Starting phenix.real_space_refine on Sun Dec 10 22:15:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/12_2023/3j8a_6124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/12_2023/3j8a_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_6124/12_2023/3j8a_6124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/12_2023/3j8a_6124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/12_2023/3j8a_6124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/12_2023/3j8a_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-1.21rc1-5172/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: 8.93, per 1000 atoms: 0.57 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: 6.42 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: 3.16 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: 4.25 Time building geometry restraints manager: 6.91 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.480 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 42.630 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.480 ------------------------------------------------------------------------------- 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 : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 33 residues processed: 590 average time/residue: 0.2544 time to fit residues: 225.4337 Evaluate side-chains 443 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 410 time to evaluate : 1.912 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.1499 time to fit residues: 11.2877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** 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 C 92 ASN C 162 ASN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 115 ASN ** D 161 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 E 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16113 Z= 0.264 Angle : 0.786 7.980 21934 Z= 0.403 Chirality : 0.045 0.164 2505 Planarity : 0.005 0.041 2828 Dihedral : 7.885 93.699 2323 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.40 % Favored : 91.77 % Rotamer: Outliers : 5.37 % Allowed : 23.11 % 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: -3.61 (0.18), residues: 1810 helix: -3.05 (0.16), residues: 635 sheet: -1.00 (0.37), residues: 200 loop : -2.24 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 340 HIS 0.012 0.002 HIS C 275 PHE 0.014 0.002 PHE D 255 TYR 0.016 0.002 TYR D 169 ARG 0.003 0.000 ARG C 254 *********************** 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 515 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 432 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 40 residues processed: 474 average time/residue: 0.2435 time to fit residues: 175.5715 Evaluate side-chains 424 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 384 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1394 time to fit residues: 12.4924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 187 optimal weight: 0.0870 chunk 202 optimal weight: 30.0000 chunk 166 optimal weight: 30.0000 chunk 185 optimal weight: 0.0870 chunk 63 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 overall best weight: 4.2342 ------------------------------------------------------------------------------- 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 40 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 263 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16113 Z= 0.248 Angle : 0.725 7.967 21934 Z= 0.359 Chirality : 0.045 0.224 2505 Planarity : 0.005 0.043 2828 Dihedral : 7.346 83.885 2323 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.52 % Favored : 92.65 % Rotamer: Outliers : 4.40 % Allowed : 25.50 % Favored : 70.10 % 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: -3.11 (0.18), residues: 1810 helix: -2.60 (0.17), residues: 635 sheet: -0.93 (0.37), residues: 200 loop : -1.91 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 340 HIS 0.012 0.002 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.012 0.001 TYR D 169 ARG 0.003 0.000 ARG E 39 *********************** 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 473 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 405 time to evaluate : 1.837 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 30 residues processed: 452 average time/residue: 0.2330 time to fit residues: 162.3979 Evaluate side-chains 403 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 373 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1380 time to fit residues: 10.1340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 20 optimal weight: 100.0000 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 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 115 ASN D 162 ASN D 246 GLN E 40 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN E 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2608 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= 0.262 Angle : 0.714 8.691 21934 Z= 0.350 Chirality : 0.045 0.214 2505 Planarity : 0.005 0.037 2828 Dihedral : 7.160 79.785 2323 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.29 % Favored : 91.88 % Rotamer: Outliers : 4.72 % Allowed : 26.47 % Favored : 68.80 % 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: -3.01 (0.18), residues: 1810 helix: -2.44 (0.17), residues: 630 sheet: -1.52 (0.41), residues: 150 loop : -1.77 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 340 HIS 0.013 0.002 HIS C 275 PHE 0.015 0.002 PHE C 255 TYR 0.020 0.001 TYR A 198 ARG 0.004 0.000 ARG D 312 *********************** 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 474 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 401 time to evaluate : 1.732 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 34 residues processed: 444 average time/residue: 0.2320 time to fit residues: 161.8581 Evaluate side-chains 408 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 374 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1452 time to fit residues: 11.4381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 110.0000 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 101 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** 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 ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16113 Z= 0.178 Angle : 0.705 12.517 21934 Z= 0.340 Chirality : 0.044 0.194 2505 Planarity : 0.004 0.039 2828 Dihedral : 6.750 76.908 2323 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.64 % Favored : 93.54 % Rotamer: Outliers : 3.30 % Allowed : 27.12 % Favored : 69.58 % 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: -2.62 (0.19), residues: 1810 helix: -2.04 (0.18), residues: 650 sheet: -1.38 (0.38), residues: 175 loop : -1.53 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 340 HIS 0.013 0.002 HIS C 275 PHE 0.012 0.001 PHE C 255 TYR 0.022 0.001 TYR A 362 ARG 0.004 0.000 ARG B 183 *********************** 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 476 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 425 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 25 residues processed: 445 average time/residue: 0.2414 time to fit residues: 165.6349 Evaluate side-chains 413 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 388 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1489 time to fit residues: 9.0677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 0.7980 chunk 179 optimal weight: 0.3980 chunk 39 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 0.0670 chunk 199 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 70.0000 chunk 65 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 overall best weight: 1.8522 ------------------------------------------------------------------------------- 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** ** B 88 HIS ** 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 115 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16113 Z= 0.178 Angle : 0.697 11.484 21934 Z= 0.336 Chirality : 0.045 0.256 2505 Planarity : 0.004 0.060 2828 Dihedral : 6.549 74.222 2323 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.75 % Favored : 93.43 % Rotamer: Outliers : 3.11 % Allowed : 28.61 % Favored : 68.28 % 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: -2.44 (0.19), residues: 1810 helix: -1.83 (0.19), residues: 635 sheet: -1.75 (0.35), residues: 200 loop : -1.37 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP D 340 HIS 0.012 0.002 HIS C 275 PHE 0.023 0.001 PHE C 31 TYR 0.027 0.001 TYR B 69 ARG 0.009 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 464 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 416 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 21 residues processed: 435 average time/residue: 0.2325 time to fit residues: 156.6817 Evaluate side-chains 407 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 386 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1444 time to fit residues: 8.1464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 0.9980 chunk 22 optimal weight: 90.0000 chunk 113 optimal weight: 8.9990 chunk 145 optimal weight: 0.0050 chunk 112 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- 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** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** 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 D 115 ASN D 297 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16113 Z= 0.228 Angle : 0.716 9.876 21934 Z= 0.347 Chirality : 0.046 0.319 2505 Planarity : 0.004 0.037 2828 Dihedral : 6.503 73.477 2323 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.97 % Favored : 93.20 % Rotamer: Outliers : 2.33 % Allowed : 29.39 % Favored : 68.28 % 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: -2.48 (0.19), residues: 1810 helix: -1.82 (0.19), residues: 630 sheet: -2.25 (0.34), residues: 205 loop : -1.30 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A 340 HIS 0.011 0.002 HIS C 275 PHE 0.019 0.001 PHE C 31 TYR 0.021 0.001 TYR D 169 ARG 0.004 0.000 ARG C 39 *********************** 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 445 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 409 time to evaluate : 1.678 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 419 average time/residue: 0.2339 time to fit residues: 151.9867 Evaluate side-chains 403 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 383 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1440 time to fit residues: 7.6703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 18 optimal weight: 120.0000 chunk 156 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN E 49 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16113 Z= 0.228 Angle : 0.724 10.096 21934 Z= 0.349 Chirality : 0.046 0.288 2505 Planarity : 0.004 0.036 2828 Dihedral : 6.514 73.585 2323 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.02 % Favored : 93.15 % Rotamer: Outliers : 2.52 % Allowed : 29.51 % Favored : 67.96 % 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: -2.43 (0.19), residues: 1810 helix: -1.81 (0.19), residues: 630 sheet: -2.11 (0.32), residues: 230 loop : -1.23 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP B 340 HIS 0.010 0.002 HIS C 275 PHE 0.016 0.001 PHE C 31 TYR 0.019 0.001 TYR D 169 ARG 0.006 0.000 ARG B 147 *********************** 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 443 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 404 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 418 average time/residue: 0.2401 time to fit residues: 155.8897 Evaluate side-chains 405 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 382 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1432 time to fit residues: 8.4225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 173 optimal weight: 0.3980 chunk 185 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 0.0870 chunk 167 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 overall best weight: 3.8964 ------------------------------------------------------------------------------- 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** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** 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 115 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3513 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= 0.238 Angle : 0.730 9.893 21934 Z= 0.352 Chirality : 0.046 0.300 2505 Planarity : 0.005 0.052 2828 Dihedral : 6.512 73.615 2323 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.57 % Favored : 92.60 % Rotamer: Outliers : 1.36 % Allowed : 30.49 % Favored : 68.16 % 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: -2.42 (0.20), residues: 1810 helix: -1.80 (0.19), residues: 630 sheet: -2.08 (0.32), residues: 230 loop : -1.24 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP A 340 HIS 0.012 0.002 HIS D 275 PHE 0.016 0.001 PHE C 255 TYR 0.020 0.001 TYR B 69 ARG 0.005 0.000 ARG D 256 *********************** 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 419 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 398 time to evaluate : 1.661 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 403 average time/residue: 0.2317 time to fit residues: 146.3502 Evaluate side-chains 399 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 385 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1431 time to fit residues: 6.2040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 92 optimal weight: 0.0980 chunk 136 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 16 optimal weight: 80.0000 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16113 Z= 0.224 Angle : 0.741 9.930 21934 Z= 0.356 Chirality : 0.047 0.311 2505 Planarity : 0.004 0.037 2828 Dihedral : 6.463 73.299 2323 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.02 % Favored : 93.15 % Rotamer: Outliers : 1.23 % Allowed : 31.59 % Favored : 67.18 % 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: -2.49 (0.19), residues: 1810 helix: -1.79 (0.19), residues: 635 sheet: -2.20 (0.34), residues: 205 loop : -1.34 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 340 HIS 0.012 0.002 HIS D 275 PHE 0.015 0.001 PHE C 255 TYR 0.021 0.001 TYR B 279 ARG 0.004 0.000 ARG D 256 ********************** 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 408 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 389 time to evaluate : 1.711 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 400 average time/residue: 0.2340 time to fit residues: 147.0142 Evaluate side-chains 383 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 375 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1499 time to fit residues: 4.4970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 24 optimal weight: 110.0000 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 20 optimal weight: 110.0000 chunk 30 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** B 371 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104244 restraints weight = 32322.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106785 restraints weight = 15558.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108665 restraints weight = 9024.971| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 16113 Z= 0.323 Angle : 0.775 10.030 21934 Z= 0.377 Chirality : 0.048 0.310 2505 Planarity : 0.005 0.040 2828 Dihedral : 6.682 73.588 2323 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.51 % Favored : 91.66 % Rotamer: Outliers : 1.49 % Allowed : 31.97 % Favored : 66.54 % 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: -2.43 (0.19), residues: 1810 helix: -1.92 (0.19), residues: 635 sheet: -0.77 (0.39), residues: 190 loop : -1.53 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP A 340 HIS 0.010 0.002 HIS D 275 PHE 0.019 0.002 PHE C 31 TYR 0.021 0.002 TYR D 169 ARG 0.005 0.000 ARG C 183 =============================================================================== Job complete usr+sys time: 3523.40 seconds wall clock time: 64 minutes 35.61 seconds (3875.61 seconds total)