Starting phenix.real_space_refine on Sat Mar 16 07:00:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcx_28998/03_2024/8fcx_28998_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcx_28998/03_2024/8fcx_28998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcx_28998/03_2024/8fcx_28998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcx_28998/03_2024/8fcx_28998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcx_28998/03_2024/8fcx_28998_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcx_28998/03_2024/8fcx_28998_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 40 5.16 5 C 8835 2.51 5 N 2440 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 95": "OE1" <-> "OE2" Residue "R GLU 272": "OE1" <-> "OE2" Residue "R GLU 321": "OE1" <-> "OE2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S GLU 321": "OE1" <-> "OE2" Residue "T GLU 10": "OE1" <-> "OE2" Residue "T GLU 71": "OE1" <-> "OE2" Residue "T GLU 76": "OE1" <-> "OE2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U GLU 38": "OE1" <-> "OE2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U GLU 71": "OE1" <-> "OE2" Residue "U GLU 76": "OE1" <-> "OE2" Residue "U GLU 95": "OE1" <-> "OE2" Residue "U GLU 108": "OE1" <-> "OE2" Residue "U GLU 144": "OE1" <-> "OE2" Residue "U GLU 172": "OE1" <-> "OE2" Residue "U GLU 333": "OE1" <-> "OE2" Residue "V GLU 71": "OE1" <-> "OE2" Residue "V GLU 157": "OE1" <-> "OE2" Residue "V GLU 210": "OE1" <-> "OE2" Residue "V GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13940 Number of models: 1 Model: "" Number of chains: 10 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.42, per 1000 atoms: 0.53 Number of scatterers: 13940 At special positions: 0 Unit cell: (77.996, 124.372, 151.776, 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 40 16.00 P 15 15.00 Mg 5 11.99 O 2605 8.00 N 2440 7.00 C 8835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.5 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 5 sheets defined 55.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'R' and resid 9 through 12 Processing helix chain 'R' and resid 16 through 25 Processing helix chain 'R' and resid 31 through 45 Processing helix chain 'R' and resid 63 through 84 Proline residue: R 80 - end of helix removed outlier: 3.634A pdb=" N SER R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 117 Processing helix chain 'R' and resid 149 through 163 Processing helix chain 'R' and resid 173 through 177 Processing helix chain 'R' and resid 182 through 199 removed outlier: 3.866A pdb=" N LEU R 185 " --> pdb=" O GLY R 182 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET R 198 " --> pdb=" O LEU R 195 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR R 199 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 219 through 223 Processing helix chain 'R' and resid 238 through 253 Processing helix chain 'R' and resid 265 through 274 removed outlier: 4.644A pdb=" N GLU R 268 " --> pdb=" O ASP R 265 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE R 270 " --> pdb=" O TRP R 267 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR R 271 " --> pdb=" O GLU R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 295 Processing helix chain 'R' and resid 302 through 307 Processing helix chain 'R' and resid 312 through 328 removed outlier: 3.849A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 342 removed outlier: 3.727A pdb=" N ASN R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 13 removed outlier: 3.661A pdb=" N LEU S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 25 Processing helix chain 'S' and resid 31 through 45 Processing helix chain 'S' and resid 63 through 82 Proline residue: S 80 - end of helix Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 149 through 163 Processing helix chain 'S' and resid 173 through 177 Processing helix chain 'S' and resid 182 through 199 removed outlier: 3.919A pdb=" N LEU S 185 " --> pdb=" O GLY S 182 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET S 198 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 209 through 214 Processing helix chain 'S' and resid 219 through 223 Processing helix chain 'S' and resid 238 through 253 Processing helix chain 'S' and resid 265 through 274 removed outlier: 4.665A pdb=" N GLU S 268 " --> pdb=" O ASP S 265 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG S 273 " --> pdb=" O PHE S 270 " (cutoff:3.500A) Processing helix chain 'S' and resid 278 through 294 Processing helix chain 'S' and resid 302 through 308 removed outlier: 3.611A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 312 through 328 Processing helix chain 'S' and resid 333 through 343 Processing helix chain 'T' and resid 9 through 12 removed outlier: 3.512A pdb=" N LEU T 12 " --> pdb=" O LEU T 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 9 through 12' Processing helix chain 'T' and resid 16 through 25 Processing helix chain 'T' and resid 31 through 45 Processing helix chain 'T' and resid 63 through 84 Proline residue: T 80 - end of helix removed outlier: 4.017A pdb=" N SER T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 117 Processing helix chain 'T' and resid 149 through 163 Processing helix chain 'T' and resid 173 through 177 Processing helix chain 'T' and resid 182 through 199 removed outlier: 4.003A pdb=" N GLN T 186 " --> pdb=" O GLY T 182 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 214 removed outlier: 3.507A pdb=" N THR T 213 " --> pdb=" O GLU T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 219 through 224 Processing helix chain 'T' and resid 238 through 253 Processing helix chain 'T' and resid 267 through 274 Processing helix chain 'T' and resid 278 through 295 Processing helix chain 'T' and resid 302 through 307 Processing helix chain 'T' and resid 312 through 328 Processing helix chain 'T' and resid 333 through 343 Processing helix chain 'U' and resid 9 through 12 Processing helix chain 'U' and resid 16 through 25 Processing helix chain 'U' and resid 31 through 45 Processing helix chain 'U' and resid 63 through 83 Proline residue: U 80 - end of helix Processing helix chain 'U' and resid 106 through 117 Processing helix chain 'U' and resid 149 through 163 Processing helix chain 'U' and resid 173 through 177 Processing helix chain 'U' and resid 183 through 199 removed outlier: 4.353A pdb=" N MET U 198 " --> pdb=" O LEU U 195 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR U 199 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 214 Processing helix chain 'U' and resid 219 through 223 Processing helix chain 'U' and resid 238 through 253 Processing helix chain 'U' and resid 264 through 274 removed outlier: 4.932A pdb=" N GLU U 268 " --> pdb=" O ASP U 265 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR U 269 " --> pdb=" O HIS U 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR U 274 " --> pdb=" O TYR U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 295 Processing helix chain 'U' and resid 302 through 307 Processing helix chain 'U' and resid 312 through 328 Processing helix chain 'U' and resid 333 through 343 Processing helix chain 'V' and resid 9 through 12 Processing helix chain 'V' and resid 16 through 25 Processing helix chain 'V' and resid 31 through 45 Processing helix chain 'V' and resid 63 through 77 Processing helix chain 'V' and resid 79 through 84 Processing helix chain 'V' and resid 106 through 117 Processing helix chain 'V' and resid 149 through 163 Processing helix chain 'V' and resid 173 through 177 Processing helix chain 'V' and resid 184 through 199 removed outlier: 4.014A pdb=" N LEU V 189 " --> pdb=" O LEU V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 209 through 214 Processing helix chain 'V' and resid 218 through 223 Processing helix chain 'V' and resid 238 through 253 Processing helix chain 'V' and resid 265 through 274 removed outlier: 4.737A pdb=" N GLU V 268 " --> pdb=" O ASP V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 294 Processing helix chain 'V' and resid 302 through 308 removed outlier: 3.605A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 328 removed outlier: 3.846A pdb=" N LYS V 317 " --> pdb=" O ALA V 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE V 319 " --> pdb=" O CYS V 315 " (cutoff:3.500A) Processing helix chain 'V' and resid 333 through 343 Processing sheet with id= A, first strand: chain 'R' and resid 225 through 230 removed outlier: 6.261A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE R 230 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR R 56 " --> pdb=" O PHE R 230 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS R 203 " --> pdb=" O ILE R 53 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL R 55 " --> pdb=" O HIS R 203 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU R 205 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLY R 57 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLY R 207 " --> pdb=" O GLY R 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL R 92 " --> pdb=" O VAL R 167 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 225 through 230 removed outlier: 6.879A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE S 230 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR S 56 " --> pdb=" O PHE S 230 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS S 203 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL S 55 " --> pdb=" O HIS S 203 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU S 205 " --> pdb=" O VAL S 55 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY S 57 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLY S 207 " --> pdb=" O GLY S 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'T' and resid 225 through 230 removed outlier: 6.792A pdb=" N PHE T 52 " --> pdb=" O VAL T 226 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS T 203 " --> pdb=" O ILE T 53 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL T 55 " --> pdb=" O HIS T 203 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU T 205 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY T 57 " --> pdb=" O LEU T 205 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'U' and resid 225 through 230 removed outlier: 6.810A pdb=" N PHE U 52 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE U 228 " --> pdb=" O PHE U 52 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE U 54 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE U 230 " --> pdb=" O PHE U 54 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR U 56 " --> pdb=" O PHE U 230 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS U 203 " --> pdb=" O ILE U 53 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL U 55 " --> pdb=" O HIS U 203 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU U 205 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY U 57 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE U 168 " --> pdb=" O CYS U 204 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU U 206 " --> pdb=" O PHE U 168 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL U 170 " --> pdb=" O LEU U 206 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'V' and resid 225 through 230 removed outlier: 6.703A pdb=" N PHE V 52 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE V 228 " --> pdb=" O PHE V 52 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE V 54 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE V 230 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR V 56 " --> pdb=" O PHE V 230 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS V 203 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL V 55 " --> pdb=" O HIS V 203 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU V 205 " --> pdb=" O VAL V 55 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLY V 57 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLY V 207 " --> pdb=" O GLY V 57 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE V 168 " --> pdb=" O CYS V 204 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU V 206 " --> pdb=" O PHE V 168 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL V 170 " --> pdb=" O LEU V 206 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL V 92 " --> pdb=" O PHE V 169 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASP V 171 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE V 94 " --> pdb=" O ASP V 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 625 hydrogen bonds defined for protein. 1620 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: 3.65 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4581 1.34 - 1.46: 1901 1.46 - 1.57: 7663 1.57 - 1.69: 25 1.69 - 1.81: 55 Bond restraints: 14225 Sorted by residual: bond pdb=" N SER V 59 " pdb=" CA SER V 59 " ideal model delta sigma weight residual 1.463 1.437 0.027 1.29e-02 6.01e+03 4.23e+00 bond pdb=" CA SER V 59 " pdb=" C SER V 59 " ideal model delta sigma weight residual 1.530 1.514 0.015 1.10e-02 8.26e+03 1.94e+00 bond pdb=" CA ASP V 127 " pdb=" CB ASP V 127 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.61e-02 3.86e+03 1.93e+00 bond pdb=" CA LEU U 82 " pdb=" C LEU U 82 " ideal model delta sigma weight residual 1.524 1.508 0.017 1.28e-02 6.10e+03 1.75e+00 bond pdb=" CG ASP V 187 " pdb=" OD1 ASP V 187 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.73e+00 ... (remaining 14220 not shown) Histogram of bond angle deviations from ideal: 98.87 - 107.05: 389 107.05 - 115.24: 8603 115.24 - 123.42: 9873 123.42 - 131.60: 390 131.60 - 139.78: 30 Bond angle restraints: 19285 Sorted by residual: angle pdb=" N THR V 299 " pdb=" CA THR V 299 " pdb=" C THR V 299 " ideal model delta sigma weight residual 108.38 115.75 -7.37 1.35e+00 5.49e-01 2.98e+01 angle pdb=" N THR U 299 " pdb=" CA THR U 299 " pdb=" C THR U 299 " ideal model delta sigma weight residual 108.74 115.57 -6.83 1.38e+00 5.25e-01 2.45e+01 angle pdb=" C VAL S 61 " pdb=" N GLY S 62 " pdb=" CA GLY S 62 " ideal model delta sigma weight residual 122.26 116.29 5.97 1.34e+00 5.57e-01 1.99e+01 angle pdb=" N SER U 59 " pdb=" CA SER U 59 " pdb=" C SER U 59 " ideal model delta sigma weight residual 109.24 102.68 6.56 1.63e+00 3.76e-01 1.62e+01 angle pdb=" N VAL U 61 " pdb=" CA VAL U 61 " pdb=" C VAL U 61 " ideal model delta sigma weight residual 109.34 117.63 -8.29 2.08e+00 2.31e-01 1.59e+01 ... (remaining 19280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7282 17.65 - 35.30: 1026 35.30 - 52.95: 297 52.95 - 70.60: 59 70.60 - 88.25: 11 Dihedral angle restraints: 8675 sinusoidal: 3660 harmonic: 5015 Sorted by residual: dihedral pdb=" CA ASP V 187 " pdb=" C ASP V 187 " pdb=" N GLN V 188 " pdb=" CA GLN V 188 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASP U 127 " pdb=" C ASP U 127 " pdb=" N TYR U 128 " pdb=" CA TYR U 128 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA LEU V 121 " pdb=" C LEU V 121 " pdb=" N ILE V 122 " pdb=" CA ILE V 122 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 8672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1496 0.033 - 0.067: 454 0.067 - 0.100: 132 0.100 - 0.134: 71 0.134 - 0.167: 7 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ASP V 127 " pdb=" N ASP V 127 " pdb=" C ASP V 127 " pdb=" CB ASP V 127 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ASP T 127 " pdb=" N ASP T 127 " pdb=" C ASP T 127 " pdb=" CB ASP T 127 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE S 94 " pdb=" N ILE S 94 " pdb=" C ILE S 94 " pdb=" CB ILE S 94 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 2157 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE V 126 " -0.013 2.00e-02 2.50e+03 2.13e-02 7.93e+00 pdb=" CG PHE V 126 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE V 126 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE V 126 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE V 126 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE V 126 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE V 126 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 297 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C ALA U 297 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA U 297 " -0.015 2.00e-02 2.50e+03 pdb=" N THR U 298 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU S 79 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO S 80 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO S 80 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 80 " 0.031 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 154 2.57 - 3.15: 11916 3.15 - 3.73: 23014 3.73 - 4.32: 30619 4.32 - 4.90: 50565 Nonbonded interactions: 116268 Sorted by model distance: nonbonded pdb=" O3A ATP V 600 " pdb="MG MG V 601 " model vdw 1.984 2.170 nonbonded pdb=" O3B ATP T 600 " pdb="MG MG T 601 " model vdw 1.995 2.170 nonbonded pdb=" O3B ATP U 600 " pdb="MG MG U 601 " model vdw 2.000 2.170 nonbonded pdb=" O3B ATP S 600 " pdb="MG MG S 601 " model vdw 2.005 2.170 nonbonded pdb=" O3A ATP U 600 " pdb="MG MG U 601 " model vdw 2.026 2.170 ... (remaining 116263 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 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.250 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 38.640 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.003 0.037 14225 Z= 0.176 Angle : 0.599 8.446 19285 Z= 0.328 Chirality : 0.040 0.167 2160 Planarity : 0.004 0.054 2455 Dihedral : 17.789 88.249 5435 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.70 % Allowed : 3.93 % Favored : 95.37 % Rotamer: Outliers : 0.61 % Allowed : 27.03 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1705 helix: 0.97 (0.17), residues: 1040 sheet: -0.54 (0.48), residues: 140 loop : -0.94 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 267 HIS 0.006 0.001 HIS S 124 PHE 0.047 0.001 PHE V 126 TYR 0.014 0.001 TYR T 128 ARG 0.011 0.000 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 254 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 156 LEU cc_start: 0.9236 (tp) cc_final: 0.8871 (tp) REVERT: R 190 ASP cc_start: 0.8941 (m-30) cc_final: 0.8691 (m-30) REVERT: S 56 TYR cc_start: 0.8152 (m-80) cc_final: 0.7225 (m-10) REVERT: S 318 MET cc_start: 0.8866 (mtm) cc_final: 0.8345 (mtt) REVERT: S 333 GLU cc_start: 0.8828 (tp30) cc_final: 0.8559 (tm-30) REVERT: T 244 PHE cc_start: 0.9532 (t80) cc_final: 0.9245 (t80) REVERT: T 277 CYS cc_start: 0.8974 (m) cc_final: 0.8420 (m) REVERT: T 333 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8698 (tp30) REVERT: U 172 GLU cc_start: 0.9175 (pt0) cc_final: 0.8756 (pm20) REVERT: U 210 GLU cc_start: 0.9000 (tt0) cc_final: 0.8783 (tt0) REVERT: V 30 HIS cc_start: 0.7327 (p90) cc_final: 0.6806 (p-80) REVERT: V 190 ASP cc_start: 0.9234 (m-30) cc_final: 0.8841 (m-30) REVERT: V 277 CYS cc_start: 0.8892 (m) cc_final: 0.8378 (m) REVERT: V 278 ILE cc_start: 0.8329 (mm) cc_final: 0.8010 (tt) REVERT: V 281 LEU cc_start: 0.8850 (tp) cc_final: 0.8625 (tt) REVERT: V 315 CYS cc_start: 0.7785 (t) cc_final: 0.7281 (p) outliers start: 9 outliers final: 4 residues processed: 261 average time/residue: 0.2716 time to fit residues: 101.2312 Evaluate side-chains 143 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain V residue 59 SER Chi-restraints excluded: chain V residue 301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 252 GLN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 242 GLN U 328 GLN V 158 ASN V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14225 Z= 0.221 Angle : 0.574 7.913 19285 Z= 0.296 Chirality : 0.040 0.165 2160 Planarity : 0.004 0.042 2455 Dihedral : 9.969 80.774 2081 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.81 % Favored : 95.84 % Rotamer: Outliers : 2.30 % Allowed : 25.81 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1705 helix: 1.07 (0.17), residues: 1060 sheet: -0.43 (0.48), residues: 140 loop : -1.00 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 267 HIS 0.005 0.001 HIS V 30 PHE 0.015 0.001 PHE U 126 TYR 0.017 0.001 TYR T 103 ARG 0.004 0.000 ARG S 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 277 CYS cc_start: 0.8517 (m) cc_final: 0.8113 (m) REVERT: S 318 MET cc_start: 0.9001 (mtm) cc_final: 0.8734 (mtt) REVERT: S 333 GLU cc_start: 0.8787 (tp30) cc_final: 0.8559 (tm-30) REVERT: T 41 MET cc_start: 0.9178 (mmm) cc_final: 0.8969 (mmt) REVERT: U 164 HIS cc_start: 0.9069 (t-90) cc_final: 0.8823 (t-90) REVERT: U 172 GLU cc_start: 0.9188 (pt0) cc_final: 0.8869 (pm20) REVERT: U 252 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: U 318 MET cc_start: 0.9384 (mtp) cc_final: 0.9148 (mtm) REVERT: V 30 HIS cc_start: 0.8071 (p90) cc_final: 0.7618 (p-80) REVERT: V 190 ASP cc_start: 0.9177 (m-30) cc_final: 0.8842 (m-30) REVERT: V 278 ILE cc_start: 0.8426 (mm) cc_final: 0.8142 (tt) REVERT: V 318 MET cc_start: 0.8713 (mtm) cc_final: 0.8325 (mtm) outliers start: 34 outliers final: 13 residues processed: 168 average time/residue: 0.2405 time to fit residues: 60.8657 Evaluate side-chains 121 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 236 ASP Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 137 ASN Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 284 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 128 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 175 HIS ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN U 158 ASN V 242 GLN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14225 Z= 0.297 Angle : 0.586 7.890 19285 Z= 0.306 Chirality : 0.041 0.161 2160 Planarity : 0.004 0.041 2455 Dihedral : 9.135 83.713 2076 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.28 % Favored : 95.37 % Rotamer: Outliers : 3.78 % Allowed : 25.47 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1705 helix: 1.01 (0.17), residues: 1055 sheet: -0.50 (0.46), residues: 140 loop : -0.99 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 267 HIS 0.004 0.001 HIS T 30 PHE 0.023 0.002 PHE U 126 TYR 0.021 0.002 TYR T 183 ARG 0.004 0.000 ARG U 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 122 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8868 (mp) REVERT: R 277 CYS cc_start: 0.8876 (m) cc_final: 0.8489 (m) REVERT: S 223 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7749 (ttp80) REVERT: S 318 MET cc_start: 0.9000 (mtm) cc_final: 0.8721 (mtt) REVERT: T 82 LEU cc_start: 0.9000 (tp) cc_final: 0.8698 (mt) REVERT: U 164 HIS cc_start: 0.9116 (t-90) cc_final: 0.8761 (t-90) REVERT: U 172 GLU cc_start: 0.9270 (pt0) cc_final: 0.8924 (pm20) REVERT: V 190 ASP cc_start: 0.9180 (m-30) cc_final: 0.8790 (m-30) outliers start: 56 outliers final: 30 residues processed: 169 average time/residue: 0.2218 time to fit residues: 58.0937 Evaluate side-chains 132 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 223 ARG Chi-restraints excluded: chain S residue 236 ASP Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 277 CYS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 138 PHE Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 266 HIS Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 137 ASN Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 124 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 284 TRP Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 337 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 0.0370 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 HIS ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS V 220 GLN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14225 Z= 0.160 Angle : 0.537 8.376 19285 Z= 0.272 Chirality : 0.039 0.176 2160 Planarity : 0.004 0.038 2455 Dihedral : 8.459 86.080 2075 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.81 % Favored : 95.84 % Rotamer: Outliers : 2.77 % Allowed : 26.62 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1705 helix: 1.30 (0.17), residues: 1050 sheet: -0.41 (0.46), residues: 140 loop : -0.92 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 267 HIS 0.008 0.001 HIS V 175 PHE 0.013 0.001 PHE U 214 TYR 0.019 0.001 TYR R 109 ARG 0.004 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9235 (tt) cc_final: 0.8889 (mp) REVERT: R 277 CYS cc_start: 0.8589 (m) cc_final: 0.8155 (m) REVERT: R 283 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8228 (t0) REVERT: S 114 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9567 (mm) REVERT: S 224 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8719 (ptp-170) REVERT: T 82 LEU cc_start: 0.8996 (tp) cc_final: 0.8691 (mt) REVERT: T 95 GLU cc_start: 0.8394 (pm20) cc_final: 0.7638 (pm20) REVERT: U 95 GLU cc_start: 0.8863 (pm20) cc_final: 0.8616 (pm20) REVERT: U 164 HIS cc_start: 0.9143 (t-90) cc_final: 0.8818 (t-90) REVERT: U 172 GLU cc_start: 0.9244 (pt0) cc_final: 0.8912 (pm20) REVERT: U 252 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8702 (tt0) REVERT: U 318 MET cc_start: 0.9501 (mtp) cc_final: 0.9166 (mtm) REVERT: V 30 HIS cc_start: 0.8384 (p90) cc_final: 0.8018 (p90) REVERT: V 190 ASP cc_start: 0.9099 (m-30) cc_final: 0.8704 (m-30) REVERT: V 220 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8357 (tp-100) REVERT: V 266 HIS cc_start: 0.9059 (OUTLIER) cc_final: 0.8772 (m90) outliers start: 41 outliers final: 19 residues processed: 151 average time/residue: 0.2225 time to fit residues: 51.8361 Evaluate side-chains 121 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 224 ARG Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 220 GLN Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 266 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 0.0370 chunk 113 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 164 HIS T 337 GLN V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14225 Z= 0.153 Angle : 0.516 7.909 19285 Z= 0.262 Chirality : 0.039 0.190 2160 Planarity : 0.004 0.038 2455 Dihedral : 8.316 84.527 2075 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.99 % Favored : 95.66 % Rotamer: Outliers : 2.23 % Allowed : 26.69 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1705 helix: 1.39 (0.17), residues: 1045 sheet: -0.31 (0.46), residues: 140 loop : -0.92 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 267 HIS 0.009 0.001 HIS T 164 PHE 0.025 0.001 PHE T 138 TYR 0.021 0.001 TYR S 109 ARG 0.002 0.000 ARG T 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9040 (mp) REVERT: R 277 CYS cc_start: 0.8616 (m) cc_final: 0.8189 (m) REVERT: R 283 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8212 (t0) REVERT: S 224 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8743 (ptp-170) REVERT: S 283 ASP cc_start: 0.9044 (m-30) cc_final: 0.8730 (t0) REVERT: T 41 MET cc_start: 0.9343 (mmm) cc_final: 0.9098 (mmt) REVERT: T 82 LEU cc_start: 0.8983 (tp) cc_final: 0.8674 (mt) REVERT: T 95 GLU cc_start: 0.8415 (pm20) cc_final: 0.7900 (pm20) REVERT: U 95 GLU cc_start: 0.8821 (pm20) cc_final: 0.8617 (pm20) REVERT: U 164 HIS cc_start: 0.9166 (t-90) cc_final: 0.8819 (t-90) REVERT: U 172 GLU cc_start: 0.9244 (pt0) cc_final: 0.8917 (pm20) REVERT: U 198 MET cc_start: 0.8389 (ptp) cc_final: 0.8046 (ptp) REVERT: U 252 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8706 (tt0) REVERT: U 318 MET cc_start: 0.9561 (mtp) cc_final: 0.9275 (mtm) REVERT: V 190 ASP cc_start: 0.9088 (m-30) cc_final: 0.8691 (m-30) outliers start: 33 outliers final: 20 residues processed: 131 average time/residue: 0.2152 time to fit residues: 44.8776 Evaluate side-chains 125 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 224 ARG Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 328 GLN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14225 Z= 0.282 Angle : 0.558 7.517 19285 Z= 0.290 Chirality : 0.040 0.160 2160 Planarity : 0.004 0.064 2455 Dihedral : 8.779 80.139 2075 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.81 % Favored : 94.84 % Rotamer: Outliers : 2.91 % Allowed : 26.55 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1705 helix: 1.33 (0.17), residues: 1045 sheet: -0.35 (0.47), residues: 140 loop : -0.89 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 267 HIS 0.005 0.001 HIS V 164 PHE 0.020 0.002 PHE U 126 TYR 0.016 0.001 TYR V 128 ARG 0.004 0.000 ARG V 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 96 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9050 (mp) REVERT: R 277 CYS cc_start: 0.8916 (m) cc_final: 0.8509 (m) REVERT: R 283 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8181 (t0) REVERT: S 283 ASP cc_start: 0.9105 (m-30) cc_final: 0.8822 (t0) REVERT: T 41 MET cc_start: 0.9366 (mmm) cc_final: 0.9108 (mmt) REVERT: T 82 LEU cc_start: 0.8974 (tp) cc_final: 0.8680 (mt) REVERT: T 95 GLU cc_start: 0.8566 (pm20) cc_final: 0.8146 (pm20) REVERT: U 95 GLU cc_start: 0.8902 (pm20) cc_final: 0.8691 (pm20) REVERT: U 164 HIS cc_start: 0.9197 (t-90) cc_final: 0.8890 (t-90) REVERT: U 172 GLU cc_start: 0.9287 (pt0) cc_final: 0.8970 (pm20) REVERT: V 190 ASP cc_start: 0.9180 (m-30) cc_final: 0.8749 (m-30) REVERT: V 281 LEU cc_start: 0.9243 (mt) cc_final: 0.8563 (tt) outliers start: 43 outliers final: 21 residues processed: 132 average time/residue: 0.2217 time to fit residues: 46.5746 Evaluate side-chains 113 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 185 LEU Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 236 ASP Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 277 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.0050 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 0.0000 chunk 120 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14225 Z= 0.145 Angle : 0.521 9.422 19285 Z= 0.264 Chirality : 0.039 0.169 2160 Planarity : 0.004 0.037 2455 Dihedral : 8.256 87.396 2075 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.75 % Favored : 95.89 % Rotamer: Outliers : 1.76 % Allowed : 27.50 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1705 helix: 1.47 (0.17), residues: 1045 sheet: -0.36 (0.48), residues: 135 loop : -0.87 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP V 284 HIS 0.007 0.001 HIS V 30 PHE 0.014 0.001 PHE T 138 TYR 0.021 0.001 TYR T 183 ARG 0.003 0.000 ARG T 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 277 CYS cc_start: 0.8615 (m) cc_final: 0.8181 (m) REVERT: R 283 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8153 (t0) REVERT: S 283 ASP cc_start: 0.9049 (m-30) cc_final: 0.8704 (t0) REVERT: S 318 MET cc_start: 0.8812 (mmm) cc_final: 0.8501 (mmt) REVERT: T 82 LEU cc_start: 0.8975 (tp) cc_final: 0.8675 (mt) REVERT: T 95 GLU cc_start: 0.8564 (pm20) cc_final: 0.7887 (pm20) REVERT: T 333 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: U 164 HIS cc_start: 0.9194 (t-90) cc_final: 0.8872 (t-90) REVERT: U 172 GLU cc_start: 0.9236 (pt0) cc_final: 0.8900 (pm20) REVERT: V 41 MET cc_start: 0.9289 (mmm) cc_final: 0.9059 (tpp) REVERT: V 190 ASP cc_start: 0.9055 (m-30) cc_final: 0.8670 (m-30) REVERT: V 251 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7968 (t80) outliers start: 26 outliers final: 19 residues processed: 133 average time/residue: 0.2367 time to fit residues: 49.2358 Evaluate side-chains 122 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 HIS Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 185 LEU Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 236 ASP Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 333 GLU Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 GLN V 164 HIS V 197 ASN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14225 Z= 0.221 Angle : 0.543 9.157 19285 Z= 0.278 Chirality : 0.039 0.191 2160 Planarity : 0.004 0.039 2455 Dihedral : 8.437 86.826 2075 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.34 % Favored : 95.31 % Rotamer: Outliers : 2.09 % Allowed : 27.57 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1705 helix: 1.49 (0.17), residues: 1025 sheet: -0.45 (0.48), residues: 135 loop : -0.68 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 284 HIS 0.006 0.001 HIS R 30 PHE 0.015 0.001 PHE U 126 TYR 0.014 0.001 TYR U 103 ARG 0.004 0.000 ARG S 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 236 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7290 (t0) REVERT: R 277 CYS cc_start: 0.8818 (m) cc_final: 0.8421 (m) REVERT: R 283 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8134 (t0) REVERT: S 283 ASP cc_start: 0.9116 (m-30) cc_final: 0.8828 (t0) REVERT: T 82 LEU cc_start: 0.8966 (tp) cc_final: 0.8646 (mm) REVERT: T 95 GLU cc_start: 0.8695 (pm20) cc_final: 0.8174 (pm20) REVERT: T 333 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8497 (tm-30) REVERT: U 19 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8514 (mtt90) REVERT: U 164 HIS cc_start: 0.9218 (t-90) cc_final: 0.8907 (t-90) REVERT: U 172 GLU cc_start: 0.9262 (pt0) cc_final: 0.8948 (pm20) REVERT: V 190 ASP cc_start: 0.9099 (m-30) cc_final: 0.8720 (m-30) REVERT: V 251 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8123 (t80) outliers start: 31 outliers final: 19 residues processed: 124 average time/residue: 0.2403 time to fit residues: 48.4288 Evaluate side-chains 118 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 236 ASP Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 236 ASP Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 333 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 278 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14225 Z= 0.272 Angle : 0.564 8.896 19285 Z= 0.291 Chirality : 0.040 0.191 2160 Planarity : 0.004 0.036 2455 Dihedral : 8.567 89.663 2075 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.63 % Favored : 95.01 % Rotamer: Outliers : 2.16 % Allowed : 27.57 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1705 helix: 1.41 (0.17), residues: 1025 sheet: -0.41 (0.49), residues: 135 loop : -0.67 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 267 HIS 0.010 0.001 HIS V 164 PHE 0.020 0.002 PHE U 126 TYR 0.031 0.002 TYR R 109 ARG 0.002 0.000 ARG R 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 236 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7304 (t0) REVERT: R 277 CYS cc_start: 0.8892 (m) cc_final: 0.8503 (m) REVERT: R 283 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8140 (t0) REVERT: S 283 ASP cc_start: 0.9099 (m-30) cc_final: 0.8821 (t0) REVERT: T 82 LEU cc_start: 0.8952 (tp) cc_final: 0.8680 (mt) REVERT: T 95 GLU cc_start: 0.8804 (pm20) cc_final: 0.8470 (pm20) REVERT: T 333 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8495 (tm-30) REVERT: U 19 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8534 (mtt90) REVERT: U 164 HIS cc_start: 0.9212 (t-90) cc_final: 0.8803 (t-90) REVERT: U 172 GLU cc_start: 0.9270 (pt0) cc_final: 0.8956 (pm20) REVERT: V 190 ASP cc_start: 0.9150 (m-30) cc_final: 0.8741 (m-30) REVERT: V 251 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8049 (t80) outliers start: 32 outliers final: 20 residues processed: 129 average time/residue: 0.2425 time to fit residues: 48.5177 Evaluate side-chains 121 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 236 ASP Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 236 ASP Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 333 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 278 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 112 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14225 Z= 0.197 Angle : 0.548 8.584 19285 Z= 0.280 Chirality : 0.040 0.179 2160 Planarity : 0.004 0.039 2455 Dihedral : 8.401 88.398 2075 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.52 % Favored : 95.13 % Rotamer: Outliers : 1.62 % Allowed : 28.18 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1705 helix: 1.41 (0.17), residues: 1035 sheet: -0.59 (0.42), residues: 185 loop : -0.53 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 267 HIS 0.006 0.001 HIS R 30 PHE 0.015 0.001 PHE U 126 TYR 0.029 0.001 TYR R 109 ARG 0.002 0.000 ARG V 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 236 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7308 (t0) REVERT: R 277 CYS cc_start: 0.8751 (m) cc_final: 0.8361 (m) REVERT: R 283 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8124 (t0) REVERT: T 82 LEU cc_start: 0.8950 (tp) cc_final: 0.8674 (mt) REVERT: T 333 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: U 19 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8563 (mtt90) REVERT: U 164 HIS cc_start: 0.9206 (t-90) cc_final: 0.8893 (t-90) REVERT: U 172 GLU cc_start: 0.9265 (pt0) cc_final: 0.8940 (pm20) REVERT: V 190 ASP cc_start: 0.9125 (m-30) cc_final: 0.8733 (m-30) REVERT: V 251 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8016 (t80) outliers start: 24 outliers final: 18 residues processed: 117 average time/residue: 0.2187 time to fit residues: 41.0024 Evaluate side-chains 118 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 236 ASP Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 236 ASP Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 333 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0770 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 56 optimal weight: 0.0040 chunk 138 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN V 220 GLN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.063719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.047423 restraints weight = 64351.788| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 5.51 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14225 Z= 0.142 Angle : 0.536 8.712 19285 Z= 0.270 Chirality : 0.039 0.178 2160 Planarity : 0.004 0.044 2455 Dihedral : 8.008 89.130 2075 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.93 % Favored : 95.72 % Rotamer: Outliers : 1.35 % Allowed : 28.11 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1705 helix: 1.65 (0.18), residues: 1005 sheet: -0.27 (0.49), residues: 135 loop : -0.19 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 267 HIS 0.006 0.001 HIS V 30 PHE 0.011 0.001 PHE U 138 TYR 0.029 0.001 TYR R 109 ARG 0.003 0.000 ARG R 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2652.10 seconds wall clock time: 49 minutes 11.15 seconds (2951.15 seconds total)