= 0.249 Angle : 0.583 7.523 19870 Z= 0.277 Chirality : 0.046 0.173 2215 Planarity : 0.004 0.037 2525 Dihedral : 9.428 132.085 2023 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.01 % Allowed : 7.91 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1780 helix: 0.36 (0.19), residues: 760 sheet: 0.56 (0.27), residues: 330 loop : 1.86 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 PHE 0.013 0.001 PHE D 262 TYR 0.009 0.001 TYR A 143 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 1.913 Fit side-chains REVERT: C 72 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: C 95 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7557 (mtm-85) REVERT: C 314 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: A 64 ILE cc_start: 0.9528 (OUTLIER) cc_final: 0.8862 (pp) REVERT: A 72 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 276 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: B 57 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: B 125 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: B 132 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7521 (tmt) REVERT: B 314 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: D 125 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: D 286 ASP cc_start: 0.7577 (m-30) cc_final: 0.7334 (m-30) REVERT: D 334 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: E 44 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.6388 (mpt) REVERT: E 64 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8619 (pp) REVERT: E 132 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7648 (ttp) outliers start: 46 outliers final: 17 residues processed: 188 average time/residue: 1.4008 time to fit residues: 289.4201 Evaluate side-chains 194 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 324 THR 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: 6.9990 chunk 166 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 chunk 106 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 92 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14630 Z= 0.130 Angle : 0.522 6.708 19870 Z= 0.245 Chirality : 0.043 0.148 2215 Planarity : 0.003 0.038 2525 Dihedral : 8.649 121.585 2023 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.96 % Allowed : 9.08 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1780 helix: 0.54 (0.19), residues: 755 sheet: 0.64 (0.27), residues: 330 loop : 1.96 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE C 255 TYR 0.011 0.001 TYR E 166 ARG 0.002 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.728 Fit side-chains REVERT: C 314 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: A 64 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.8867 (pp) REVERT: A 72 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: A 276 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: B 125 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: B 314 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: E 44 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.6454 (mpt) REVERT: E 64 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8540 (pp) outliers start: 30 outliers final: 9 residues processed: 185 average time/residue: 1.3204 time to fit residues: 268.1895 Evaluate side-chains 183 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 0.1980 chunk 165 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 92 ASN E 92 ASN E 128 ASN E 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14630 Z= 0.159 Angle : 0.537 6.596 19870 Z= 0.252 Chirality : 0.043 0.150 2215 Planarity : 0.003 0.038 2525 Dihedral : 8.695 123.086 2023 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.31 % Allowed : 9.74 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1780 helix: 0.56 (0.19), residues: 760 sheet: 0.64 (0.27), residues: 330 loop : 2.00 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 340 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.011 0.001 TYR E 166 ARG 0.002 0.000 ARG B 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.669 Fit side-chains REVERT: C 314 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: A 72 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: A 276 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: B 125 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: B 314 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: E 44 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.6450 (mpt) REVERT: E 64 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8544 (pp) outliers start: 20 outliers final: 7 residues processed: 176 average time/residue: 1.3193 time to fit residues: 254.8752 Evaluate side-chains 177 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 92 ASN E 128 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.084912 restraints weight = 15474.485| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.27 r_work: 0.2802 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14630 Z= 0.314 Angle : 0.614 8.154 19870 Z= 0.293 Chirality : 0.047 0.182 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.593 133.942 2023 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.70 % Allowed : 9.22 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1780 helix: 0.42 (0.19), residues: 760 sheet: 0.58 (0.27), residues: 330 loop : 1.94 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.014 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.004 0.000 ARG B 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5400.00 seconds wall clock time: 96 minutes 22.05 seconds (5782.05 seconds total)