Starting phenix.real_space_refine on Mon Mar 18 09:14:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/03_2024/8f8s_28935_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/03_2024/8f8s_28935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/03_2024/8f8s_28935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/03_2024/8f8s_28935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/03_2024/8f8s_28935_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/03_2024/8f8s_28935_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 14 5.49 5 Mg 7 5.21 5 S 143 5.16 5 C 12848 2.51 5 N 3434 2.21 5 O 3925 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 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20371 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2811 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} 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: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2819 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 19, 'TRANS': 340} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 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: "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: "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: "F" 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: "G" 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} Time building chain proxies: 11.12, per 1000 atoms: 0.55 Number of scatterers: 20371 At special positions: 0 Unit cell: (84.24, 104.76, 241.92, 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 143 16.00 P 14 15.00 Mg 7 11.99 O 3925 8.00 N 3434 7.00 C 12848 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: 7.76 Conformation dependent library (CDL) restraints added in 3.7 seconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 30 sheets defined 42.3% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.591A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.922A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) 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 194 removed outlier: 3.520A pdb=" N ASP A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.648A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.834A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.755A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.513A 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: 3.712A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 338 through 348 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 365 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.895A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.501A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) 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 194 Processing helix chain 'B' and resid 204 through 216 removed outlier: 3.785A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.523A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.753A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.624A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.550A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 345 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.638A pdb=" N ASP B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 removed outlier: 4.234A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.519A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) 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 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: 3.839A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.758A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.743A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.578A 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: 4.848A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.513A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.637A 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 365 Processing helix chain 'C' and resid 369 through 373 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 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.950A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.812A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.608A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.509A 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 347 removed outlier: 3.514A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 373 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 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.963A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.709A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.875A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.535A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 295 " --> pdb=" O ASP E 292 " (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: 3.633A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.908A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.718A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.846A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 294 removed outlier: 3.651A pdb=" N ARG F 290 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F 294 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 347 removed outlier: 5.278A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 196 removed outlier: 4.008A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 removed outlier: 3.651A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 252 through 261 removed outlier: 3.859A pdb=" N ARG G 256 " --> pdb=" O GLU G 253 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 287 through 294 removed outlier: 3.612A pdb=" N ARG G 290 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS G 291 " --> pdb=" O ASP G 288 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR G 294 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.555A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 346 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 347 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 369 through 373 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 10 Processing sheet with id= B, first strand: chain 'A' and resid 16 through 19 Processing sheet with id= C, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.217A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.749A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 250 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.881A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= H, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.260A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.737A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.327A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= N, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.770A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= P, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.217A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= R, first strand: chain 'E' and resid 8 through 12 Processing sheet with id= S, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= T, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= U, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.327A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= W, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.494A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 34 through 38 Processing sheet with id= Y, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.171A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= AA, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.511A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 34 through 38 Processing sheet with id= AC, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.281A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 711 hydrogen bonds defined for protein. 1764 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: 6.50 Time building geometry restraints manager: 8.46 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: 6603 1.34 - 1.46: 3207 1.46 - 1.57: 10733 1.57 - 1.69: 21 1.69 - 1.81: 251 Bond restraints: 20815 Sorted by residual: bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.44e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.38e+00 ... (remaining 20810 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.82: 581 105.82 - 113.44: 11436 113.44 - 121.05: 10282 121.05 - 128.67: 5820 128.67 - 136.29: 135 Bond angle restraints: 28254 Sorted by residual: angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.24 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" N HIC F 73 " pdb=" CA HIC F 73 " pdb=" CB HIC F 73 " ideal model delta sigma weight residual 110.50 115.82 -5.32 1.70e+00 3.46e-01 9.79e+00 angle pdb=" N HIC E 73 " pdb=" CA HIC E 73 " pdb=" CB HIC E 73 " ideal model delta sigma weight residual 110.50 115.78 -5.28 1.70e+00 3.46e-01 9.64e+00 angle pdb=" C ILE B 71 " pdb=" N GLU B 72 " pdb=" CA GLU B 72 " ideal model delta sigma weight residual 121.70 127.12 -5.42 1.80e+00 3.09e-01 9.05e+00 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 115.55 -5.05 1.70e+00 3.46e-01 8.84e+00 ... (remaining 28249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 12206 33.77 - 67.54: 294 67.54 - 101.31: 11 101.31 - 135.08: 7 135.08 - 168.85: 2 Dihedral angle restraints: 12520 sinusoidal: 5060 harmonic: 7460 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.86 -168.85 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.96 -147.96 1 2.00e+01 2.50e-03 4.43e+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 -60.00 65.95 -125.95 1 2.00e+01 2.50e-03 3.81e+01 ... (remaining 12517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1590 0.029 - 0.057: 945 0.057 - 0.086: 342 0.086 - 0.114: 216 0.114 - 0.143: 48 Chirality restraints: 3141 Sorted by residual: chirality pdb=" CA ILE G 165 " pdb=" N ILE G 165 " pdb=" C ILE G 165 " pdb=" CB ILE G 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE F 165 " pdb=" N ILE F 165 " pdb=" C ILE F 165 " pdb=" CB ILE F 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE C 165 " pdb=" N ILE C 165 " pdb=" C ILE C 165 " pdb=" CB ILE C 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 3138 not shown) Planarity restraints: 3609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 322 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 321 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO E 322 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 322 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 322 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 321 " 0.041 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO F 322 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 322 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 322 " 0.035 5.00e-02 4.00e+02 ... (remaining 3606 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 140 2.58 - 3.16: 15777 3.16 - 3.74: 31663 3.74 - 4.32: 45694 4.32 - 4.90: 75780 Nonbonded interactions: 169054 Sorted by model distance: nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.002 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.039 2.170 nonbonded pdb=" O3B ADP G 401 " pdb="MG MG G 402 " model vdw 2.042 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.146 2.170 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.232 2.440 ... (remaining 169049 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' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'C' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'D' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'E' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'F' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'G' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.220 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: 0.020 Extract box with map and model: 13.620 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 55.130 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 0.057 20815 Z= 0.247 Angle : 0.613 6.945 28254 Z= 0.306 Chirality : 0.046 0.143 3141 Planarity : 0.005 0.064 3609 Dihedral : 14.041 168.855 7742 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.94 % Allowed : 7.85 % Favored : 89.22 % 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: -0.35 (0.17), residues: 2540 helix: -0.79 (0.15), residues: 1065 sheet: 0.58 (0.24), residues: 473 loop : 0.29 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.005 0.001 HIS C 161 PHE 0.013 0.001 PHE D 255 TYR 0.012 0.001 TYR F 143 ARG 0.006 0.001 ARG F 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 621 time to evaluate : 2.369 Fit side-chains REVERT: A 61 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7920 (pttp) REVERT: A 71 ILE cc_start: 0.8137 (mm) cc_final: 0.7868 (mt) REVERT: A 82 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7613 (tpp) REVERT: A 94 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7575 (tm) REVERT: A 99 GLU cc_start: 0.7474 (mp0) cc_final: 0.7256 (mp0) REVERT: A 116 ARG cc_start: 0.7376 (ttp80) cc_final: 0.6710 (ttp80) REVERT: A 122 ILE cc_start: 0.8450 (mm) cc_final: 0.8236 (mp) REVERT: A 214 GLU cc_start: 0.7899 (tt0) cc_final: 0.7659 (mt-10) REVERT: A 215 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7772 (ttmm) REVERT: A 224 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7239 (tp30) REVERT: A 299 MET cc_start: 0.8651 (mtp) cc_final: 0.8323 (mtp) REVERT: A 316 GLU cc_start: 0.8736 (tp30) cc_final: 0.8497 (tp30) REVERT: A 355 MET cc_start: 0.7153 (mpp) cc_final: 0.6917 (mpp) REVERT: B 61 LYS cc_start: 0.8081 (mmtp) cc_final: 0.7832 (mmtp) REVERT: B 83 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: B 116 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7556 (ptm160) REVERT: B 117 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 118 LYS cc_start: 0.7876 (tptt) cc_final: 0.7620 (tptt) REVERT: B 184 ASP cc_start: 0.8086 (m-30) cc_final: 0.7874 (m-30) REVERT: B 205 GLU cc_start: 0.7378 (mp0) cc_final: 0.7145 (mp0) REVERT: B 207 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 248 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8092 (pt) REVERT: B 291 LYS cc_start: 0.8581 (tttp) cc_final: 0.8321 (tttm) REVERT: C 72 GLU cc_start: 0.7694 (tt0) cc_final: 0.7430 (tp30) REVERT: C 98 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8560 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7518 (pm20) cc_final: 0.7273 (pm20) REVERT: C 118 LYS cc_start: 0.8423 (mtpp) cc_final: 0.8168 (mttm) REVERT: C 227 MET cc_start: 0.8814 (mmm) cc_final: 0.8607 (mmm) REVERT: C 334 GLU cc_start: 0.7734 (pm20) cc_final: 0.7434 (pm20) REVERT: D 44 MET cc_start: 0.7811 (tpp) cc_final: 0.7550 (tpp) REVERT: D 90 PHE cc_start: 0.8594 (m-80) cc_final: 0.8360 (m-80) REVERT: D 117 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7793 (mt-10) REVERT: D 227 MET cc_start: 0.8516 (mmm) cc_final: 0.8313 (mmp) REVERT: D 284 LYS cc_start: 0.8571 (mttp) cc_final: 0.8328 (mtpm) REVERT: E 99 GLU cc_start: 0.7566 (pm20) cc_final: 0.7298 (pp20) REVERT: E 121 GLN cc_start: 0.8395 (tt0) cc_final: 0.8146 (tt0) REVERT: E 147 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8716 (ptp-170) REVERT: E 288 ASP cc_start: 0.7758 (m-30) cc_final: 0.7499 (m-30) REVERT: E 313 MET cc_start: 0.8488 (mmm) cc_final: 0.8219 (tpt) REVERT: E 337 TYR cc_start: 0.8774 (m-10) cc_final: 0.8568 (m-80) REVERT: F 68 LYS cc_start: 0.8708 (mmtp) cc_final: 0.8453 (mmtp) REVERT: F 96 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8554 (m) REVERT: F 99 GLU cc_start: 0.7742 (mp0) cc_final: 0.7410 (mp0) REVERT: F 167 GLU cc_start: 0.8039 (mp0) cc_final: 0.7820 (mp0) REVERT: F 210 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7999 (ttm110) REVERT: F 222 ASP cc_start: 0.7979 (t0) cc_final: 0.7745 (t0) REVERT: F 354 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7244 (mm-40) REVERT: F 355 MET cc_start: 0.8216 (mtp) cc_final: 0.8002 (mtm) REVERT: F 364 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7248 (mm-30) REVERT: F 373 LYS cc_start: 0.8625 (tttp) cc_final: 0.8246 (mtpt) REVERT: G 117 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: G 147 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7907 (ptm160) REVERT: G 270 GLU cc_start: 0.6394 (mp0) cc_final: 0.5622 (mp0) REVERT: G 283 MET cc_start: 0.8209 (mmt) cc_final: 0.7760 (mmt) REVERT: G 311 ASP cc_start: 0.7838 (p0) cc_final: 0.7584 (p0) outliers start: 64 outliers final: 21 residues processed: 654 average time/residue: 1.5417 time to fit residues: 1115.3462 Evaluate side-chains 620 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 589 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 232 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 111 ASN B 115 ASN B 162 ASN B 297 ASN B 360 GLN C 12 ASN C 115 ASN C 137 GLN C 246 GLN D 12 ASN D 115 ASN D 137 GLN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 246 GLN F 59 GLN F 137 GLN F 246 GLN F 297 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20815 Z= 0.231 Angle : 0.591 9.574 28254 Z= 0.282 Chirality : 0.045 0.221 3141 Planarity : 0.005 0.055 3609 Dihedral : 10.445 175.720 2967 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.50 % Allowed : 15.92 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2540 helix: -0.26 (0.16), residues: 1047 sheet: 0.72 (0.23), residues: 498 loop : 0.31 (0.22), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.004 0.001 HIS F 161 PHE 0.018 0.001 PHE A 223 TYR 0.016 0.001 TYR A 198 ARG 0.008 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 593 time to evaluate : 1.869 Fit side-chains REVERT: A 16 LEU cc_start: 0.8143 (mp) cc_final: 0.7916 (mm) REVERT: A 61 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7913 (pttp) REVERT: A 82 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (tpp) REVERT: A 99 GLU cc_start: 0.7547 (mp0) cc_final: 0.7322 (mp0) REVERT: A 103 THR cc_start: 0.8316 (t) cc_final: 0.8095 (m) REVERT: A 167 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7992 (tp30) REVERT: A 213 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7602 (ttpt) REVERT: A 214 GLU cc_start: 0.7862 (tt0) cc_final: 0.7542 (mt-10) REVERT: A 215 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7823 (ttmm) REVERT: A 236 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8095 (pp) REVERT: A 254 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8100 (mmm-85) REVERT: A 299 MET cc_start: 0.8619 (mtp) cc_final: 0.8278 (mtp) REVERT: A 316 GLU cc_start: 0.8792 (tp30) cc_final: 0.8552 (tp30) REVERT: B 21 PHE cc_start: 0.8589 (m-80) cc_final: 0.8319 (m-80) REVERT: B 61 LYS cc_start: 0.8086 (mmtp) cc_final: 0.7842 (mmtp) REVERT: B 117 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6696 (mm-30) REVERT: B 118 LYS cc_start: 0.7667 (tptt) cc_final: 0.7301 (tptt) REVERT: B 184 ASP cc_start: 0.8142 (m-30) cc_final: 0.7939 (m-30) REVERT: B 205 GLU cc_start: 0.7228 (mp0) cc_final: 0.6982 (mp0) REVERT: B 215 LYS cc_start: 0.8418 (mttp) cc_final: 0.8079 (mttp) REVERT: C 44 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6922 (mmm) REVERT: C 72 GLU cc_start: 0.7704 (tt0) cc_final: 0.7434 (tp30) REVERT: C 99 GLU cc_start: 0.7511 (pm20) cc_final: 0.7297 (pm20) REVERT: C 118 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8157 (mttm) REVERT: C 224 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7807 (mm-30) REVERT: C 297 ASN cc_start: 0.8411 (m110) cc_final: 0.8137 (m110) REVERT: C 334 GLU cc_start: 0.7761 (pm20) cc_final: 0.7422 (pm20) REVERT: D 44 MET cc_start: 0.7848 (tpp) cc_final: 0.7498 (tpp) REVERT: D 90 PHE cc_start: 0.8575 (m-80) cc_final: 0.8350 (m-80) REVERT: D 99 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: D 132 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7924 (ppp) REVERT: D 227 MET cc_start: 0.8526 (mmm) cc_final: 0.8298 (mmp) REVERT: D 284 LYS cc_start: 0.8566 (mttp) cc_final: 0.8302 (mtpm) REVERT: E 121 GLN cc_start: 0.8400 (tt0) cc_final: 0.8134 (tt0) REVERT: E 237 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: E 313 MET cc_start: 0.8487 (mmm) cc_final: 0.8204 (tpt) REVERT: F 68 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8464 (mmtp) REVERT: F 96 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8599 (m) REVERT: F 99 GLU cc_start: 0.7744 (mp0) cc_final: 0.7390 (mp0) REVERT: F 210 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8002 (ttm110) REVERT: F 222 ASP cc_start: 0.7970 (t0) cc_final: 0.7759 (t0) REVERT: F 354 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7319 (mm-40) REVERT: F 355 MET cc_start: 0.8221 (mtp) cc_final: 0.7992 (mtm) REVERT: F 364 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7236 (mm-30) REVERT: G 116 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.8028 (ttm-80) REVERT: G 117 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: G 147 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8309 (ptm160) REVERT: G 270 GLU cc_start: 0.6429 (mp0) cc_final: 0.5672 (mp0) REVERT: G 283 MET cc_start: 0.8166 (mmt) cc_final: 0.7809 (mmt) REVERT: G 311 ASP cc_start: 0.7817 (p0) cc_final: 0.7582 (p0) outliers start: 98 outliers final: 43 residues processed: 633 average time/residue: 1.5194 time to fit residues: 1064.8301 Evaluate side-chains 620 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 565 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 115 ASN A 354 GLN B 111 ASN B 297 ASN C 12 ASN C 101 HIS C 115 ASN C 137 GLN C 162 ASN C 246 GLN D 12 ASN D 115 ASN D 137 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 297 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 246 GLN F 137 GLN F 246 GLN F 353 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 225 ASN G 297 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20815 Z= 0.263 Angle : 0.589 7.519 28254 Z= 0.281 Chirality : 0.046 0.185 3141 Planarity : 0.005 0.054 3609 Dihedral : 9.995 179.637 2948 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.73 % Allowed : 17.67 % Favored : 77.60 % 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: 0.15 (0.17), residues: 2540 helix: -0.13 (0.16), residues: 1050 sheet: 0.67 (0.23), residues: 494 loop : 0.32 (0.22), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.004 0.001 HIS C 161 PHE 0.014 0.001 PHE B 31 TYR 0.015 0.001 TYR A 198 ARG 0.007 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 578 time to evaluate : 2.439 Fit side-chains REVERT: A 61 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7915 (pttp) REVERT: A 99 GLU cc_start: 0.7542 (mp0) cc_final: 0.7303 (mp0) REVERT: A 115 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7958 (t0) REVERT: A 167 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8089 (mm-30) REVERT: A 214 GLU cc_start: 0.7885 (tt0) cc_final: 0.7634 (mt-10) REVERT: A 215 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7861 (ttmm) REVERT: A 299 MET cc_start: 0.8628 (mtp) cc_final: 0.8217 (mtm) REVERT: A 316 GLU cc_start: 0.8790 (tp30) cc_final: 0.8537 (tp30) REVERT: A 326 LYS cc_start: 0.8111 (mttp) cc_final: 0.7901 (mttp) REVERT: B 11 ASP cc_start: 0.8715 (t0) cc_final: 0.8166 (t70) REVERT: B 21 PHE cc_start: 0.8587 (m-80) cc_final: 0.8340 (m-80) REVERT: B 61 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7838 (mmtp) REVERT: B 89 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8418 (t) REVERT: B 117 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6762 (mm-30) REVERT: B 118 LYS cc_start: 0.7722 (tptt) cc_final: 0.7408 (tptt) REVERT: B 184 ASP cc_start: 0.8190 (m-30) cc_final: 0.7979 (m-30) REVERT: B 205 GLU cc_start: 0.7340 (mp0) cc_final: 0.7008 (mp0) REVERT: C 44 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: C 72 GLU cc_start: 0.7702 (tt0) cc_final: 0.7416 (tp30) REVERT: C 99 GLU cc_start: 0.7521 (pm20) cc_final: 0.7295 (pm20) REVERT: C 118 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8186 (mttm) REVERT: C 334 GLU cc_start: 0.7782 (pm20) cc_final: 0.7437 (pm20) REVERT: D 44 MET cc_start: 0.7903 (tpp) cc_final: 0.7695 (tpp) REVERT: D 80 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: D 90 PHE cc_start: 0.8568 (m-80) cc_final: 0.8356 (m-80) REVERT: D 132 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8034 (ppp) REVERT: D 227 MET cc_start: 0.8546 (mmm) cc_final: 0.8316 (mmp) REVERT: D 276 GLU cc_start: 0.8059 (tt0) cc_final: 0.7846 (tt0) REVERT: D 284 LYS cc_start: 0.8557 (mttp) cc_final: 0.8295 (mtpm) REVERT: E 121 GLN cc_start: 0.8395 (tt0) cc_final: 0.8076 (tt0) REVERT: E 256 ARG cc_start: 0.8595 (mtp180) cc_final: 0.8344 (mtm180) REVERT: E 313 MET cc_start: 0.8495 (mmm) cc_final: 0.8226 (tpt) REVERT: F 68 LYS cc_start: 0.8708 (mmtp) cc_final: 0.8458 (mmtp) REVERT: F 96 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8556 (m) REVERT: F 128 ASN cc_start: 0.7683 (p0) cc_final: 0.7368 (p0) REVERT: F 210 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8025 (ttm110) REVERT: F 299 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8321 (mtm) REVERT: F 354 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7291 (mm-40) REVERT: F 355 MET cc_start: 0.8222 (mtp) cc_final: 0.7981 (mtm) REVERT: F 364 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7232 (mm-30) REVERT: G 116 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7991 (ttm-80) REVERT: G 117 GLU cc_start: 0.8107 (tt0) cc_final: 0.7779 (tp30) REVERT: G 147 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8317 (ptm160) REVERT: G 270 GLU cc_start: 0.6473 (mp0) cc_final: 0.5743 (mp0) outliers start: 103 outliers final: 51 residues processed: 621 average time/residue: 1.5786 time to fit residues: 1083.8858 Evaluate side-chains 634 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 572 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 221 optimal weight: 0.5980 chunk 66 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN B 297 ASN C 115 ASN C 137 GLN C 246 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 137 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 246 GLN G 12 ASN G 92 ASN G 128 ASN G 225 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20815 Z= 0.283 Angle : 0.603 10.018 28254 Z= 0.287 Chirality : 0.046 0.165 3141 Planarity : 0.005 0.053 3609 Dihedral : 9.769 172.081 2940 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.86 % Allowed : 17.85 % Favored : 77.28 % 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: 0.17 (0.17), residues: 2540 helix: -0.09 (0.16), residues: 1050 sheet: 0.63 (0.23), residues: 495 loop : 0.32 (0.22), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 79 HIS 0.005 0.001 HIS C 101 PHE 0.013 0.001 PHE F 255 TYR 0.013 0.001 TYR A 198 ARG 0.007 0.001 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 584 time to evaluate : 2.379 Fit side-chains REVERT: A 61 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7897 (pttp) REVERT: A 81 ASP cc_start: 0.7817 (p0) cc_final: 0.7585 (p0) REVERT: A 99 GLU cc_start: 0.7553 (mp0) cc_final: 0.7273 (mp0) REVERT: A 167 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8130 (mm-30) REVERT: A 214 GLU cc_start: 0.7908 (tt0) cc_final: 0.7684 (mt-10) REVERT: A 215 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7877 (ttmm) REVERT: A 236 LEU cc_start: 0.8307 (pp) cc_final: 0.8034 (pt) REVERT: A 299 MET cc_start: 0.8622 (mtp) cc_final: 0.8261 (mtm) REVERT: A 316 GLU cc_start: 0.8787 (tp30) cc_final: 0.8532 (tp30) REVERT: A 326 LYS cc_start: 0.8105 (mttp) cc_final: 0.7888 (mttp) REVERT: B 21 PHE cc_start: 0.8560 (m-80) cc_final: 0.8330 (m-80) REVERT: B 61 LYS cc_start: 0.8045 (mmtp) cc_final: 0.7823 (mmtp) REVERT: B 117 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6670 (mm-30) REVERT: B 118 LYS cc_start: 0.7729 (tptt) cc_final: 0.7425 (tptt) REVERT: B 184 ASP cc_start: 0.8199 (m-30) cc_final: 0.7984 (m-30) REVERT: B 205 GLU cc_start: 0.7401 (mp0) cc_final: 0.7066 (mp0) REVERT: B 215 LYS cc_start: 0.8373 (mttp) cc_final: 0.8063 (mtmm) REVERT: B 325 MET cc_start: 0.8812 (mmp) cc_final: 0.8602 (mmm) REVERT: C 44 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7072 (mpp) REVERT: C 72 GLU cc_start: 0.7681 (tt0) cc_final: 0.7407 (tp30) REVERT: C 99 GLU cc_start: 0.7522 (pm20) cc_final: 0.7289 (pm20) REVERT: C 113 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8174 (mtmm) REVERT: C 118 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8208 (mttm) REVERT: C 297 ASN cc_start: 0.8468 (m110) cc_final: 0.8186 (m110) REVERT: C 334 GLU cc_start: 0.7770 (pm20) cc_final: 0.7473 (pm20) REVERT: C 360 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7193 (tm-30) REVERT: D 44 MET cc_start: 0.7927 (tpp) cc_final: 0.7522 (tpp) REVERT: D 80 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: D 90 PHE cc_start: 0.8581 (m-80) cc_final: 0.8353 (m-80) REVERT: D 132 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7983 (ppp) REVERT: D 227 MET cc_start: 0.8566 (mmm) cc_final: 0.8324 (mmp) REVERT: D 276 GLU cc_start: 0.8059 (tt0) cc_final: 0.7836 (tt0) REVERT: D 284 LYS cc_start: 0.8555 (mttp) cc_final: 0.8290 (mtpm) REVERT: E 121 GLN cc_start: 0.8399 (tt0) cc_final: 0.8085 (tt0) REVERT: E 147 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8665 (ptp-170) REVERT: E 256 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8404 (mtm180) REVERT: E 313 MET cc_start: 0.8500 (mmm) cc_final: 0.8230 (tpt) REVERT: F 68 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8453 (mmtp) REVERT: F 96 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8579 (m) REVERT: F 113 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7669 (mmtp) REVERT: F 210 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8049 (ttm110) REVERT: F 222 ASP cc_start: 0.7977 (t0) cc_final: 0.7767 (t0) REVERT: F 241 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: F 299 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8325 (mtm) REVERT: F 354 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7243 (mm-40) REVERT: F 355 MET cc_start: 0.8218 (mtp) cc_final: 0.7972 (mtm) REVERT: F 364 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7234 (mm-30) REVERT: G 83 GLU cc_start: 0.7664 (tt0) cc_final: 0.7408 (mt-10) REVERT: G 116 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8031 (ttm-80) REVERT: G 117 GLU cc_start: 0.8144 (tt0) cc_final: 0.7786 (tp30) REVERT: G 147 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7560 (ptm160) REVERT: G 270 GLU cc_start: 0.6480 (mp0) cc_final: 0.5712 (mp0) outliers start: 106 outliers final: 55 residues processed: 630 average time/residue: 1.5534 time to fit residues: 1080.9730 Evaluate side-chains 648 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 580 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 3 optimal weight: 0.0010 chunk 184 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 126 optimal weight: 0.3980 chunk 222 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 111 ASN B 297 ASN C 115 ASN C 137 GLN C 246 GLN D 12 ASN D 137 GLN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 137 GLN F 246 GLN F 353 GLN G 12 ASN G 92 ASN G 101 HIS G 128 ASN G 225 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20815 Z= 0.217 Angle : 0.586 7.664 28254 Z= 0.277 Chirality : 0.045 0.175 3141 Planarity : 0.004 0.052 3609 Dihedral : 9.556 169.710 2938 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.64 % Allowed : 18.68 % Favored : 76.69 % 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: 0.26 (0.17), residues: 2540 helix: -0.04 (0.16), residues: 1056 sheet: 0.76 (0.24), residues: 484 loop : 0.36 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.004 0.001 HIS C 161 PHE 0.013 0.001 PHE F 255 TYR 0.012 0.001 TYR A 198 ARG 0.008 0.000 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 590 time to evaluate : 2.464 Fit side-chains REVERT: A 61 LYS cc_start: 0.8260 (pttp) cc_final: 0.7852 (pttp) REVERT: A 81 ASP cc_start: 0.7870 (p0) cc_final: 0.7567 (p0) REVERT: A 99 GLU cc_start: 0.7556 (mp0) cc_final: 0.7266 (mp0) REVERT: A 167 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8001 (mm-30) REVERT: A 214 GLU cc_start: 0.7897 (tt0) cc_final: 0.7680 (mt-10) REVERT: A 265 SER cc_start: 0.8747 (m) cc_final: 0.8406 (t) REVERT: A 299 MET cc_start: 0.8610 (mtp) cc_final: 0.8254 (mtm) REVERT: A 316 GLU cc_start: 0.8780 (tp30) cc_final: 0.8528 (tp30) REVERT: A 326 LYS cc_start: 0.8101 (mttp) cc_final: 0.7862 (mttp) REVERT: B 21 PHE cc_start: 0.8557 (m-80) cc_final: 0.8318 (m-80) REVERT: B 61 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7821 (mmtp) REVERT: B 117 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6640 (mm-30) REVERT: B 118 LYS cc_start: 0.7716 (tptt) cc_final: 0.7386 (tptt) REVERT: B 205 GLU cc_start: 0.7428 (mp0) cc_final: 0.7065 (mp0) REVERT: B 211 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7276 (t70) REVERT: B 215 LYS cc_start: 0.8363 (mttp) cc_final: 0.8144 (mtmm) REVERT: C 44 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7024 (mpp) REVERT: C 72 GLU cc_start: 0.7664 (tt0) cc_final: 0.7413 (tp30) REVERT: C 99 GLU cc_start: 0.7501 (pm20) cc_final: 0.7284 (pm20) REVERT: C 113 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8143 (mtmm) REVERT: C 118 LYS cc_start: 0.8418 (mtpp) cc_final: 0.8201 (mttm) REVERT: C 297 ASN cc_start: 0.8470 (m110) cc_final: 0.8193 (m110) REVERT: C 334 GLU cc_start: 0.7775 (pm20) cc_final: 0.7487 (pm20) REVERT: C 360 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7180 (tm-30) REVERT: D 44 MET cc_start: 0.7944 (tpp) cc_final: 0.7538 (tpp) REVERT: D 80 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: D 90 PHE cc_start: 0.8545 (m-80) cc_final: 0.8312 (m-80) REVERT: D 132 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7981 (ppp) REVERT: D 227 MET cc_start: 0.8549 (mmm) cc_final: 0.8311 (mmp) REVERT: D 276 GLU cc_start: 0.8054 (tt0) cc_final: 0.7831 (tt0) REVERT: D 284 LYS cc_start: 0.8548 (mttp) cc_final: 0.8283 (mtpm) REVERT: E 147 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8602 (ptp-170) REVERT: E 256 ARG cc_start: 0.8608 (mtp180) cc_final: 0.8407 (mtm180) REVERT: E 313 MET cc_start: 0.8487 (mmm) cc_final: 0.8225 (tpt) REVERT: F 68 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8465 (mmtp) REVERT: F 113 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7766 (mmtp) REVERT: F 210 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8044 (ttm110) REVERT: F 222 ASP cc_start: 0.7955 (t0) cc_final: 0.7746 (t0) REVERT: F 299 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8344 (mtm) REVERT: F 314 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: F 354 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7291 (mm-40) REVERT: F 364 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7229 (mm-30) REVERT: G 83 GLU cc_start: 0.7696 (tt0) cc_final: 0.7438 (mt-10) REVERT: G 117 GLU cc_start: 0.8117 (tt0) cc_final: 0.7774 (tp30) REVERT: G 147 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7686 (ptm160) REVERT: G 270 GLU cc_start: 0.6428 (mp0) cc_final: 0.5644 (mp0) outliers start: 101 outliers final: 61 residues processed: 627 average time/residue: 1.5356 time to fit residues: 1066.1530 Evaluate side-chains 650 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 578 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 291 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.6980 chunk 222 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 247 optimal weight: 0.0030 chunk 205 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 111 ASN B 297 ASN C 115 ASN C 137 GLN C 246 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 246 GLN G 12 ASN G 92 ASN G 128 ASN G 225 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20815 Z= 0.276 Angle : 0.610 9.183 28254 Z= 0.288 Chirality : 0.046 0.188 3141 Planarity : 0.005 0.052 3609 Dihedral : 9.459 164.578 2930 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.82 % Allowed : 19.32 % Favored : 75.86 % 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: 0.23 (0.17), residues: 2540 helix: -0.05 (0.16), residues: 1054 sheet: 0.76 (0.24), residues: 484 loop : 0.32 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.004 0.001 HIS C 101 PHE 0.013 0.001 PHE F 255 TYR 0.012 0.001 TYR A 198 ARG 0.010 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 588 time to evaluate : 2.207 Fit side-chains REVERT: A 61 LYS cc_start: 0.8264 (pttp) cc_final: 0.7862 (pttp) REVERT: A 81 ASP cc_start: 0.7925 (p0) cc_final: 0.7604 (p0) REVERT: A 99 GLU cc_start: 0.7581 (mp0) cc_final: 0.7277 (mp0) REVERT: A 154 ASP cc_start: 0.7710 (t70) cc_final: 0.7466 (t70) REVERT: A 167 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8060 (mm-30) REVERT: A 265 SER cc_start: 0.8747 (m) cc_final: 0.8421 (t) REVERT: A 299 MET cc_start: 0.8609 (mtp) cc_final: 0.8248 (mtm) REVERT: A 316 GLU cc_start: 0.8776 (tp30) cc_final: 0.8532 (tp30) REVERT: A 326 LYS cc_start: 0.8111 (mttp) cc_final: 0.7859 (mttp) REVERT: A 361 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6790 (mt-10) REVERT: A 364 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6091 (pt0) REVERT: B 21 PHE cc_start: 0.8562 (m-80) cc_final: 0.8308 (m-80) REVERT: B 61 LYS cc_start: 0.8069 (mmtp) cc_final: 0.7846 (mmtp) REVERT: B 117 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6699 (mm-30) REVERT: B 118 LYS cc_start: 0.7740 (tptt) cc_final: 0.7425 (tptt) REVERT: B 205 GLU cc_start: 0.7462 (mp0) cc_final: 0.7078 (mp0) REVERT: B 211 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7263 (t70) REVERT: B 215 LYS cc_start: 0.8359 (mttp) cc_final: 0.8118 (mtmm) REVERT: C 44 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7110 (mpp) REVERT: C 72 GLU cc_start: 0.7669 (tt0) cc_final: 0.7417 (tp30) REVERT: C 99 GLU cc_start: 0.7513 (pm20) cc_final: 0.7273 (pm20) REVERT: C 113 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8177 (mtmm) REVERT: C 118 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8191 (mttm) REVERT: C 297 ASN cc_start: 0.8507 (m110) cc_final: 0.8230 (m110) REVERT: C 334 GLU cc_start: 0.7782 (pm20) cc_final: 0.7487 (pm20) REVERT: C 360 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7187 (tm-30) REVERT: D 44 MET cc_start: 0.7912 (tpp) cc_final: 0.7709 (tpp) REVERT: D 80 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: D 90 PHE cc_start: 0.8557 (m-80) cc_final: 0.8345 (m-80) REVERT: D 132 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7978 (ppp) REVERT: D 227 MET cc_start: 0.8574 (mmm) cc_final: 0.8328 (mmp) REVERT: D 276 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: D 284 LYS cc_start: 0.8559 (mttp) cc_final: 0.8280 (mtpm) REVERT: E 147 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8603 (ptp-170) REVERT: E 313 MET cc_start: 0.8491 (mmm) cc_final: 0.8229 (tpt) REVERT: F 68 LYS cc_start: 0.8707 (mmtp) cc_final: 0.8467 (mmtp) REVERT: F 113 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7752 (mmtp) REVERT: F 210 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8036 (ttm110) REVERT: F 241 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: F 299 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: F 314 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: F 354 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7233 (mm-40) REVERT: F 364 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7230 (mm-30) REVERT: G 117 GLU cc_start: 0.8150 (tt0) cc_final: 0.7798 (tp30) REVERT: G 147 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7559 (ptm160) REVERT: G 270 GLU cc_start: 0.6427 (mp0) cc_final: 0.5587 (mp0) outliers start: 105 outliers final: 64 residues processed: 630 average time/residue: 1.5513 time to fit residues: 1078.3323 Evaluate side-chains 662 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 584 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 291 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 208 optimal weight: 0.6980 chunk 138 optimal weight: 0.3980 chunk 246 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 111 ASN B 297 ASN C 115 ASN C 137 GLN C 246 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 225 ASN D 371 HIS E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN F 353 GLN G 12 ASN G 92 ASN G 128 ASN G 225 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20815 Z= 0.250 Angle : 0.608 8.616 28254 Z= 0.285 Chirality : 0.046 0.188 3141 Planarity : 0.005 0.052 3609 Dihedral : 9.333 158.827 2930 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.05 % Allowed : 19.64 % Favored : 75.31 % 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: 0.31 (0.17), residues: 2540 helix: 0.02 (0.16), residues: 1046 sheet: 0.76 (0.24), residues: 484 loop : 0.40 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 79 HIS 0.004 0.001 HIS C 161 PHE 0.013 0.001 PHE F 255 TYR 0.014 0.001 TYR D 166 ARG 0.009 0.001 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 587 time to evaluate : 2.330 Fit side-chains REVERT: A 61 LYS cc_start: 0.8256 (pttp) cc_final: 0.7855 (pttp) REVERT: A 82 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7549 (tpp) REVERT: A 99 GLU cc_start: 0.7575 (mp0) cc_final: 0.7268 (mp0) REVERT: A 154 ASP cc_start: 0.7712 (t70) cc_final: 0.7466 (t70) REVERT: A 265 SER cc_start: 0.8759 (m) cc_final: 0.8429 (t) REVERT: A 299 MET cc_start: 0.8610 (mtp) cc_final: 0.8252 (mtm) REVERT: A 316 GLU cc_start: 0.8776 (tp30) cc_final: 0.8556 (tp30) REVERT: A 326 LYS cc_start: 0.8100 (mttp) cc_final: 0.7861 (mttp) REVERT: A 359 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7968 (mmmm) REVERT: A 361 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6758 (mt-10) REVERT: A 364 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6065 (pt0) REVERT: B 21 PHE cc_start: 0.8561 (m-80) cc_final: 0.8304 (m-80) REVERT: B 61 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7814 (mmtp) REVERT: B 89 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8250 (t) REVERT: B 117 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6684 (mm-30) REVERT: B 118 LYS cc_start: 0.7736 (tptt) cc_final: 0.7402 (tptt) REVERT: B 205 GLU cc_start: 0.7470 (mp0) cc_final: 0.7086 (mp0) REVERT: B 211 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7239 (t70) REVERT: B 215 LYS cc_start: 0.8352 (mttp) cc_final: 0.8109 (mtmm) REVERT: C 44 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7038 (mpp) REVERT: C 72 GLU cc_start: 0.7656 (tt0) cc_final: 0.7398 (tp30) REVERT: C 99 GLU cc_start: 0.7511 (pm20) cc_final: 0.7280 (pm20) REVERT: C 113 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8166 (mtmm) REVERT: C 118 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8174 (mttm) REVERT: C 297 ASN cc_start: 0.8503 (m110) cc_final: 0.8228 (m110) REVERT: C 334 GLU cc_start: 0.7781 (pm20) cc_final: 0.7485 (pm20) REVERT: C 360 GLN cc_start: 0.7513 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 44 MET cc_start: 0.7922 (tpp) cc_final: 0.7722 (tpp) REVERT: D 132 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7970 (ppp) REVERT: D 227 MET cc_start: 0.8580 (mmm) cc_final: 0.8339 (mmp) REVERT: D 276 GLU cc_start: 0.8055 (tt0) cc_final: 0.7832 (tt0) REVERT: D 284 LYS cc_start: 0.8554 (mttp) cc_final: 0.8278 (mtpm) REVERT: D 305 MET cc_start: 0.8948 (mmp) cc_final: 0.8695 (mmm) REVERT: E 283 MET cc_start: 0.8530 (mmp) cc_final: 0.8303 (tpt) REVERT: E 313 MET cc_start: 0.8484 (mmm) cc_final: 0.8225 (tpt) REVERT: F 68 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8465 (mmtp) REVERT: F 113 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7750 (mmtp) REVERT: F 210 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8036 (ttm110) REVERT: F 241 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: F 299 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8351 (mtm) REVERT: F 314 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: F 354 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7294 (mm-40) REVERT: F 364 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7227 (mm-30) REVERT: G 116 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8040 (ttm-80) REVERT: G 117 GLU cc_start: 0.8151 (tt0) cc_final: 0.7790 (tp30) REVERT: G 147 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7642 (ptm160) REVERT: G 270 GLU cc_start: 0.6296 (mp0) cc_final: 0.5418 (mp0) outliers start: 110 outliers final: 65 residues processed: 633 average time/residue: 1.5930 time to fit residues: 1114.0043 Evaluate side-chains 658 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 578 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 291 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 147 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 111 ASN B 297 ASN C 115 ASN C 137 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 137 GLN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN G 12 ASN G 92 ASN G 128 ASN G 225 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20815 Z= 0.264 Angle : 0.624 10.823 28254 Z= 0.292 Chirality : 0.046 0.184 3141 Planarity : 0.005 0.052 3609 Dihedral : 9.225 153.297 2927 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.45 % Allowed : 20.61 % Favored : 74.94 % 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: 0.17 (0.17), residues: 2540 helix: -0.15 (0.16), residues: 1090 sheet: 0.74 (0.24), residues: 459 loop : 0.40 (0.21), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.004 0.001 HIS C 161 PHE 0.013 0.001 PHE F 255 TYR 0.013 0.001 TYR A 240 ARG 0.010 0.001 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 585 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8255 (pttp) cc_final: 0.7819 (pttp) REVERT: A 82 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7569 (tpp) REVERT: A 99 GLU cc_start: 0.7595 (mp0) cc_final: 0.7266 (mp0) REVERT: A 154 ASP cc_start: 0.7720 (t70) cc_final: 0.7483 (t70) REVERT: A 265 SER cc_start: 0.8758 (m) cc_final: 0.8437 (t) REVERT: A 299 MET cc_start: 0.8610 (mtp) cc_final: 0.8247 (mtm) REVERT: A 326 LYS cc_start: 0.8101 (mttp) cc_final: 0.7856 (mttp) REVERT: A 359 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7977 (mmmm) REVERT: B 21 PHE cc_start: 0.8562 (m-80) cc_final: 0.8344 (m-80) REVERT: B 61 LYS cc_start: 0.8041 (mmtp) cc_final: 0.7819 (mmtp) REVERT: B 89 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8231 (t) REVERT: B 117 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6737 (mm-30) REVERT: B 118 LYS cc_start: 0.7736 (tptt) cc_final: 0.7439 (tptt) REVERT: B 205 GLU cc_start: 0.7475 (mp0) cc_final: 0.7088 (mp0) REVERT: B 211 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7576 (t70) REVERT: B 291 LYS cc_start: 0.8560 (tttm) cc_final: 0.8240 (tttm) REVERT: C 44 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7047 (mpp) REVERT: C 72 GLU cc_start: 0.7657 (tt0) cc_final: 0.7393 (tp30) REVERT: C 99 GLU cc_start: 0.7513 (pm20) cc_final: 0.7279 (pm20) REVERT: C 113 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8170 (mtmm) REVERT: C 118 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8176 (mttm) REVERT: C 297 ASN cc_start: 0.8511 (m110) cc_final: 0.8234 (m110) REVERT: C 334 GLU cc_start: 0.7791 (pm20) cc_final: 0.7480 (pm20) REVERT: C 360 GLN cc_start: 0.7517 (tm-30) cc_final: 0.7202 (tm-30) REVERT: D 132 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8026 (ppp) REVERT: D 227 MET cc_start: 0.8583 (mmm) cc_final: 0.8339 (mmp) REVERT: D 276 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: D 284 LYS cc_start: 0.8557 (mttp) cc_final: 0.8279 (mtpm) REVERT: D 305 MET cc_start: 0.8944 (mmp) cc_final: 0.8688 (mmm) REVERT: E 283 MET cc_start: 0.8497 (mmp) cc_final: 0.8278 (tpt) REVERT: E 313 MET cc_start: 0.8483 (mmm) cc_final: 0.8227 (tpt) REVERT: F 68 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8466 (mmtp) REVERT: F 113 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7750 (mmtp) REVERT: F 210 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8039 (ttm110) REVERT: F 241 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: F 299 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8367 (mtm) REVERT: F 314 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: F 354 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7216 (mm-40) REVERT: F 364 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7227 (mm-30) REVERT: G 116 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8049 (ttm-80) REVERT: G 117 GLU cc_start: 0.8152 (tt0) cc_final: 0.7790 (tp30) REVERT: G 147 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7673 (ptm160) REVERT: G 270 GLU cc_start: 0.6288 (mp0) cc_final: 0.5232 (mp0) REVERT: G 276 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7753 (mt-10) outliers start: 97 outliers final: 66 residues processed: 622 average time/residue: 1.5465 time to fit residues: 1063.4004 Evaluate side-chains 672 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 591 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 291 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 chunk 229 optimal weight: 0.7980 chunk 138 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 70 optimal weight: 0.0970 chunk 207 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 111 ASN B 173 HIS B 297 ASN C 115 ASN C 137 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN G 12 ASN G 92 ASN G 128 ASN G 225 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20815 Z= 0.223 Angle : 0.618 10.230 28254 Z= 0.288 Chirality : 0.045 0.183 3141 Planarity : 0.005 0.052 3609 Dihedral : 9.106 148.961 2927 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.13 % Allowed : 21.16 % Favored : 74.71 % 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: 0.23 (0.17), residues: 2540 helix: -0.11 (0.16), residues: 1090 sheet: 0.77 (0.24), residues: 459 loop : 0.44 (0.21), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.005 0.001 HIS C 161 PHE 0.014 0.001 PHE F 255 TYR 0.016 0.001 TYR E 143 ARG 0.010 0.001 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 588 time to evaluate : 2.402 Fit side-chains REVERT: A 61 LYS cc_start: 0.8249 (pttp) cc_final: 0.7811 (pttp) REVERT: A 82 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7584 (tpp) REVERT: A 99 GLU cc_start: 0.7598 (mp0) cc_final: 0.7280 (mp0) REVERT: A 154 ASP cc_start: 0.7701 (t70) cc_final: 0.7473 (t70) REVERT: A 265 SER cc_start: 0.8753 (m) cc_final: 0.8445 (t) REVERT: A 299 MET cc_start: 0.8603 (mtp) cc_final: 0.8243 (mtm) REVERT: A 316 GLU cc_start: 0.8774 (tp30) cc_final: 0.8530 (tp30) REVERT: A 326 LYS cc_start: 0.8100 (mttp) cc_final: 0.7860 (mttp) REVERT: A 359 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7981 (mmmm) REVERT: A 361 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6982 (mt-10) REVERT: B 21 PHE cc_start: 0.8559 (m-80) cc_final: 0.8295 (m-80) REVERT: B 61 LYS cc_start: 0.8033 (mmtp) cc_final: 0.7810 (mmtp) REVERT: B 89 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8196 (t) REVERT: B 117 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6729 (mm-30) REVERT: B 118 LYS cc_start: 0.7718 (tptt) cc_final: 0.7414 (tptt) REVERT: B 205 GLU cc_start: 0.7471 (mp0) cc_final: 0.7089 (mp0) REVERT: B 211 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7571 (t70) REVERT: B 346 LEU cc_start: 0.8467 (tp) cc_final: 0.8193 (tt) REVERT: C 44 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7051 (mpp) REVERT: C 72 GLU cc_start: 0.7639 (tt0) cc_final: 0.7358 (tp30) REVERT: C 99 GLU cc_start: 0.7514 (pm20) cc_final: 0.7291 (pm20) REVERT: C 113 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8149 (mtmm) REVERT: C 118 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8172 (mttm) REVERT: C 297 ASN cc_start: 0.8492 (m110) cc_final: 0.8214 (m110) REVERT: C 334 GLU cc_start: 0.7776 (pm20) cc_final: 0.7470 (pm20) REVERT: C 360 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7212 (tm-30) REVERT: D 132 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7963 (ppp) REVERT: D 227 MET cc_start: 0.8570 (mmm) cc_final: 0.8330 (mmp) REVERT: D 276 GLU cc_start: 0.8053 (tt0) cc_final: 0.7832 (tt0) REVERT: D 284 LYS cc_start: 0.8552 (mttp) cc_final: 0.8274 (mtpm) REVERT: D 305 MET cc_start: 0.8922 (mmp) cc_final: 0.8675 (mmm) REVERT: E 283 MET cc_start: 0.8520 (mmp) cc_final: 0.8299 (tpt) REVERT: E 313 MET cc_start: 0.8475 (mmm) cc_final: 0.8221 (tpt) REVERT: F 68 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8463 (mmtp) REVERT: F 113 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7758 (mmtp) REVERT: F 210 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8062 (ttm110) REVERT: F 241 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: F 299 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8358 (mtm) REVERT: F 314 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: F 354 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7233 (mm-40) REVERT: F 364 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7227 (mm-30) REVERT: G 44 MET cc_start: 0.8339 (mtp) cc_final: 0.7857 (mmm) REVERT: G 117 GLU cc_start: 0.8151 (tt0) cc_final: 0.7788 (tp30) REVERT: G 147 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7629 (ptm160) REVERT: G 270 GLU cc_start: 0.6234 (mp0) cc_final: 0.5149 (mp0) REVERT: G 276 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7763 (mt-10) outliers start: 90 outliers final: 64 residues processed: 621 average time/residue: 1.5745 time to fit residues: 1087.6449 Evaluate side-chains 661 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 584 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 0.1980 chunk 169 optimal weight: 0.9990 chunk 255 optimal weight: 0.0970 chunk 234 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 161 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN B 297 ASN C 115 ASN C 137 GLN C 162 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 225 ASN E 59 GLN E 78 ASN E 92 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN G 92 ASN G 128 ASN G 225 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20815 Z= 0.213 Angle : 0.623 10.164 28254 Z= 0.290 Chirality : 0.045 0.216 3141 Planarity : 0.004 0.052 3609 Dihedral : 8.970 144.082 2924 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.95 % Allowed : 21.48 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2540 helix: -0.02 (0.16), residues: 1076 sheet: 0.79 (0.24), residues: 459 loop : 0.39 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 356 HIS 0.004 0.001 HIS C 161 PHE 0.014 0.001 PHE F 255 TYR 0.016 0.001 TYR A 240 ARG 0.011 0.001 ARG D 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 593 time to evaluate : 2.237 Fit side-chains REVERT: A 61 LYS cc_start: 0.8234 (pttp) cc_final: 0.7844 (pttp) REVERT: A 82 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7585 (tpp) REVERT: A 99 GLU cc_start: 0.7600 (mp0) cc_final: 0.7285 (mp0) REVERT: A 124 PHE cc_start: 0.8065 (m-80) cc_final: 0.7820 (m-80) REVERT: A 154 ASP cc_start: 0.7697 (t70) cc_final: 0.7467 (t70) REVERT: A 223 PHE cc_start: 0.8022 (t80) cc_final: 0.7770 (t80) REVERT: A 265 SER cc_start: 0.8766 (m) cc_final: 0.8465 (t) REVERT: A 299 MET cc_start: 0.8610 (mtp) cc_final: 0.8257 (mtm) REVERT: A 316 GLU cc_start: 0.8770 (tp30) cc_final: 0.8541 (tp30) REVERT: A 326 LYS cc_start: 0.8071 (mttp) cc_final: 0.7824 (mttp) REVERT: A 352 PHE cc_start: 0.8092 (t80) cc_final: 0.7789 (t80) REVERT: A 359 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7813 (mmmm) REVERT: A 361 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6922 (mt-10) REVERT: B 21 PHE cc_start: 0.8560 (m-80) cc_final: 0.8294 (m-80) REVERT: B 61 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7779 (mmtp) REVERT: B 89 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8177 (t) REVERT: B 117 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6730 (mm-30) REVERT: B 118 LYS cc_start: 0.7706 (tptt) cc_final: 0.7397 (tptt) REVERT: B 205 GLU cc_start: 0.7473 (mp0) cc_final: 0.7084 (mp0) REVERT: B 211 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7578 (t70) REVERT: B 284 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8303 (mtmm) REVERT: B 291 LYS cc_start: 0.8540 (tttm) cc_final: 0.8279 (tttm) REVERT: B 346 LEU cc_start: 0.8467 (tp) cc_final: 0.8211 (tt) REVERT: C 44 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7064 (mpp) REVERT: C 72 GLU cc_start: 0.7634 (tt0) cc_final: 0.7353 (tp30) REVERT: C 99 GLU cc_start: 0.7512 (pm20) cc_final: 0.7295 (pm20) REVERT: C 113 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8145 (mtmm) REVERT: C 118 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8185 (mttm) REVERT: C 297 ASN cc_start: 0.8483 (m110) cc_final: 0.8210 (m110) REVERT: C 334 GLU cc_start: 0.7768 (pm20) cc_final: 0.7527 (pm20) REVERT: C 360 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7194 (tm-30) REVERT: D 90 PHE cc_start: 0.8333 (m-80) cc_final: 0.7658 (m-80) REVERT: D 227 MET cc_start: 0.8567 (mmm) cc_final: 0.8327 (mmp) REVERT: D 276 GLU cc_start: 0.8052 (tt0) cc_final: 0.7832 (tt0) REVERT: D 284 LYS cc_start: 0.8548 (mttp) cc_final: 0.8271 (mtpm) REVERT: D 305 MET cc_start: 0.8908 (mmp) cc_final: 0.8664 (mmm) REVERT: E 99 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: E 283 MET cc_start: 0.8522 (mmp) cc_final: 0.8300 (tpt) REVERT: E 313 MET cc_start: 0.8469 (mmm) cc_final: 0.8215 (tpt) REVERT: F 68 LYS cc_start: 0.8694 (mmtp) cc_final: 0.8453 (mmtp) REVERT: F 113 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7752 (mmtp) REVERT: F 210 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8056 (ttm110) REVERT: F 241 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: F 299 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8363 (mtm) REVERT: F 314 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: F 354 GLN cc_start: 0.7449 (mm-40) cc_final: 0.7231 (mm-40) REVERT: F 364 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7240 (mm-30) REVERT: G 44 MET cc_start: 0.8339 (mtp) cc_final: 0.8109 (mmm) REVERT: G 117 GLU cc_start: 0.8148 (tt0) cc_final: 0.7786 (tp30) REVERT: G 270 GLU cc_start: 0.6250 (mp0) cc_final: 0.5158 (mp0) REVERT: G 276 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7758 (mt-10) outliers start: 86 outliers final: 65 residues processed: 624 average time/residue: 1.5501 time to fit residues: 1069.6357 Evaluate side-chains 662 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 585 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN B 297 ASN C 115 ASN C 137 GLN C 162 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 225 ASN E 59 GLN E 78 ASN E 92 ASN E 115 ASN E 225 ASN F 59 GLN F 246 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 128 ASN G 225 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.091211 restraints weight = 29435.955| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.61 r_work: 0.2995 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20815 Z= 0.305 Angle : 0.665 14.151 28254 Z= 0.311 Chirality : 0.048 0.247 3141 Planarity : 0.005 0.056 3609 Dihedral : 8.966 128.507 2920 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.76 % Allowed : 21.98 % Favored : 74.25 % 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 (0.17), residues: 2540 helix: -0.18 (0.16), residues: 1090 sheet: 0.76 (0.24), residues: 458 loop : 0.36 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.005 0.001 HIS C 101 PHE 0.013 0.001 PHE F 255 TYR 0.019 0.001 TYR A 240 ARG 0.011 0.001 ARG D 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13597.60 seconds wall clock time: 238 minutes 40.21 seconds (14320.21 seconds total)