Starting phenix.real_space_refine on Sat Mar 16 16:53:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcw_28997/03_2024/8fcw_28997_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcw_28997/03_2024/8fcw_28997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcw_28997/03_2024/8fcw_28997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcw_28997/03_2024/8fcw_28997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcw_28997/03_2024/8fcw_28997_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcw_28997/03_2024/8fcw_28997_updated.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 75 5.49 5 Mg 5 5.21 5 S 40 5.16 5 C 9420 2.51 5 N 2665 2.21 5 O 2965 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 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 294": "OD1" <-> "OD2" Residue "V GLU 296": "OE1" <-> "OE2" Residue "V GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15170 Number of models: 1 Model: "" Number of chains: 12 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: "N" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "O" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} 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: 8.29, per 1000 atoms: 0.55 Number of scatterers: 15170 At special positions: 0 Unit cell: (112.778, 124.372, 153.884, 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 75 15.00 Mg 5 11.99 O 2965 8.00 N 2665 7.00 C 9420 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: 6.82 Conformation dependent library (CDL) restraints added in 2.4 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 54.7% alpha, 6.5% beta 30 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 6.46 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: 3.625A 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: 3.798A pdb=" N LEU R 185 " --> pdb=" O GLY R 182 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET R 198 " --> pdb=" O LEU R 195 " (cutoff:3.500A) removed outlier: 3.523A 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: 4.648A pdb=" N GLU R 268 " --> pdb=" O ASP R 265 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR R 274 " --> pdb=" O TYR R 271 " (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: 3.822A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 342 removed outlier: 3.690A pdb=" N ASN R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 13 removed outlier: 3.710A 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: 3.928A pdb=" N LEU S 185 " --> pdb=" O GLY S 182 " (cutoff:3.500A) removed outlier: 3.994A 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 272 removed outlier: 4.643A pdb=" N GLU S 268 " --> pdb=" O ASP S 265 " (cutoff:3.500A) Processing helix chain 'S' and resid 278 through 294 Processing helix chain 'S' and resid 302 through 308 removed outlier: 3.590A 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: 3.547A 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: 4.104A pdb=" N SER T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 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: 4.055A pdb=" N GLN T 186 " --> pdb=" O GLY T 182 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 214 Processing helix chain 'T' and resid 219 through 223 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 82 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 182 through 199 removed outlier: 4.212A pdb=" N MET U 198 " --> pdb=" O LEU U 195 " (cutoff:3.500A) removed outlier: 4.136A 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 267 through 274 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: 4.041A 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 264 through 274 removed outlier: 3.538A pdb=" N TRP V 267 " --> pdb=" O VAL V 264 " (cutoff:3.500A) removed outlier: 4.698A 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: 3.658A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 328 removed outlier: 3.821A pdb=" N LYS V 317 " --> pdb=" O ALA V 313 " (cutoff:3.500A) removed outlier: 3.544A 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: 6.279A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE R 230 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR R 56 " --> pdb=" O PHE R 230 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS R 203 " --> pdb=" O ILE R 53 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL R 55 " --> pdb=" O HIS R 203 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU R 205 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY R 57 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY R 207 " --> pdb=" O GLY R 57 " (cutoff:3.500A) removed outlier: 3.582A 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: 6.869A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE S 230 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR S 56 " --> pdb=" O PHE S 230 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS S 203 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL S 55 " --> pdb=" O HIS S 203 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU S 205 " --> pdb=" O VAL S 55 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY S 57 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 5.866A 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: 6.738A pdb=" N PHE T 52 " --> pdb=" O VAL T 226 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS T 203 " --> pdb=" O ILE T 53 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL T 55 " --> pdb=" O HIS T 203 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU T 205 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 7.720A 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: 6.759A pdb=" N PHE U 52 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE U 228 " --> pdb=" O PHE U 52 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE U 54 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE U 230 " --> pdb=" O PHE U 54 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR U 56 " --> pdb=" O PHE U 230 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N HIS U 203 " --> pdb=" O ILE U 53 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL U 55 " --> pdb=" O HIS U 203 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU U 205 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLY U 57 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL U 92 " --> pdb=" O VAL U 167 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'V' and resid 225 through 230 removed outlier: 6.662A pdb=" N PHE V 52 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE V 228 " --> pdb=" O PHE V 52 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE V 54 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE V 230 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR V 56 " --> pdb=" O PHE V 230 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS V 203 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL V 55 " --> pdb=" O HIS V 203 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU V 205 " --> pdb=" O VAL V 55 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLY V 57 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY V 207 " --> pdb=" O GLY V 57 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL V 92 " --> pdb=" O PHE V 169 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASP V 171 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE V 94 " --> pdb=" O ASP V 171 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 4.72 Time building geometry restraints manager: 7.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2365 1.31 - 1.43: 4382 1.43 - 1.56: 8655 1.56 - 1.69: 146 1.69 - 1.81: 55 Bond restraints: 15603 Sorted by residual: bond pdb=" O2B ATP U 600 " pdb=" PB ATP U 600 " ideal model delta sigma weight residual 1.529 1.284 0.245 2.20e-02 2.07e+03 1.24e+02 bond pdb=" O2B ATP S 600 " pdb=" PB ATP S 600 " ideal model delta sigma weight residual 1.529 1.337 0.192 2.20e-02 2.07e+03 7.61e+01 bond pdb=" O2B ATP T 600 " pdb=" PB ATP T 600 " ideal model delta sigma weight residual 1.529 1.378 0.151 2.20e-02 2.07e+03 4.71e+01 bond pdb=" C4 ATP R 600 " pdb=" C5 ATP R 600 " ideal model delta sigma weight residual 1.388 1.447 -0.059 1.00e-02 1.00e+04 3.50e+01 bond pdb=" C4 ATP S 600 " pdb=" N9 ATP S 600 " ideal model delta sigma weight residual 1.374 1.316 0.058 1.00e-02 1.00e+04 3.31e+01 ... (remaining 15598 not shown) Histogram of bond angle deviations from ideal: 98.96 - 106.98: 790 106.98 - 114.99: 9233 114.99 - 123.01: 10291 123.01 - 131.03: 999 131.03 - 139.04: 94 Bond angle restraints: 21407 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 108.38 116.17 -7.79 1.35e+00 5.49e-01 3.33e+01 angle pdb=" PA ATP V 600 " pdb=" O3A ATP V 600 " pdb=" PB ATP V 600 " ideal model delta sigma weight residual 136.83 131.73 5.10 1.00e+00 1.00e+00 2.60e+01 angle pdb=" N GLU U 100 " pdb=" CA GLU U 100 " pdb=" C GLU U 100 " ideal model delta sigma weight residual 112.87 107.07 5.80 1.20e+00 6.94e-01 2.33e+01 angle pdb=" PA ATP T 600 " pdb=" O3A ATP T 600 " pdb=" PB ATP T 600 " ideal model delta sigma weight residual 136.83 132.07 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" N THR U 299 " pdb=" CA THR U 299 " pdb=" C THR U 299 " ideal model delta sigma weight residual 108.74 115.19 -6.45 1.38e+00 5.25e-01 2.19e+01 ... (remaining 21402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7450 17.72 - 35.44: 1187 35.44 - 53.16: 551 53.16 - 70.88: 127 70.88 - 88.60: 14 Dihedral angle restraints: 9329 sinusoidal: 4314 harmonic: 5015 Sorted by residual: dihedral pdb=" CA PHE U 214 " pdb=" C PHE U 214 " pdb=" N ARG U 215 " pdb=" CA ARG U 215 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PHE T 214 " pdb=" C PHE T 214 " pdb=" N ARG T 215 " pdb=" CA ARG T 215 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE S 214 " pdb=" C PHE S 214 " pdb=" N ARG S 215 " pdb=" CA ARG S 215 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1773 0.063 - 0.125: 559 0.125 - 0.188: 61 0.188 - 0.250: 5 0.250 - 0.313: 2 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CB VAL V 167 " pdb=" CA VAL V 167 " pdb=" CG1 VAL V 167 " pdb=" CG2 VAL V 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL V 336 " pdb=" CA VAL V 336 " pdb=" CG1 VAL V 336 " pdb=" CG2 VAL V 336 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU V 248 " pdb=" CB LEU V 248 " pdb=" CD1 LEU V 248 " pdb=" CD2 LEU V 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2397 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE V 319 " -0.023 2.00e-02 2.50e+03 2.01e-02 7.06e+00 pdb=" CG PHE V 319 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE V 319 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE V 319 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE V 319 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE V 319 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE V 319 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 142 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ASN R 142 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN R 142 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 143 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 126 " 0.006 2.00e-02 2.50e+03 1.60e-02 4.48e+00 pdb=" CG PHE V 126 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE V 126 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE V 126 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE V 126 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE V 126 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE V 126 " -0.002 2.00e-02 2.50e+03 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 165 2.57 - 3.15: 13092 3.15 - 3.74: 25637 3.74 - 4.32: 35154 4.32 - 4.90: 54938 Nonbonded interactions: 128986 Sorted by model distance: nonbonded pdb=" O3B ATP T 600 " pdb="MG MG T 601 " model vdw 1.989 2.170 nonbonded pdb=" O1G ATP V 600 " pdb="MG MG V 601 " model vdw 2.005 2.170 nonbonded pdb=" O3B ATP S 600 " pdb="MG MG S 601 " model vdw 2.007 2.170 nonbonded pdb=" O3B ATP U 600 " pdb="MG MG U 601 " model vdw 2.008 2.170 nonbonded pdb=" O3A ATP V 600 " pdb="MG MG V 601 " model vdw 2.042 2.170 ... (remaining 128981 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: 0.690 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: 4.310 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 45.310 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.010 0.245 15603 Z= 0.629 Angle : 0.903 10.196 21407 Z= 0.553 Chirality : 0.058 0.313 2400 Planarity : 0.005 0.048 2515 Dihedral : 20.726 88.596 6089 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.64 % Favored : 95.95 % Rotamer: Outliers : 2.09 % Allowed : 25.61 % Favored : 72.30 % 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: -0.40 (0.20), residues: 1705 helix: 0.35 (0.16), residues: 1055 sheet: -0.59 (0.47), residues: 140 loop : -1.27 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP S 106 HIS 0.013 0.003 HIS T 203 PHE 0.036 0.005 PHE V 319 TYR 0.025 0.004 TYR S 128 ARG 0.016 0.001 ARG U 223 *********************** 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 288 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 257 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 LEU cc_start: 0.9763 (mt) cc_final: 0.9513 (pp) REVERT: R 277 CYS cc_start: 0.8642 (m) cc_final: 0.8369 (m) REVERT: R 318 MET cc_start: 0.8733 (mmt) cc_final: 0.8010 (mmt) REVERT: R 321 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8911 (pp20) REVERT: S 41 MET cc_start: 0.9449 (tpp) cc_final: 0.9244 (mmm) REVERT: S 71 GLU cc_start: 0.9354 (tt0) cc_final: 0.9149 (pp20) REVERT: S 103 TYR cc_start: 0.8392 (p90) cc_final: 0.8132 (OUTLIER) REVERT: S 138 PHE cc_start: 0.9244 (m-80) cc_final: 0.8921 (m-80) REVERT: S 190 ASP cc_start: 0.9364 (m-30) cc_final: 0.9096 (m-30) REVERT: S 216 ASN cc_start: 0.8105 (m-40) cc_final: 0.7875 (m-40) REVERT: S 234 CYS cc_start: 0.9308 (m) cc_final: 0.9009 (m) REVERT: S 318 MET cc_start: 0.9110 (mtm) cc_final: 0.8515 (mtp) REVERT: T 105 ASN cc_start: 0.9168 (t0) cc_final: 0.8898 (p0) REVERT: T 164 HIS cc_start: 0.9197 (t-170) cc_final: 0.8780 (t-90) REVERT: T 321 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8621 (OUTLIER) REVERT: U 108 GLU cc_start: 0.9114 (tp30) cc_final: 0.8843 (tp30) REVERT: U 126 PHE cc_start: 0.8281 (t80) cc_final: 0.7966 (t80) REVERT: U 321 GLU cc_start: 0.9363 (tp30) cc_final: 0.8902 (mt-10) REVERT: V 41 MET cc_start: 0.9340 (mmm) cc_final: 0.9051 (mmm) REVERT: V 121 LEU cc_start: 0.9324 (tt) cc_final: 0.9010 (tm) REVERT: V 158 ASN cc_start: 0.9657 (m-40) cc_final: 0.9419 (m110) outliers start: 31 outliers final: 8 residues processed: 276 average time/residue: 1.1434 time to fit residues: 350.2868 Evaluate side-chains 130 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain U 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: 176 random chunks: chunk 148 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 102 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 GLN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 252 GLN T 25 ASN T 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15603 Z= 0.180 Angle : 0.606 10.474 21407 Z= 0.309 Chirality : 0.039 0.179 2400 Planarity : 0.004 0.045 2515 Dihedral : 19.255 82.333 2740 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.93 % Favored : 96.72 % Rotamer: Outliers : 3.24 % Allowed : 27.30 % Favored : 69.46 % 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: 0.18 (0.21), residues: 1705 helix: 0.93 (0.16), residues: 1065 sheet: -0.55 (0.46), residues: 140 loop : -1.35 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.021 0.001 PHE U 138 TYR 0.018 0.001 TYR U 103 ARG 0.010 0.000 ARG U 102 *********************** 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 203 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 155 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: R 195 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8274 (mm) REVERT: R 248 LEU cc_start: 0.9777 (mt) cc_final: 0.9506 (pp) REVERT: R 277 CYS cc_start: 0.8643 (m) cc_final: 0.8375 (m) REVERT: R 318 MET cc_start: 0.8543 (mmt) cc_final: 0.7740 (mmt) REVERT: R 321 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8808 (pp20) REVERT: S 71 GLU cc_start: 0.9350 (tt0) cc_final: 0.9121 (tm-30) REVERT: S 103 TYR cc_start: 0.8305 (p90) cc_final: 0.7905 (OUTLIER) REVERT: S 138 PHE cc_start: 0.9212 (m-80) cc_final: 0.8935 (m-80) REVERT: S 146 LYS cc_start: 0.8727 (pttp) cc_final: 0.8363 (pptt) REVERT: S 190 ASP cc_start: 0.9409 (m-30) cc_final: 0.9169 (m-30) REVERT: S 234 CYS cc_start: 0.9332 (m) cc_final: 0.9067 (m) REVERT: S 318 MET cc_start: 0.9058 (mtm) cc_final: 0.8670 (mtp) REVERT: S 328 GLN cc_start: 0.9221 (mt0) cc_final: 0.9001 (mt0) REVERT: S 337 GLN cc_start: 0.9409 (mm-40) cc_final: 0.8659 (tm-30) REVERT: T 102 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7339 (pmm-80) REVERT: T 103 TYR cc_start: 0.8603 (p90) cc_final: 0.7880 (p90) REVERT: T 108 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8844 (mm-30) REVERT: T 146 LYS cc_start: 0.9388 (mtmm) cc_final: 0.9086 (mtmm) REVERT: T 164 HIS cc_start: 0.9266 (t-170) cc_final: 0.8854 (t-90) REVERT: T 190 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.9063 (m-30) REVERT: T 210 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: T 311 SER cc_start: 0.9274 (m) cc_final: 0.9019 (p) REVERT: U 41 MET cc_start: 0.9187 (tpp) cc_final: 0.8895 (mmm) REVERT: U 108 GLU cc_start: 0.9132 (tp30) cc_final: 0.8786 (tp30) REVERT: U 197 ASN cc_start: 0.8981 (m-40) cc_final: 0.8658 (m-40) REVERT: U 321 GLU cc_start: 0.9261 (tp30) cc_final: 0.8822 (mt-10) REVERT: V 51 SER cc_start: 0.9053 (m) cc_final: 0.8798 (p) REVERT: V 121 LEU cc_start: 0.9248 (tt) cc_final: 0.9031 (tm) REVERT: V 158 ASN cc_start: 0.9634 (m-40) cc_final: 0.9384 (m110) REVERT: V 210 GLU cc_start: 0.8960 (mp0) cc_final: 0.8734 (mp0) REVERT: V 321 GLU cc_start: 0.9152 (mp0) cc_final: 0.8872 (mm-30) outliers start: 48 outliers final: 13 residues processed: 194 average time/residue: 1.0105 time to fit residues: 221.1594 Evaluate side-chains 141 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 190 ASP Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 145 SER Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 ASN S 216 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15603 Z= 0.266 Angle : 0.601 11.638 21407 Z= 0.310 Chirality : 0.040 0.146 2400 Planarity : 0.004 0.047 2515 Dihedral : 18.745 84.937 2734 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.11 % Favored : 96.54 % Rotamer: Outliers : 3.51 % Allowed : 26.49 % Favored : 70.00 % 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: 0.50 (0.22), residues: 1705 helix: 1.15 (0.17), residues: 1065 sheet: -0.45 (0.45), residues: 140 loop : -1.14 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.024 0.002 PHE V 126 TYR 0.013 0.001 TYR T 128 ARG 0.010 0.001 ARG R 153 *********************** 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 181 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 129 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 195 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8573 (mm) REVERT: R 198 MET cc_start: 0.8778 (pmm) cc_final: 0.8547 (pmm) REVERT: R 248 LEU cc_start: 0.9776 (mt) cc_final: 0.9512 (pp) REVERT: R 277 CYS cc_start: 0.8702 (m) cc_final: 0.8459 (m) REVERT: S 71 GLU cc_start: 0.9342 (tt0) cc_final: 0.9101 (tm-30) REVERT: S 95 GLU cc_start: 0.8550 (pm20) cc_final: 0.8219 (pm20) REVERT: S 103 TYR cc_start: 0.8413 (p90) cc_final: 0.7870 (OUTLIER) REVERT: S 138 PHE cc_start: 0.9275 (m-80) cc_final: 0.9032 (m-80) REVERT: S 144 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: S 146 LYS cc_start: 0.9078 (pttp) cc_final: 0.8615 (pptt) REVERT: S 186 GLN cc_start: 0.8604 (mp10) cc_final: 0.8386 (mp10) REVERT: S 190 ASP cc_start: 0.9392 (m-30) cc_final: 0.9127 (m-30) REVERT: S 318 MET cc_start: 0.9051 (mtm) cc_final: 0.8810 (mtp) REVERT: S 337 GLN cc_start: 0.9320 (mm-40) cc_final: 0.8680 (tm-30) REVERT: T 146 LYS cc_start: 0.9443 (mtmm) cc_final: 0.9235 (mtmm) REVERT: T 164 HIS cc_start: 0.9314 (t-170) cc_final: 0.8848 (t-90) REVERT: T 210 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8672 (mp0) REVERT: T 311 SER cc_start: 0.9328 (m) cc_final: 0.9094 (p) REVERT: T 321 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8863 (mt-10) REVERT: U 19 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8662 (mtp85) REVERT: U 108 GLU cc_start: 0.9218 (tp30) cc_final: 0.8819 (tp30) REVERT: U 164 HIS cc_start: 0.8550 (t-90) cc_final: 0.8340 (t-90) REVERT: U 190 ASP cc_start: 0.9384 (m-30) cc_final: 0.9093 (m-30) REVERT: U 197 ASN cc_start: 0.9133 (m-40) cc_final: 0.8775 (m-40) REVERT: U 321 GLU cc_start: 0.9319 (tp30) cc_final: 0.8900 (mt-10) REVERT: V 121 LEU cc_start: 0.9269 (tt) cc_final: 0.9063 (tm) REVERT: V 158 ASN cc_start: 0.9611 (m-40) cc_final: 0.9367 (m110) REVERT: V 210 GLU cc_start: 0.8940 (mp0) cc_final: 0.8693 (mp0) REVERT: V 321 GLU cc_start: 0.9257 (mp0) cc_final: 0.8977 (mm-30) REVERT: V 339 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8804 (tp) REVERT: V 345 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8716 (mp) outliers start: 52 outliers final: 17 residues processed: 172 average time/residue: 0.9945 time to fit residues: 193.4553 Evaluate side-chains 135 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 236 ASP Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 76 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 323 GLN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 338 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15603 Z= 0.179 Angle : 0.563 12.479 21407 Z= 0.288 Chirality : 0.038 0.153 2400 Planarity : 0.004 0.043 2515 Dihedral : 18.459 89.620 2729 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.82 % Favored : 96.83 % Rotamer: Outliers : 3.51 % Allowed : 26.15 % 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: 0.66 (0.22), residues: 1705 helix: 1.26 (0.17), residues: 1065 sheet: -0.45 (0.46), residues: 140 loop : -1.01 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 267 HIS 0.005 0.001 HIS R 229 PHE 0.016 0.001 PHE V 138 TYR 0.024 0.001 TYR T 103 ARG 0.004 0.000 ARG V 112 *********************** 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 181 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 129 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 248 LEU cc_start: 0.9782 (mt) cc_final: 0.9525 (pp) REVERT: R 277 CYS cc_start: 0.8728 (m) cc_final: 0.8333 (m) REVERT: S 71 GLU cc_start: 0.9342 (tt0) cc_final: 0.9101 (tm-30) REVERT: S 103 TYR cc_start: 0.8344 (p90) cc_final: 0.7812 (OUTLIER) REVERT: S 138 PHE cc_start: 0.9286 (m-80) cc_final: 0.9066 (m-80) REVERT: S 190 ASP cc_start: 0.9352 (m-30) cc_final: 0.9091 (m-30) REVERT: S 318 MET cc_start: 0.9088 (mtm) cc_final: 0.8779 (mtp) REVERT: S 337 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8653 (tm-30) REVERT: T 164 HIS cc_start: 0.9309 (t-170) cc_final: 0.8860 (t-90) REVERT: T 190 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.9052 (m-30) REVERT: T 210 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8726 (mp0) REVERT: T 311 SER cc_start: 0.9284 (m) cc_final: 0.9032 (p) REVERT: U 19 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8943 (mpp80) REVERT: U 164 HIS cc_start: 0.8620 (t-90) cc_final: 0.8291 (t-90) REVERT: U 190 ASP cc_start: 0.9357 (m-30) cc_final: 0.9052 (m-30) REVERT: U 197 ASN cc_start: 0.9048 (m-40) cc_final: 0.8710 (m-40) REVERT: U 321 GLU cc_start: 0.9306 (tp30) cc_final: 0.8890 (mt-10) REVERT: V 51 SER cc_start: 0.9339 (m) cc_final: 0.8991 (p) REVERT: V 121 LEU cc_start: 0.9308 (tt) cc_final: 0.9065 (tm) REVERT: V 158 ASN cc_start: 0.9594 (m-40) cc_final: 0.9373 (m110) REVERT: V 210 GLU cc_start: 0.8928 (mp0) cc_final: 0.8706 (mp0) REVERT: V 321 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8923 (mm-30) REVERT: V 339 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8744 (tp) REVERT: V 345 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8680 (mp) outliers start: 52 outliers final: 24 residues processed: 166 average time/residue: 0.9228 time to fit residues: 174.7812 Evaluate side-chains 139 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 190 ASP Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 189 LEU Chi-restraints excluded: chain U residue 236 ASP Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 158 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15603 Z= 0.328 Angle : 0.612 10.725 21407 Z= 0.318 Chirality : 0.040 0.184 2400 Planarity : 0.004 0.046 2515 Dihedral : 18.526 85.307 2729 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.01 % Rotamer: Outliers : 3.78 % Allowed : 26.82 % Favored : 69.39 % 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: 0.63 (0.22), residues: 1705 helix: 1.29 (0.17), residues: 1050 sheet: -1.00 (0.39), residues: 190 loop : -0.84 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 267 HIS 0.004 0.001 HIS R 229 PHE 0.020 0.002 PHE U 126 TYR 0.015 0.001 TYR S 26 ARG 0.004 0.000 ARG S 215 *********************** 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 172 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 116 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: R 248 LEU cc_start: 0.9785 (mt) cc_final: 0.9497 (pp) REVERT: S 71 GLU cc_start: 0.9346 (tt0) cc_final: 0.9131 (tm-30) REVERT: S 103 TYR cc_start: 0.8354 (p90) cc_final: 0.7791 (OUTLIER) REVERT: S 116 THR cc_start: 0.9554 (t) cc_final: 0.9321 (p) REVERT: S 138 PHE cc_start: 0.9392 (m-80) cc_final: 0.9188 (m-80) REVERT: S 144 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8656 (mp0) REVERT: S 146 LYS cc_start: 0.9389 (pttp) cc_final: 0.8923 (pptt) REVERT: S 190 ASP cc_start: 0.9377 (m-30) cc_final: 0.9122 (m-30) REVERT: S 324 GLU cc_start: 0.9120 (pp20) cc_final: 0.8901 (tm-30) REVERT: S 337 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8670 (tm-30) REVERT: T 164 HIS cc_start: 0.9366 (t-170) cc_final: 0.8885 (t-90) REVERT: T 210 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8658 (mp0) REVERT: U 19 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8547 (mtp85) REVERT: U 164 HIS cc_start: 0.8813 (t-90) cc_final: 0.8500 (t-90) REVERT: U 190 ASP cc_start: 0.9404 (m-30) cc_final: 0.9038 (m-30) REVERT: U 321 GLU cc_start: 0.9352 (tp30) cc_final: 0.9019 (mm-30) REVERT: V 103 TYR cc_start: 0.8639 (p90) cc_final: 0.8234 (p90) REVERT: V 121 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9100 (tm) REVERT: V 158 ASN cc_start: 0.9629 (m-40) cc_final: 0.9374 (m110) REVERT: V 210 GLU cc_start: 0.8920 (mp0) cc_final: 0.8663 (mp0) REVERT: V 321 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9053 (mm-30) REVERT: V 339 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8924 (tp) REVERT: V 345 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8878 (mp) outliers start: 56 outliers final: 28 residues processed: 160 average time/residue: 1.0041 time to fit residues: 183.9944 Evaluate side-chains 137 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 134 SER Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 236 ASP Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 170 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 56 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15603 Z= 0.167 Angle : 0.563 10.122 21407 Z= 0.289 Chirality : 0.039 0.186 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.074 88.926 2729 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.93 % Favored : 96.72 % Rotamer: Outliers : 3.18 % Allowed : 27.70 % Favored : 69.12 % 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: 0.82 (0.22), residues: 1705 helix: 1.37 (0.17), residues: 1055 sheet: -0.44 (0.46), residues: 140 loop : -0.83 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 267 HIS 0.004 0.001 HIS T 254 PHE 0.021 0.001 PHE U 138 TYR 0.029 0.001 TYR T 103 ARG 0.003 0.000 ARG R 327 *********************** 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 169 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 122 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: R 248 LEU cc_start: 0.9770 (mt) cc_final: 0.9495 (pp) REVERT: R 277 CYS cc_start: 0.8554 (m) cc_final: 0.8217 (m) REVERT: S 71 GLU cc_start: 0.9359 (tt0) cc_final: 0.9100 (tm-30) REVERT: S 103 TYR cc_start: 0.8201 (p90) cc_final: 0.7618 (OUTLIER) REVERT: S 116 THR cc_start: 0.9492 (t) cc_final: 0.9236 (p) REVERT: S 138 PHE cc_start: 0.9409 (m-80) cc_final: 0.9201 (m-80) REVERT: S 190 ASP cc_start: 0.9371 (m-30) cc_final: 0.9103 (m-30) REVERT: S 324 GLU cc_start: 0.9076 (pp20) cc_final: 0.8789 (tm-30) REVERT: S 337 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8644 (tm-30) REVERT: T 164 HIS cc_start: 0.9315 (t-170) cc_final: 0.8847 (t-90) REVERT: T 198 MET cc_start: 0.7900 (mtt) cc_final: 0.7681 (mtm) REVERT: T 210 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8715 (mp0) REVERT: U 19 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8959 (mpp80) REVERT: U 41 MET cc_start: 0.9150 (tpp) cc_final: 0.8836 (mmm) REVERT: U 164 HIS cc_start: 0.8870 (t-90) cc_final: 0.8471 (t-90) REVERT: U 190 ASP cc_start: 0.9380 (m-30) cc_final: 0.9085 (m-30) REVERT: U 252 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.9091 (tt0) REVERT: V 51 SER cc_start: 0.9347 (m) cc_final: 0.8959 (p) REVERT: V 103 TYR cc_start: 0.8642 (p90) cc_final: 0.8217 (p90) REVERT: V 121 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9064 (tm) REVERT: V 158 ASN cc_start: 0.9627 (m-40) cc_final: 0.9342 (m110) REVERT: V 210 GLU cc_start: 0.8965 (mp0) cc_final: 0.8727 (mp0) REVERT: V 321 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.9015 (mm-30) REVERT: V 339 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8765 (tp) REVERT: V 345 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8886 (mp) outliers start: 47 outliers final: 15 residues processed: 157 average time/residue: 0.9749 time to fit residues: 173.9739 Evaluate side-chains 129 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 338 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15603 Z= 0.184 Angle : 0.576 9.590 21407 Z= 0.295 Chirality : 0.038 0.186 2400 Planarity : 0.004 0.045 2515 Dihedral : 18.044 89.960 2729 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.11 % Favored : 96.54 % Rotamer: Outliers : 3.04 % Allowed : 28.24 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1705 helix: 1.44 (0.17), residues: 1045 sheet: -0.42 (0.46), residues: 140 loop : -0.81 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 267 HIS 0.004 0.001 HIS T 254 PHE 0.017 0.001 PHE U 138 TYR 0.013 0.001 TYR T 128 ARG 0.003 0.000 ARG T 131 *********************** 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 162 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 117 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: R 248 LEU cc_start: 0.9770 (mt) cc_final: 0.9483 (pp) REVERT: R 277 CYS cc_start: 0.8579 (m) cc_final: 0.8265 (m) REVERT: S 71 GLU cc_start: 0.9354 (tt0) cc_final: 0.8925 (tm-30) REVERT: S 103 TYR cc_start: 0.8176 (p90) cc_final: 0.7616 (OUTLIER) REVERT: S 146 LYS cc_start: 0.9344 (pttp) cc_final: 0.8969 (pptt) REVERT: S 190 ASP cc_start: 0.9368 (m-30) cc_final: 0.9123 (m-30) REVERT: S 324 GLU cc_start: 0.9085 (pp20) cc_final: 0.8620 (tm-30) REVERT: S 337 GLN cc_start: 0.9322 (mm-40) cc_final: 0.8623 (tm-30) REVERT: T 164 HIS cc_start: 0.9310 (t-170) cc_final: 0.8837 (t-90) REVERT: T 210 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8715 (mp0) REVERT: U 19 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8953 (mpp80) REVERT: U 41 MET cc_start: 0.9151 (tpp) cc_final: 0.8832 (mmm) REVERT: U 164 HIS cc_start: 0.8901 (t-90) cc_final: 0.8456 (t-90) REVERT: U 190 ASP cc_start: 0.9399 (m-30) cc_final: 0.9099 (m-30) REVERT: U 252 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9018 (tt0) REVERT: V 51 SER cc_start: 0.9401 (m) cc_final: 0.9045 (p) REVERT: V 103 TYR cc_start: 0.8684 (p90) cc_final: 0.8302 (p90) REVERT: V 121 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9062 (tm) REVERT: V 158 ASN cc_start: 0.9610 (m-40) cc_final: 0.9354 (m110) REVERT: V 210 GLU cc_start: 0.8954 (mp0) cc_final: 0.8702 (mp0) REVERT: V 321 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.9035 (mm-30) REVERT: V 339 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8790 (tp) REVERT: V 345 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8885 (mp) outliers start: 45 outliers final: 25 residues processed: 151 average time/residue: 0.9096 time to fit residues: 157.4363 Evaluate side-chains 136 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15603 Z= 0.282 Angle : 0.611 9.461 21407 Z= 0.314 Chirality : 0.040 0.180 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.100 86.478 2729 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.81 % Favored : 95.84 % Rotamer: Outliers : 2.84 % Allowed : 28.85 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1705 helix: 1.44 (0.17), residues: 1045 sheet: -0.88 (0.40), residues: 190 loop : -0.81 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.021 0.002 PHE V 138 TYR 0.028 0.001 TYR T 103 ARG 0.005 0.000 ARG U 131 *********************** 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 153 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: R 41 MET cc_start: 0.8856 (mmm) cc_final: 0.8593 (tpt) REVERT: R 248 LEU cc_start: 0.9796 (mt) cc_final: 0.9501 (pp) REVERT: R 277 CYS cc_start: 0.8680 (m) cc_final: 0.8360 (m) REVERT: S 71 GLU cc_start: 0.9368 (tt0) cc_final: 0.8955 (tm-30) REVERT: S 103 TYR cc_start: 0.8320 (p90) cc_final: 0.7731 (OUTLIER) REVERT: S 144 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: S 146 LYS cc_start: 0.9454 (pttp) cc_final: 0.8983 (pptt) REVERT: S 190 ASP cc_start: 0.9347 (m-30) cc_final: 0.9056 (m-30) REVERT: S 324 GLU cc_start: 0.9151 (pp20) cc_final: 0.8712 (tm-30) REVERT: S 337 GLN cc_start: 0.9333 (mm-40) cc_final: 0.8669 (tm-30) REVERT: T 164 HIS cc_start: 0.9360 (t-170) cc_final: 0.8879 (t-90) REVERT: T 210 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: T 333 GLU cc_start: 0.8617 (pp20) cc_final: 0.8403 (tm-30) REVERT: U 19 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8866 (mpp80) REVERT: U 164 HIS cc_start: 0.8956 (t-90) cc_final: 0.8540 (t-90) REVERT: U 190 ASP cc_start: 0.9404 (m-30) cc_final: 0.9060 (m-30) REVERT: U 321 GLU cc_start: 0.9314 (tp30) cc_final: 0.9004 (mm-30) REVERT: V 51 SER cc_start: 0.9319 (m) cc_final: 0.8942 (p) REVERT: V 103 TYR cc_start: 0.8802 (p90) cc_final: 0.8375 (p90) REVERT: V 121 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9139 (tm) REVERT: V 128 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: V 158 ASN cc_start: 0.9599 (m-40) cc_final: 0.9353 (m110) REVERT: V 210 GLU cc_start: 0.8928 (mp0) cc_final: 0.8658 (mp0) REVERT: V 321 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9060 (mm-30) REVERT: V 339 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8894 (tp) REVERT: V 345 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8911 (mp) outliers start: 42 outliers final: 24 residues processed: 145 average time/residue: 0.9766 time to fit residues: 161.2623 Evaluate side-chains 132 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15603 Z= 0.241 Angle : 0.604 10.236 21407 Z= 0.308 Chirality : 0.039 0.179 2400 Planarity : 0.004 0.045 2515 Dihedral : 18.000 86.539 2729 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.70 % Favored : 95.95 % Rotamer: Outliers : 2.91 % Allowed : 29.26 % Favored : 67.84 % 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: 0.81 (0.22), residues: 1705 helix: 1.46 (0.17), residues: 1040 sheet: -0.82 (0.40), residues: 190 loop : -0.84 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 267 HIS 0.003 0.001 HIS T 254 PHE 0.027 0.001 PHE S 138 TYR 0.014 0.001 TYR S 128 ARG 0.003 0.000 ARG U 131 *********************** 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 150 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 107 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 LEU cc_start: 0.9784 (mt) cc_final: 0.9494 (pp) REVERT: R 277 CYS cc_start: 0.8499 (m) cc_final: 0.8156 (m) REVERT: S 71 GLU cc_start: 0.9370 (tt0) cc_final: 0.8950 (tm-30) REVERT: S 103 TYR cc_start: 0.8322 (p90) cc_final: 0.7704 (OUTLIER) REVERT: S 144 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: S 146 LYS cc_start: 0.9410 (pttp) cc_final: 0.8947 (pptt) REVERT: S 190 ASP cc_start: 0.9350 (m-30) cc_final: 0.9034 (m-30) REVERT: S 324 GLU cc_start: 0.9152 (pp20) cc_final: 0.8738 (tm-30) REVERT: S 337 GLN cc_start: 0.9330 (mm-40) cc_final: 0.8643 (tm-30) REVERT: T 164 HIS cc_start: 0.9355 (t-170) cc_final: 0.8904 (t-90) REVERT: T 198 MET cc_start: 0.8481 (mtm) cc_final: 0.8255 (mtm) REVERT: T 210 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8723 (mp0) REVERT: U 19 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8886 (mpp80) REVERT: U 41 MET cc_start: 0.9177 (tpp) cc_final: 0.8881 (mmm) REVERT: U 164 HIS cc_start: 0.8957 (t-90) cc_final: 0.8531 (t-90) REVERT: U 252 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.9047 (tt0) REVERT: U 321 GLU cc_start: 0.9311 (tp30) cc_final: 0.9005 (mm-30) REVERT: V 51 SER cc_start: 0.9321 (m) cc_final: 0.8887 (p) REVERT: V 103 TYR cc_start: 0.8826 (p90) cc_final: 0.8448 (p90) REVERT: V 121 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9090 (tm) REVERT: V 128 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: V 158 ASN cc_start: 0.9602 (m-40) cc_final: 0.9332 (m110) REVERT: V 187 ASP cc_start: 0.9381 (p0) cc_final: 0.9167 (p0) REVERT: V 197 ASN cc_start: 0.9194 (m110) cc_final: 0.8981 (p0) REVERT: V 210 GLU cc_start: 0.8964 (mp0) cc_final: 0.8706 (mp0) REVERT: V 321 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.9052 (mm-30) REVERT: V 339 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8800 (tp) REVERT: V 345 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8923 (mp) outliers start: 43 outliers final: 25 residues processed: 138 average time/residue: 0.9776 time to fit residues: 153.6744 Evaluate side-chains 134 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 79 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 175 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15603 Z= 0.283 Angle : 0.624 10.336 21407 Z= 0.319 Chirality : 0.040 0.176 2400 Planarity : 0.004 0.046 2515 Dihedral : 18.025 86.687 2729 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 2.91 % Allowed : 29.39 % Favored : 67.70 % 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: 0.78 (0.22), residues: 1705 helix: 1.40 (0.17), residues: 1040 sheet: -0.74 (0.41), residues: 190 loop : -0.82 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 267 HIS 0.003 0.001 HIS T 254 PHE 0.027 0.002 PHE T 138 TYR 0.029 0.001 TYR T 103 ARG 0.003 0.000 ARG T 131 ********************** 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 146 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 103 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 MET cc_start: 0.8851 (mmm) cc_final: 0.8590 (tpt) REVERT: R 277 CYS cc_start: 0.8489 (m) cc_final: 0.8164 (m) REVERT: S 71 GLU cc_start: 0.9363 (tt0) cc_final: 0.8962 (tm-30) REVERT: S 103 TYR cc_start: 0.8305 (p90) cc_final: 0.7786 (p90) REVERT: S 144 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: S 146 LYS cc_start: 0.9482 (pttp) cc_final: 0.9006 (pptt) REVERT: S 324 GLU cc_start: 0.9151 (pp20) cc_final: 0.8735 (tm-30) REVERT: S 337 GLN cc_start: 0.9335 (mm-40) cc_final: 0.8665 (tm-30) REVERT: T 164 HIS cc_start: 0.9376 (t-170) cc_final: 0.8922 (t-90) REVERT: T 210 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8733 (mp0) REVERT: T 293 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9210 (mt) REVERT: U 19 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8874 (mpp80) REVERT: U 164 HIS cc_start: 0.9011 (t-90) cc_final: 0.8599 (t-90) REVERT: U 190 ASP cc_start: 0.9401 (m-30) cc_final: 0.9034 (m-30) REVERT: U 252 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.9091 (tt0) REVERT: U 321 GLU cc_start: 0.9313 (tp30) cc_final: 0.9012 (mm-30) REVERT: V 51 SER cc_start: 0.9298 (m) cc_final: 0.8873 (p) REVERT: V 103 TYR cc_start: 0.8876 (p90) cc_final: 0.8509 (p90) REVERT: V 128 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: V 158 ASN cc_start: 0.9597 (m-40) cc_final: 0.9327 (m110) REVERT: V 187 ASP cc_start: 0.9388 (p0) cc_final: 0.9179 (p0) REVERT: V 210 GLU cc_start: 0.8926 (mp0) cc_final: 0.8656 (mp0) REVERT: V 321 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9058 (mm-30) REVERT: V 339 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8895 (tp) REVERT: V 345 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8930 (mp) outliers start: 43 outliers final: 22 residues processed: 138 average time/residue: 1.0106 time to fit residues: 158.3342 Evaluate side-chains 132 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 0.0070 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 142 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.082161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051784 restraints weight = 51994.872| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.84 r_work: 0.2815 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15603 Z= 0.173 Angle : 0.612 10.875 21407 Z= 0.306 Chirality : 0.039 0.181 2400 Planarity : 0.004 0.044 2515 Dihedral : 17.846 85.611 2729 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.70 % Favored : 95.95 % Rotamer: Outliers : 2.36 % Allowed : 30.00 % Favored : 67.64 % 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: 0.90 (0.22), residues: 1705 helix: 1.45 (0.17), residues: 1050 sheet: -0.77 (0.40), residues: 190 loop : -0.66 (0.32), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 267 HIS 0.003 0.001 HIS V 30 PHE 0.026 0.001 PHE S 138 TYR 0.013 0.001 TYR S 128 ARG 0.003 0.000 ARG S 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4248.49 seconds wall clock time: 76 minutes 33.79 seconds (4593.79 seconds total)