Starting phenix.real_space_refine on Sat Mar 16 21:29:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/03_2024/3j8a_6124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/03_2024/3j8a_6124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/03_2024/3j8a_6124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/03_2024/3j8a_6124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/03_2024/3j8a_6124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/03_2024/3j8a_6124_updated.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.038 sd= 1.493 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9925 2.51 5 N 2700 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} 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: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} 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: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} 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: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} 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: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} 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} Time building chain proxies: 8.49, per 1000 atoms: 0.54 Number of scatterers: 15800 At special positions: 0 Unit cell: (103.04, 97.44, 207.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 O 3060 8.00 N 2700 7.00 C 9925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.03 Conformation dependent library (CDL) restraints added in 2.5 seconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 23 sheets defined 48.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'F' and resid 98 through 230 removed outlier: 3.829A pdb=" N UNK F 129 " --> pdb=" O UNK F 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK F 143 " --> pdb=" O UNK F 139 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK F 164 " --> pdb=" O UNK F 160 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N UNK F 170 " --> pdb=" O UNK F 166 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK F 177 " --> pdb=" O UNK F 173 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK F 178 " --> pdb=" O UNK F 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK F 205 " --> pdb=" O UNK F 201 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK F 209 " --> pdb=" O UNK F 205 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK F 220 " --> pdb=" O UNK F 216 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N UNK F 223 " --> pdb=" O UNK F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 230 removed outlier: 3.577A pdb=" N UNK G 123 " --> pdb=" O UNK G 119 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK G 129 " --> pdb=" O UNK G 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK G 143 " --> pdb=" O UNK G 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK G 164 " --> pdb=" O UNK G 160 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK G 198 " --> pdb=" O UNK G 194 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N UNK G 219 " --> pdb=" O UNK G 215 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK G 226 " --> pdb=" O UNK G 222 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK G 227 " --> pdb=" O UNK G 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.922A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.888A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 142' Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.753A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 223 through 231 removed outlier: 4.209A 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: 4.645A 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 274 through 284 removed outlier: 3.922A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.380A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 344 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.846A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.911A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 223 through 231 removed outlier: 4.052A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 4.558A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.920A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.741A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.380A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 344 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 348 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.886A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.768A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 142' Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 223 through 231 removed outlier: 4.444A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.488A 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 274 through 284 removed outlier: 3.994A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 311 through 320 removed outlier: 3.542A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.414A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER C 344 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 355 Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.775A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.697A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 removed outlier: 3.959A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 removed outlier: 4.250A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 4.603A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.909A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 311 through 320 removed outlier: 3.606A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.374A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER D 344 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 348 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 355 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'E' and resid 79 through 92 removed outlier: 3.883A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.871A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 142' Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.764A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 214 Processing helix chain 'E' and resid 223 through 230 removed outlier: 4.401A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 4.589A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.816A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 311 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.414A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER E 344 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER E 348 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 355 Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.689A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 66 through 69 removed outlier: 3.910A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 35 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.971A pdb=" N GLU A 107 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 159 through 165 removed outlier: 3.946A pdb=" N GLY A 156 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 298 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SER A 155 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER A 300 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.528A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 250 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 134 through 136 removed outlier: 7.765A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 20 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.726A pdb=" N VAL B 35 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 159 through 165 removed outlier: 4.023A pdb=" N GLY B 156 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 298 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N SER B 155 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER B 300 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.806A pdb=" N ILE B 250 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 134 through 136 removed outlier: 7.768A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 20 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.830A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 159 through 165 removed outlier: 3.921A pdb=" N GLY C 156 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 298 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER C 155 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER C 300 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.871A pdb=" N ILE C 250 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 8 through 11 removed outlier: 3.714A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.670A pdb=" N VAL D 35 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 105 through 107 removed outlier: 3.773A pdb=" N GLU D 107 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 159 through 165 removed outlier: 3.895A pdb=" N GLY D 156 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 298 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N SER D 155 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER D 300 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.833A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 8 through 11 removed outlier: 3.604A pdb=" N VAL E 9 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY E 20 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 34 through 38 removed outlier: 3.773A pdb=" N VAL E 35 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 105 through 107 removed outlier: 3.850A pdb=" N GLU E 107 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 159 through 165 removed outlier: 3.944A pdb=" N GLY E 156 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL E 298 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER E 155 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER E 300 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 238 through 241 removed outlier: 3.526A pdb=" N LYS E 238 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E 250 " --> pdb=" O LYS E 238 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5092 1.33 - 1.45: 2089 1.45 - 1.57: 8736 1.57 - 1.69: 16 1.69 - 1.81: 180 Bond restraints: 16113 Sorted by residual: bond pdb=" NE2 HIC A 73 " pdb=" CZ HIC A 73 " ideal model delta sigma weight residual 1.444 1.273 0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" NE2 HIC B 73 " pdb=" CZ HIC B 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" NE2 HIC D 73 " pdb=" CZ HIC D 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" NE2 HIC C 73 " pdb=" CZ HIC C 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" NE2 HIC E 73 " pdb=" CZ HIC E 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.20e+01 ... (remaining 16108 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.92: 494 105.92 - 113.96: 9218 113.96 - 122.01: 8695 122.01 - 130.05: 3418 130.05 - 138.10: 109 Bond angle restraints: 21934 Sorted by residual: angle pdb=" C GLN E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta sigma weight residual 119.84 109.99 9.85 1.25e+00 6.40e-01 6.21e+01 angle pdb=" N VAL E 201 " pdb=" CA VAL E 201 " pdb=" C VAL E 201 " ideal model delta sigma weight residual 110.62 118.31 -7.69 1.02e+00 9.61e-01 5.69e+01 angle pdb=" N LEU A 236 " pdb=" CA LEU A 236 " pdb=" C LEU A 236 " ideal model delta sigma weight residual 112.72 104.27 8.45 1.14e+00 7.69e-01 5.49e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 110.62 117.99 -7.37 1.02e+00 9.61e-01 5.22e+01 angle pdb=" N LEU D 236 " pdb=" CA LEU D 236 " pdb=" C LEU D 236 " ideal model delta sigma weight residual 112.72 104.70 8.02 1.14e+00 7.69e-01 4.95e+01 ... (remaining 21929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 8963 21.37 - 42.74: 579 42.74 - 64.11: 125 64.11 - 85.48: 1 85.48 - 106.85: 10 Dihedral angle restraints: 9678 sinusoidal: 3570 harmonic: 6108 Sorted by residual: dihedral pdb=" CA HIS C 101 " pdb=" C HIS C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 -166.86 106.85 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 -163.67 103.66 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 9675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1645 0.038 - 0.075: 522 0.075 - 0.113: 232 0.113 - 0.150: 90 0.150 - 0.188: 16 Chirality restraints: 2505 Sorted by residual: chirality pdb=" CA VAL B 54 " pdb=" N VAL B 54 " pdb=" C VAL B 54 " pdb=" CB VAL B 54 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA GLN E 263 " pdb=" N GLN E 263 " pdb=" C GLN E 263 " pdb=" CB GLN E 263 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA VAL D 54 " pdb=" N VAL D 54 " pdb=" C VAL D 54 " pdb=" CB VAL D 54 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 2502 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 263 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" CD GLN A 263 " 0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN A 263 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN A 263 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 102 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 102 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.024 5.00e-02 4.00e+02 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 753 2.70 - 3.25: 16773 3.25 - 3.80: 23998 3.80 - 4.35: 32004 4.35 - 4.90: 49125 Nonbonded interactions: 122653 Sorted by model distance: nonbonded pdb=" OD2 ASP A 286 " pdb=" NH2 ARG C 39 " model vdw 2.145 2.520 nonbonded pdb=" OG SER B 52 " pdb=" NZ LYS B 84 " model vdw 2.153 2.520 nonbonded pdb=" OD2 ASP D 286 " pdb=" NH2 ARG E 39 " model vdw 2.169 2.520 nonbonded pdb=" O PRO C 332 " pdb=" NH1 ARG C 335 " model vdw 2.213 2.520 nonbonded pdb=" O LEU E 221 " pdb=" NZ LYS E 315 " model vdw 2.220 2.520 ... (remaining 122648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 1.460 Check model and map are aligned: 0.220 Set scattering table: 0.170 Process input model: 42.610 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.006 0.171 16113 Z= 0.385 Angle : 1.270 13.096 21934 Z= 0.851 Chirality : 0.049 0.188 2505 Planarity : 0.005 0.047 2828 Dihedral : 14.877 106.855 5748 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.38 % Allowed : 11.22 % Favored : 87.40 % Rotamer: Outliers : 6.28 % Allowed : 15.08 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -5.31 (0.15), residues: 1810 helix: -4.21 (0.10), residues: 670 sheet: -2.64 (0.32), residues: 200 loop : -3.20 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.016 0.002 HIS C 275 PHE 0.016 0.002 PHE D 255 TYR 0.013 0.002 TYR A 169 ARG 0.005 0.001 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 535 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9725 (OUTLIER) cc_final: 0.9510 (m) REVERT: A 10 CYS cc_start: 0.9116 (t) cc_final: 0.8704 (p) REVERT: A 100 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: A 111 ASN cc_start: 0.9228 (t0) cc_final: 0.9027 (t0) REVERT: A 123 MET cc_start: 0.8236 (ttt) cc_final: 0.8010 (ttp) REVERT: B 47 MET cc_start: 0.7148 (ptm) cc_final: 0.6928 (ptp) REVERT: B 100 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: B 132 MET cc_start: 0.8874 (tpp) cc_final: 0.8606 (tpt) REVERT: B 153 LEU cc_start: 0.9330 (tp) cc_final: 0.9105 (tp) REVERT: B 162 ASN cc_start: 0.9274 (t0) cc_final: 0.8757 (t0) REVERT: B 183 ARG cc_start: 0.9271 (mtt-85) cc_final: 0.8834 (ttm-80) REVERT: B 196 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8607 (mtt90) REVERT: B 199 SER cc_start: 0.9005 (p) cc_final: 0.8804 (p) REVERT: B 256 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8771 (ttm-80) REVERT: B 334 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8452 (pt0) REVERT: B 337 TYR cc_start: 0.9183 (m-10) cc_final: 0.8952 (m-10) REVERT: B 345 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9192 (mt) REVERT: C 61 LYS cc_start: 0.9140 (mttt) cc_final: 0.8929 (mttt) REVERT: C 103 THR cc_start: 0.9462 (t) cc_final: 0.9253 (t) REVERT: C 111 ASN cc_start: 0.9108 (t0) cc_final: 0.8848 (t0) REVERT: C 121 GLN cc_start: 0.9326 (tt0) cc_final: 0.9117 (tm-30) REVERT: C 248 ILE cc_start: 0.9426 (mt) cc_final: 0.9128 (tt) REVERT: C 277 THR cc_start: 0.9439 (p) cc_final: 0.8960 (t) REVERT: C 325 MET cc_start: 0.9064 (tpp) cc_final: 0.8660 (tpt) REVERT: C 328 LYS cc_start: 0.8830 (mttt) cc_final: 0.8574 (mptt) REVERT: C 334 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: D 16 LEU cc_start: 0.9610 (mm) cc_final: 0.9406 (mp) REVERT: D 44 MET cc_start: 0.8567 (ttt) cc_final: 0.8085 (tmm) REVERT: D 115 ASN cc_start: 0.9107 (t0) cc_final: 0.8511 (t0) REVERT: D 132 MET cc_start: 0.8977 (tpp) cc_final: 0.8558 (mmm) REVERT: D 154 ASP cc_start: 0.8857 (t0) cc_final: 0.8523 (t0) REVERT: D 183 ARG cc_start: 0.9279 (mtt-85) cc_final: 0.8740 (tpp80) REVERT: D 213 LYS cc_start: 0.9555 (tttt) cc_final: 0.9221 (tttm) REVERT: D 316 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: D 336 LYS cc_start: 0.9428 (tttt) cc_final: 0.9202 (tttp) REVERT: D 340 TRP cc_start: 0.9250 (t60) cc_final: 0.8831 (t60) REVERT: D 345 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9258 (mt) REVERT: E 132 MET cc_start: 0.9093 (tpp) cc_final: 0.8847 (tpp) REVERT: E 167 GLU cc_start: 0.9056 (tt0) cc_final: 0.8816 (tm-30) REVERT: E 280 ASN cc_start: 0.9446 (t0) cc_final: 0.9238 (t0) REVERT: E 288 ASP cc_start: 0.9296 (t0) cc_final: 0.8998 (t0) REVERT: E 289 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9349 (mm) REVERT: E 329 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9295 (mp) REVERT: E 334 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8674 (pt0) outliers start: 97 outliers final: 33 residues processed: 590 average time/residue: 0.2474 time to fit residues: 219.1492 Evaluate side-chains 467 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 422 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 30.0000 chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 0.0570 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16113 Z= 0.230 Angle : 0.765 7.801 21934 Z= 0.389 Chirality : 0.044 0.191 2505 Planarity : 0.005 0.040 2828 Dihedral : 9.891 93.524 2421 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.19 % Favored : 92.98 % Rotamer: Outliers : 7.12 % Allowed : 21.36 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % 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: -3.51 (0.18), residues: 1810 helix: -2.97 (0.16), residues: 635 sheet: -0.97 (0.37), residues: 200 loop : -2.16 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 340 HIS 0.013 0.001 HIS C 275 PHE 0.013 0.002 PHE B 255 TYR 0.017 0.001 TYR D 169 ARG 0.012 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 450 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9646 (OUTLIER) cc_final: 0.9399 (m) REVERT: A 39 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8607 (ptt180) REVERT: A 64 ILE cc_start: 0.9359 (tt) cc_final: 0.9157 (tt) REVERT: A 242 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8993 (mp) REVERT: B 100 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6562 (tp30) REVERT: B 286 ASP cc_start: 0.9233 (m-30) cc_final: 0.8646 (m-30) REVERT: B 329 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9083 (mm) REVERT: B 337 TYR cc_start: 0.9226 (m-10) cc_final: 0.8890 (m-10) REVERT: B 364 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8449 (pp20) REVERT: C 18 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8935 (mmtp) REVERT: C 39 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8171 (ptt180) REVERT: C 121 GLN cc_start: 0.9215 (tt0) cc_final: 0.8988 (tm-30) REVERT: C 248 ILE cc_start: 0.9387 (mt) cc_final: 0.9147 (tt) REVERT: C 259 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8877 (tm-30) REVERT: C 325 MET cc_start: 0.8913 (tpp) cc_final: 0.8537 (tpt) REVERT: C 328 LYS cc_start: 0.8613 (mttt) cc_final: 0.8204 (mptt) REVERT: D 100 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: D 115 ASN cc_start: 0.8998 (t0) cc_final: 0.8652 (t0) REVERT: D 154 ASP cc_start: 0.8624 (t0) cc_final: 0.8367 (t0) REVERT: D 183 ARG cc_start: 0.9132 (mtt-85) cc_final: 0.8877 (tpp80) REVERT: D 213 LYS cc_start: 0.9422 (tttt) cc_final: 0.9168 (tttm) REVERT: D 242 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9027 (mp) REVERT: D 325 MET cc_start: 0.9171 (mmm) cc_final: 0.8553 (tpp) REVERT: D 334 GLU cc_start: 0.8556 (pt0) cc_final: 0.8307 (pt0) REVERT: D 336 LYS cc_start: 0.9449 (tttt) cc_final: 0.9161 (tttp) REVERT: D 340 TRP cc_start: 0.9091 (t60) cc_final: 0.8405 (t60) REVERT: E 39 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7974 (ptt180) REVERT: E 115 ASN cc_start: 0.9169 (t0) cc_final: 0.8586 (t0) REVERT: E 167 GLU cc_start: 0.9024 (tt0) cc_final: 0.8738 (tm-30) REVERT: E 288 ASP cc_start: 0.9263 (t0) cc_final: 0.9031 (t0) REVERT: E 289 ILE cc_start: 0.9624 (OUTLIER) cc_final: 0.9347 (mm) outliers start: 110 outliers final: 58 residues processed: 509 average time/residue: 0.2453 time to fit residues: 187.9015 Evaluate side-chains 465 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 394 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16113 Z= 0.271 Angle : 0.730 7.792 21934 Z= 0.363 Chirality : 0.045 0.229 2505 Planarity : 0.005 0.044 2828 Dihedral : 9.222 84.657 2387 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.13 % Favored : 92.04 % Rotamer: Outliers : 7.44 % Allowed : 23.95 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % 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: -3.09 (0.18), residues: 1810 helix: -2.59 (0.17), residues: 635 sheet: -0.92 (0.37), residues: 200 loop : -1.89 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 340 HIS 0.011 0.002 HIS C 275 PHE 0.015 0.002 PHE C 255 TYR 0.012 0.001 TYR D 169 ARG 0.004 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 406 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8515 (ptt180) REVERT: B 121 GLN cc_start: 0.9117 (tt0) cc_final: 0.8863 (tm-30) REVERT: B 124 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: B 329 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9119 (mm) REVERT: B 337 TYR cc_start: 0.9206 (m-10) cc_final: 0.8822 (m-10) REVERT: B 364 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8432 (pp20) REVERT: C 246 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8902 (tm-30) REVERT: C 259 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8800 (tm-30) REVERT: C 325 MET cc_start: 0.8897 (tpp) cc_final: 0.8554 (tpt) REVERT: D 100 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: D 115 ASN cc_start: 0.8988 (t0) cc_final: 0.8634 (t0) REVERT: D 154 ASP cc_start: 0.8634 (t0) cc_final: 0.8295 (t0) REVERT: D 183 ARG cc_start: 0.9123 (mtt-85) cc_final: 0.8793 (tpp80) REVERT: D 242 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8995 (mp) REVERT: D 289 ILE cc_start: 0.9733 (OUTLIER) cc_final: 0.9442 (mm) REVERT: D 325 MET cc_start: 0.9197 (mmm) cc_final: 0.8558 (tpp) REVERT: D 340 TRP cc_start: 0.9089 (t60) cc_final: 0.8614 (t60) REVERT: E 39 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8301 (ptt180) REVERT: E 115 ASN cc_start: 0.9233 (t0) cc_final: 0.8600 (t0) REVERT: E 167 GLU cc_start: 0.9024 (tt0) cc_final: 0.8713 (tm-30) REVERT: E 263 GLN cc_start: 0.8722 (mt0) cc_final: 0.8388 (mt0) REVERT: E 289 ILE cc_start: 0.9623 (OUTLIER) cc_final: 0.9389 (mm) outliers start: 115 outliers final: 71 residues processed: 475 average time/residue: 0.2438 time to fit residues: 175.4286 Evaluate side-chains 449 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 368 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 20 optimal weight: 100.0000 chunk 89 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16113 Z= 0.252 Angle : 0.702 8.142 21934 Z= 0.344 Chirality : 0.044 0.185 2505 Planarity : 0.004 0.040 2828 Dihedral : 8.871 79.972 2378 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.96 % Favored : 92.21 % Rotamer: Outliers : 8.74 % Allowed : 24.01 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % 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: -2.89 (0.19), residues: 1810 helix: -2.38 (0.17), residues: 635 sheet: -1.82 (0.32), residues: 260 loop : -1.48 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 340 HIS 0.009 0.001 HIS C 275 PHE 0.016 0.002 PHE C 255 TYR 0.015 0.001 TYR A 198 ARG 0.004 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 401 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8505 (ptt180) REVERT: B 44 MET cc_start: 0.8477 (ttp) cc_final: 0.8165 (ttm) REVERT: B 121 GLN cc_start: 0.9118 (tt0) cc_final: 0.8851 (tm-30) REVERT: B 124 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: B 329 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9124 (mm) REVERT: B 334 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: B 337 TYR cc_start: 0.9152 (m-10) cc_final: 0.8702 (m-10) REVERT: B 364 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8529 (tm-30) REVERT: C 259 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8822 (tm-30) REVERT: C 283 MET cc_start: 0.9109 (tpp) cc_final: 0.8627 (mpp) REVERT: C 325 MET cc_start: 0.8790 (tpp) cc_final: 0.8461 (tpt) REVERT: D 115 ASN cc_start: 0.8998 (t0) cc_final: 0.8635 (t0) REVERT: D 132 MET cc_start: 0.8714 (mmm) cc_final: 0.8436 (mmm) REVERT: D 154 ASP cc_start: 0.8603 (t0) cc_final: 0.8359 (t0) REVERT: D 242 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8944 (mp) REVERT: D 289 ILE cc_start: 0.9715 (OUTLIER) cc_final: 0.9444 (mm) REVERT: D 340 TRP cc_start: 0.9190 (t60) cc_final: 0.8752 (t60) REVERT: E 167 GLU cc_start: 0.9009 (tt0) cc_final: 0.8689 (tm-30) REVERT: E 289 ILE cc_start: 0.9621 (OUTLIER) cc_final: 0.9341 (mm) outliers start: 135 outliers final: 81 residues processed: 478 average time/residue: 0.2428 time to fit residues: 176.8693 Evaluate side-chains 474 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 384 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 110.0000 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 169 optimal weight: 0.4980 chunk 137 optimal weight: 0.0970 chunk 0 optimal weight: 70.0000 chunk 101 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16113 Z= 0.173 Angle : 0.692 9.753 21934 Z= 0.334 Chirality : 0.044 0.180 2505 Planarity : 0.004 0.037 2828 Dihedral : 8.412 77.848 2376 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.86 % Favored : 93.31 % Rotamer: Outliers : 6.93 % Allowed : 26.93 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.67 (0.19), residues: 1810 helix: -2.08 (0.18), residues: 635 sheet: -1.79 (0.35), residues: 200 loop : -1.48 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.022 0.001 TYR A 362 ARG 0.003 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 425 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8484 (ptt180) REVERT: A 237 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8633 (pt0) REVERT: A 262 PHE cc_start: 0.9061 (m-80) cc_final: 0.8789 (m-80) REVERT: B 44 MET cc_start: 0.8425 (ttp) cc_final: 0.8135 (ttm) REVERT: B 66 THR cc_start: 0.9383 (p) cc_final: 0.9163 (t) REVERT: B 100 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: B 121 GLN cc_start: 0.9067 (tt0) cc_final: 0.8789 (tm-30) REVERT: B 124 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: B 159 VAL cc_start: 0.9344 (t) cc_final: 0.9076 (p) REVERT: B 329 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9091 (mm) REVERT: B 334 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: B 337 TYR cc_start: 0.9148 (m-10) cc_final: 0.8908 (m-10) REVERT: B 340 TRP cc_start: 0.8891 (t60) cc_final: 0.8548 (t60) REVERT: B 364 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8618 (pp20) REVERT: C 225 ASN cc_start: 0.8590 (t0) cc_final: 0.8333 (t0) REVERT: C 259 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8986 (tm-30) REVERT: C 283 MET cc_start: 0.9109 (tpp) cc_final: 0.8615 (mpp) REVERT: C 325 MET cc_start: 0.8758 (tpp) cc_final: 0.8422 (tpt) REVERT: D 115 ASN cc_start: 0.8921 (t0) cc_final: 0.8584 (t0) REVERT: D 124 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: D 132 MET cc_start: 0.8718 (mmm) cc_final: 0.8286 (mmm) REVERT: D 242 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8867 (mp) REVERT: D 289 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9398 (mm) REVERT: D 325 MET cc_start: 0.8838 (mmm) cc_final: 0.8505 (tpp) REVERT: D 340 TRP cc_start: 0.9135 (t60) cc_final: 0.8570 (t60) REVERT: E 129 VAL cc_start: 0.8836 (t) cc_final: 0.8613 (p) REVERT: E 167 GLU cc_start: 0.8946 (tt0) cc_final: 0.8656 (tm-30) REVERT: E 193 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8692 (mt) REVERT: E 267 ILE cc_start: 0.9393 (mm) cc_final: 0.9161 (tp) REVERT: E 270 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8232 (mt-10) REVERT: E 275 HIS cc_start: 0.9438 (OUTLIER) cc_final: 0.8788 (p-80) outliers start: 107 outliers final: 64 residues processed: 483 average time/residue: 0.2357 time to fit residues: 174.3004 Evaluate side-chains 463 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 387 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 70.0000 chunk 65 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16113 Z= 0.202 Angle : 0.695 12.465 21934 Z= 0.334 Chirality : 0.044 0.184 2505 Planarity : 0.004 0.044 2828 Dihedral : 7.885 75.133 2367 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.97 % Favored : 93.20 % Rotamer: Outliers : 7.12 % Allowed : 27.12 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.35 (0.20), residues: 1810 helix: -1.79 (0.19), residues: 635 sheet: -1.66 (0.36), residues: 200 loop : -1.29 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 340 HIS 0.009 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.018 0.001 TYR D 169 ARG 0.005 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 395 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8472 (ptt180) REVERT: A 237 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8615 (pt0) REVERT: B 66 THR cc_start: 0.9398 (p) cc_final: 0.9193 (t) REVERT: B 121 GLN cc_start: 0.9066 (tt0) cc_final: 0.8780 (tm-30) REVERT: B 124 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: B 329 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9104 (mm) REVERT: B 334 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: B 364 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: C 225 ASN cc_start: 0.8615 (t0) cc_final: 0.8337 (t0) REVERT: C 259 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8972 (tm-30) REVERT: C 283 MET cc_start: 0.9097 (tpp) cc_final: 0.8549 (mpp) REVERT: C 325 MET cc_start: 0.8779 (tpp) cc_final: 0.8454 (tpt) REVERT: D 47 MET cc_start: 0.7462 (ttp) cc_final: 0.7167 (mtp) REVERT: D 115 ASN cc_start: 0.8940 (t0) cc_final: 0.8620 (t0) REVERT: D 124 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: D 190 MET cc_start: 0.9080 (tpp) cc_final: 0.8574 (ttm) REVERT: D 242 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8874 (mp) REVERT: D 275 HIS cc_start: 0.9492 (OUTLIER) cc_final: 0.9058 (p-80) REVERT: D 289 ILE cc_start: 0.9690 (OUTLIER) cc_final: 0.9413 (mm) REVERT: D 340 TRP cc_start: 0.9150 (t60) cc_final: 0.8591 (t60) REVERT: E 39 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8209 (ptt180) REVERT: E 167 GLU cc_start: 0.8947 (tt0) cc_final: 0.8648 (tm-30) REVERT: E 193 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8633 (mt) REVERT: E 275 HIS cc_start: 0.9433 (OUTLIER) cc_final: 0.8922 (p-80) REVERT: E 289 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9330 (mm) outliers start: 110 outliers final: 74 residues processed: 454 average time/residue: 0.2340 time to fit residues: 163.4005 Evaluate side-chains 468 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 380 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 9.9990 chunk 22 optimal weight: 90.0000 chunk 113 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 chunk 91 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16113 Z= 0.280 Angle : 0.712 11.537 21934 Z= 0.346 Chirality : 0.045 0.183 2505 Planarity : 0.005 0.067 2828 Dihedral : 7.707 75.877 2359 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.69 % Favored : 92.49 % Rotamer: Outliers : 7.77 % Allowed : 26.08 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.35 (0.20), residues: 1810 helix: -1.85 (0.19), residues: 635 sheet: -1.22 (0.35), residues: 230 loop : -1.34 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 340 HIS 0.007 0.001 HIS C 275 PHE 0.017 0.002 PHE E 255 TYR 0.042 0.001 TYR B 69 ARG 0.008 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 392 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8544 (ptt180) REVERT: B 66 THR cc_start: 0.9409 (p) cc_final: 0.9189 (t) REVERT: B 121 GLN cc_start: 0.9108 (tt0) cc_final: 0.8795 (tm-30) REVERT: B 124 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: B 132 MET cc_start: 0.8769 (tpt) cc_final: 0.8470 (tpt) REVERT: B 190 MET cc_start: 0.8657 (ttt) cc_final: 0.8412 (ttt) REVERT: B 329 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9115 (mm) REVERT: B 334 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: B 364 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: C 190 MET cc_start: 0.8715 (ttt) cc_final: 0.8488 (ttt) REVERT: C 225 ASN cc_start: 0.8632 (t0) cc_final: 0.8336 (t0) REVERT: C 259 GLU cc_start: 0.9283 (tm-30) cc_final: 0.8877 (tm-30) REVERT: C 325 MET cc_start: 0.8746 (tpp) cc_final: 0.8452 (tpt) REVERT: D 47 MET cc_start: 0.7553 (ttp) cc_final: 0.7291 (mtp) REVERT: D 115 ASN cc_start: 0.9026 (t0) cc_final: 0.8685 (t0) REVERT: D 124 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: D 242 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8924 (mp) REVERT: D 275 HIS cc_start: 0.9512 (OUTLIER) cc_final: 0.9193 (p-80) REVERT: D 289 ILE cc_start: 0.9702 (OUTLIER) cc_final: 0.9414 (mm) REVERT: D 325 MET cc_start: 0.8909 (mmm) cc_final: 0.8498 (tpp) REVERT: E 39 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8175 (ptt180) REVERT: E 167 GLU cc_start: 0.8970 (tt0) cc_final: 0.8664 (tm-30) REVERT: E 193 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8576 (mt) REVERT: E 275 HIS cc_start: 0.9470 (OUTLIER) cc_final: 0.8951 (p-80) REVERT: E 289 ILE cc_start: 0.9601 (OUTLIER) cc_final: 0.9344 (mm) outliers start: 120 outliers final: 87 residues processed: 460 average time/residue: 0.2345 time to fit residues: 165.7942 Evaluate side-chains 479 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 379 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 126 optimal weight: 0.0570 chunk 135 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 18 optimal weight: 120.0000 chunk 156 optimal weight: 8.9990 overall best weight: 3.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16113 Z= 0.218 Angle : 0.707 12.244 21934 Z= 0.340 Chirality : 0.044 0.178 2505 Planarity : 0.005 0.063 2828 Dihedral : 7.619 74.551 2358 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.02 % Favored : 93.15 % Rotamer: Outliers : 7.44 % Allowed : 27.12 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.40 (0.19), residues: 1810 helix: -1.78 (0.19), residues: 635 sheet: -1.66 (0.36), residues: 200 loop : -1.37 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 340 HIS 0.008 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.031 0.001 TYR B 69 ARG 0.008 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 392 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8459 (ptt180) REVERT: A 237 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8638 (pt0) REVERT: B 66 THR cc_start: 0.9441 (p) cc_final: 0.9230 (t) REVERT: B 121 GLN cc_start: 0.9064 (tt0) cc_final: 0.8776 (tm-30) REVERT: B 124 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: B 132 MET cc_start: 0.8769 (tpt) cc_final: 0.8459 (tpt) REVERT: B 329 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9076 (mm) REVERT: B 334 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: B 364 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: C 225 ASN cc_start: 0.8612 (t0) cc_final: 0.8307 (t0) REVERT: C 259 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8881 (tm-30) REVERT: C 325 MET cc_start: 0.8783 (tpp) cc_final: 0.8476 (tpt) REVERT: D 47 MET cc_start: 0.7506 (ttp) cc_final: 0.7232 (mtp) REVERT: D 115 ASN cc_start: 0.9035 (t0) cc_final: 0.8724 (t0) REVERT: D 124 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: D 190 MET cc_start: 0.9079 (tpp) cc_final: 0.8257 (ttt) REVERT: D 242 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8897 (mp) REVERT: E 39 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8093 (ptt180) REVERT: E 167 GLU cc_start: 0.8929 (tt0) cc_final: 0.8640 (tm-30) REVERT: E 193 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8551 (mt) REVERT: E 275 HIS cc_start: 0.9438 (OUTLIER) cc_final: 0.9027 (p-80) REVERT: E 289 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9209 (mm) outliers start: 115 outliers final: 86 residues processed: 457 average time/residue: 0.2303 time to fit residues: 161.9006 Evaluate side-chains 477 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 379 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 173 optimal weight: 0.0170 chunk 185 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16113 Z= 0.235 Angle : 0.720 11.063 21934 Z= 0.347 Chirality : 0.045 0.227 2505 Planarity : 0.004 0.045 2828 Dihedral : 7.510 73.566 2356 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.41 % Favored : 92.76 % Rotamer: Outliers : 7.12 % Allowed : 27.77 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.38 (0.19), residues: 1810 helix: -1.76 (0.19), residues: 635 sheet: -1.67 (0.36), residues: 200 loop : -1.36 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 340 HIS 0.008 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.019 0.001 TYR B 69 ARG 0.004 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 383 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8516 (ptt180) REVERT: A 237 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8676 (pt0) REVERT: B 66 THR cc_start: 0.9434 (p) cc_final: 0.9219 (t) REVERT: B 121 GLN cc_start: 0.9069 (tt0) cc_final: 0.8799 (tm-30) REVERT: B 124 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: B 329 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9027 (mm) REVERT: B 337 TYR cc_start: 0.9077 (m-10) cc_final: 0.8824 (m-10) REVERT: B 364 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: C 225 ASN cc_start: 0.8622 (t0) cc_final: 0.8309 (t0) REVERT: C 259 GLU cc_start: 0.9292 (tm-30) cc_final: 0.8894 (tm-30) REVERT: C 325 MET cc_start: 0.8809 (tpp) cc_final: 0.8526 (tpt) REVERT: D 44 MET cc_start: 0.8907 (ttp) cc_final: 0.8663 (ttm) REVERT: D 47 MET cc_start: 0.7529 (ttp) cc_final: 0.7249 (mtp) REVERT: D 124 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: D 190 MET cc_start: 0.9038 (tpp) cc_final: 0.8298 (ttt) REVERT: E 39 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8135 (ptt180) REVERT: E 167 GLU cc_start: 0.8931 (tt0) cc_final: 0.8640 (tm-30) REVERT: E 193 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8557 (mt) REVERT: E 275 HIS cc_start: 0.9465 (OUTLIER) cc_final: 0.9012 (p-80) REVERT: E 289 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9313 (mm) outliers start: 110 outliers final: 92 residues processed: 446 average time/residue: 0.2327 time to fit residues: 158.8989 Evaluate side-chains 478 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 376 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 40.0000 chunk 195 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 205 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 16 optimal weight: 80.0000 chunk 126 optimal weight: 0.0670 chunk 100 optimal weight: 10.0000 overall best weight: 3.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16113 Z= 0.232 Angle : 0.718 10.975 21934 Z= 0.346 Chirality : 0.045 0.225 2505 Planarity : 0.005 0.057 2828 Dihedral : 7.498 73.136 2356 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.57 % Favored : 92.60 % Rotamer: Outliers : 7.18 % Allowed : 27.90 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.36 (0.19), residues: 1810 helix: -1.74 (0.20), residues: 635 sheet: -1.65 (0.36), residues: 200 loop : -1.35 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 340 HIS 0.008 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.019 0.001 TYR B 69 ARG 0.004 0.000 ARG B 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 383 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8513 (ptt180) REVERT: A 237 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8665 (pt0) REVERT: B 66 THR cc_start: 0.9426 (p) cc_final: 0.9213 (t) REVERT: B 121 GLN cc_start: 0.9078 (tt0) cc_final: 0.8791 (tm-30) REVERT: B 124 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: B 132 MET cc_start: 0.8595 (tpt) cc_final: 0.8361 (tpt) REVERT: B 329 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9020 (mm) REVERT: B 337 TYR cc_start: 0.9046 (m-10) cc_final: 0.8750 (m-10) REVERT: B 364 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: C 124 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: C 225 ASN cc_start: 0.8642 (t0) cc_final: 0.8320 (t0) REVERT: C 259 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8695 (tm-30) REVERT: C 325 MET cc_start: 0.8805 (tpp) cc_final: 0.8527 (tpt) REVERT: D 47 MET cc_start: 0.7558 (ttp) cc_final: 0.7277 (mtp) REVERT: D 124 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: D 275 HIS cc_start: 0.9381 (OUTLIER) cc_final: 0.9132 (p-80) REVERT: E 39 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8150 (ptt180) REVERT: E 167 GLU cc_start: 0.8927 (tt0) cc_final: 0.8637 (tm-30) REVERT: E 193 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8565 (mt) REVERT: E 275 HIS cc_start: 0.9458 (OUTLIER) cc_final: 0.9060 (p-80) REVERT: E 289 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9195 (mm) outliers start: 111 outliers final: 92 residues processed: 448 average time/residue: 0.2432 time to fit residues: 168.5190 Evaluate side-chains 481 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 377 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.0770 chunk 174 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 24 optimal weight: 110.0000 chunk 45 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 168 optimal weight: 8.9990 chunk 20 optimal weight: 110.0000 chunk 30 optimal weight: 10.0000 overall best weight: 2.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107000 restraints weight = 32022.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109568 restraints weight = 15266.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.111470 restraints weight = 8915.244| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16113 Z= 0.198 Angle : 0.711 11.611 21934 Z= 0.341 Chirality : 0.044 0.208 2505 Planarity : 0.004 0.045 2828 Dihedral : 7.304 72.034 2354 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.02 % Favored : 93.15 % Rotamer: Outliers : 6.86 % Allowed : 28.67 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % 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: -2.20 (0.20), residues: 1810 helix: -1.69 (0.20), residues: 635 sheet: -1.45 (0.38), residues: 190 loop : -1.23 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 340 HIS 0.008 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.015 0.001 TYR B 279 ARG 0.004 0.000 ARG A 183 =============================================================================== Job complete usr+sys time: 3562.98 seconds wall clock time: 64 minutes 58.78 seconds (3898.78 seconds total)