Starting phenix.real_space_refine on Thu Aug 6 11:54:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d46_46550/08_2026/9d46_46550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d46_46550/08_2026/9d46_46550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d46_46550/08_2026/9d46_46550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d46_46550/08_2026/9d46_46550.map" model { file = "/net/cci-nas-00/data/ceres_data/9d46_46550/08_2026/9d46_46550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d46_46550/08_2026/9d46_46550.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 sd= 0.045 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 36 5.49 5 Mg 12 5.21 5 S 108 5.16 5 C 9396 2.51 5 N 2650 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15188 Number of models: 1 Model: "" Number of chains: 13 Chain: "X" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "B" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2431 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "E" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2431 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "D" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" 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: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.32, per 1000 atoms: 0.22 Number of scatterers: 15188 At special positions: 0 Unit cell: (109.98, 113.364, 159.894, 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 108 16.00 P 36 15.00 Mg 12 11.99 O 2986 8.00 N 2650 7.00 C 9396 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 - 3.00 Amino acid : True - 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: 0.87 Conformation dependent library (CDL) restraints added in 589.1 milliseconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 18 sheets defined 52.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 92 through 102 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 114 through 121 removed outlier: 3.641A pdb=" N ILE C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.664A pdb=" N GLU C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.703A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 254 through 270 removed outlier: 3.919A pdb=" N LEU C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 removed outlier: 4.414A pdb=" N TYR C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.839A pdb=" N MET C 335 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 336 " --> pdb=" O GLY C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 332 through 336' Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.517A pdb=" N MET C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 92 through 102 Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 114 through 120 Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 190 through 202 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.715A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 254 through 270 removed outlier: 3.905A pdb=" N LEU F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 290 removed outlier: 4.471A pdb=" N TYR F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 318 Processing helix chain 'F' and resid 332 through 336 removed outlier: 4.042A pdb=" N MET F 335 " --> pdb=" O ASP F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 354 removed outlier: 3.616A pdb=" N MET F 350 " --> pdb=" O GLY F 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.560A pdb=" N LYS B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.543A pdb=" N ILE B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.686A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.947A pdb=" N LEU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 290 removed outlier: 4.761A pdb=" N LEU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 114 through 120 Processing helix chain 'E' and resid 125 through 140 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 190 through 202 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.653A pdb=" N LEU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 254 through 272 removed outlier: 3.926A pdb=" N LEU E 262 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU E 271 " --> pdb=" O GLN E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 290 removed outlier: 4.321A pdb=" N TYR E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR E 288 " --> pdb=" O ALA E 284 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 318 Processing helix chain 'E' and resid 332 through 336 removed outlier: 3.987A pdb=" N MET E 335 " --> pdb=" O ASP E 332 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 336 " --> pdb=" O GLY E 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 332 through 336' Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.622A pdb=" N MET E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.595A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.677A pdb=" N GLU A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.667A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 254 through 270 removed outlier: 4.018A pdb=" N LEU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 4.678A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 318 Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.612A pdb=" N MET A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 147 through 156 removed outlier: 3.740A pdb=" N GLU D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 171 Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 225 through 237 removed outlier: 3.627A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 254 through 270 removed outlier: 3.984A pdb=" N LEU D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 290 removed outlier: 4.676A pdb=" N LEU D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 318 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.628A pdb=" N MET D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 145 through 146 removed outlier: 5.381A pdb=" N LYS B 214 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 276 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER B 275 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL B 322 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE B 277 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR B 324 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 279 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG B 357 " --> pdb=" O VAL B 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 391 through 393 removed outlier: 6.573A pdb=" N ARG C 357 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER C 275 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL C 322 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE C 277 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR C 324 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 279 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS C 214 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU C 276 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AA5, first strand: chain 'F' and resid 145 through 146 removed outlier: 6.650A pdb=" N CYS E 215 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ALA E 250 " --> pdb=" O CYS E 215 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR E 217 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS E 214 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 276 " --> pdb=" O LYS E 214 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER E 275 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL E 322 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE E 277 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR E 324 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL E 279 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 185 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG E 357 " --> pdb=" O VAL E 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AA7, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.534A pdb=" N CYS F 215 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ALA F 250 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR F 217 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS F 214 " --> pdb=" O PHE F 274 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU F 276 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER F 275 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL F 322 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE F 277 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR F 324 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL F 279 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG F 357 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 327 through 329 Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 removed outlier: 6.540A pdb=" N CYS A 215 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA A 250 " --> pdb=" O CYS A 215 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR A 217 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS A 214 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 276 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER A 275 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 322 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE A 277 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N THR A 324 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 279 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG A 357 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB2, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AB3, first strand: chain 'E' and resid 145 through 146 removed outlier: 5.228A pdb=" N LYS D 214 " --> pdb=" O PHE D 274 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 276 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER D 275 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL D 322 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE D 277 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR D 324 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL D 279 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG D 357 " --> pdb=" O VAL D 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AB6, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AB7, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'D' and resid 327 through 329 799 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5016 1.34 - 1.46: 1936 1.46 - 1.58: 8258 1.58 - 1.70: 65 1.70 - 1.81: 168 Bond restraints: 15443 Sorted by residual: bond pdb=" C1' DT X 17 " pdb=" N1 DT X 17 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.43e+01 bond pdb=" C3' DT X 9 " pdb=" C2' DT X 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT X 18 " pdb=" C2' DT X 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT X 6 " pdb=" C2' DT X 6 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.05e+00 bond pdb=" C1' DT X 12 " pdb=" N1 DT X 12 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.99e+00 ... (remaining 15438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 20662 2.01 - 4.01: 267 4.01 - 6.02: 13 6.02 - 8.02: 7 8.02 - 10.03: 3 Bond angle restraints: 20952 Sorted by residual: angle pdb=" N3 DT X 13 " pdb=" C4 DT X 13 " pdb=" O4 DT X 13 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT X 8 " pdb=" C4 DT X 8 " pdb=" O4 DT X 8 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT X 16 " pdb=" C4 DT X 16 " pdb=" O4 DT X 16 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT X 5 " pdb=" C4 DT X 5 " pdb=" O4 DT X 5 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT X 2 " pdb=" C4 DT X 2 " pdb=" O4 DT X 2 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 20947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 8511 17.40 - 34.80: 637 34.80 - 52.21: 221 52.21 - 69.61: 56 69.61 - 87.01: 24 Dihedral angle restraints: 9449 sinusoidal: 3995 harmonic: 5454 Sorted by residual: dihedral pdb=" CB MET E 269 " pdb=" CG MET E 269 " pdb=" SD MET E 269 " pdb=" CE MET E 269 " ideal model delta sinusoidal sigma weight residual 180.00 122.39 57.61 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG ARG D 312 " pdb=" CD ARG D 312 " pdb=" NE ARG D 312 " pdb=" CZ ARG D 312 " ideal model delta sinusoidal sigma weight residual -90.00 -49.83 -40.17 2 1.50e+01 4.44e-03 8.88e+00 dihedral pdb=" CG ARG D 115 " pdb=" CD ARG D 115 " pdb=" NE ARG D 115 " pdb=" CZ ARG D 115 " ideal model delta sinusoidal sigma weight residual -90.00 -49.88 -40.12 2 1.50e+01 4.44e-03 8.86e+00 ... (remaining 9446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1645 0.033 - 0.067: 470 0.067 - 0.100: 184 0.100 - 0.134: 74 0.134 - 0.167: 7 Chirality restraints: 2380 Sorted by residual: chirality pdb=" CA ARG B 188 " pdb=" N ARG B 188 " pdb=" C ARG B 188 " pdb=" CB ARG B 188 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA ARG A 188 " pdb=" N ARG A 188 " pdb=" C ARG A 188 " pdb=" CB ARG A 188 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA ILE E 345 " pdb=" N ILE E 345 " pdb=" C ILE E 345 " pdb=" CB ILE E 345 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 2377 not shown) Planarity restraints: 2666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 187 " -0.016 2.00e-02 2.50e+03 1.87e-02 6.11e+00 pdb=" CG PHE A 187 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 187 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 187 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 187 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 187 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 187 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 187 " -0.014 2.00e-02 2.50e+03 1.72e-02 5.15e+00 pdb=" CG PHE B 187 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 187 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 187 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 187 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 187 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 187 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 287 " -0.138 9.50e-02 1.11e+02 6.19e-02 2.40e+00 pdb=" NE ARG E 287 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 287 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 287 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 287 " -0.006 2.00e-02 2.50e+03 ... (remaining 2663 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 197 2.54 - 3.13: 11618 3.13 - 3.72: 25924 3.72 - 4.31: 36400 4.31 - 4.90: 59743 Nonbonded interactions: 133882 Sorted by model distance: nonbonded pdb=" O1G ATP B 501 " pdb="MG MG B 503 " model vdw 1.946 2.170 nonbonded pdb=" O1B ATP B 501 " pdb="MG MG B 503 " model vdw 1.963 2.170 nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 503 " model vdw 1.971 2.170 nonbonded pdb=" OG SER B 192 " pdb="MG MG B 503 " model vdw 1.972 2.170 nonbonded pdb=" OG SER D 192 " pdb="MG MG D 503 " model vdw 1.999 2.170 ... (remaining 133877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 81 through 502) selection = (chain 'B' and resid 81 through 502) selection = (chain 'C' and resid 81 through 502) selection = (chain 'D' and resid 81 through 502) selection = (chain 'E' and resid 81 through 502) selection = (chain 'F' and resid 81 through 502) } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.780 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 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 : 0.002 0.053 15443 Z= 0.159 Angle : 0.503 10.025 20952 Z= 0.324 Chirality : 0.040 0.167 2380 Planarity : 0.003 0.062 2666 Dihedral : 14.998 87.012 5949 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1912 helix: 1.28 (0.18), residues: 894 sheet: 0.55 (0.31), residues: 328 loop : 0.59 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 312 TYR 0.012 0.001 TYR B 217 PHE 0.043 0.001 PHE A 187 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.16 (15443) covalent geometry : angle 0.50263 / 0.32 (20952) hydrogen bonds : bond 0.17019 / 15.50 ( 799) hydrogen bonds : angle 6.53939 / 5.42 ( 2235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.561 Fit side-chains REVERT: C 134 ASN cc_start: 0.9149 (m110) cc_final: 0.8914 (m110) REVERT: F 89 ASN cc_start: 0.8852 (m110) cc_final: 0.8591 (m110) REVERT: F 166 ASN cc_start: 0.9478 (m-40) cc_final: 0.9212 (m110) REVERT: B 152 MET cc_start: 0.7772 (tmm) cc_final: 0.7393 (tmm) REVERT: B 293 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7551 (ttm170) REVERT: E 126 GLU cc_start: 0.8288 (tp30) cc_final: 0.8002 (tp30) REVERT: E 149 ASP cc_start: 0.8353 (t70) cc_final: 0.8006 (t0) REVERT: E 166 ASN cc_start: 0.9236 (m110) cc_final: 0.8901 (m110) REVERT: E 335 MET cc_start: 0.4954 (ppp) cc_final: 0.4155 (ppp) REVERT: A 112 TYR cc_start: 0.8796 (m-10) cc_final: 0.7395 (m-80) REVERT: A 142 MET cc_start: 0.7803 (mmm) cc_final: 0.7174 (tpt) REVERT: A 166 ASN cc_start: 0.9351 (m110) cc_final: 0.9144 (m110) REVERT: A 335 MET cc_start: 0.1939 (pmm) cc_final: 0.1686 (pmm) REVERT: D 301 MET cc_start: 0.8498 (tpp) cc_final: 0.8194 (tpp) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1213 time to fit residues: 22.5747 Evaluate side-chains 108 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0570 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.054843 restraints weight = 38436.892| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.48 r_work: 0.2702 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15443 Z= 0.180 Angle : 0.531 10.230 20952 Z= 0.283 Chirality : 0.043 0.146 2380 Planarity : 0.004 0.048 2666 Dihedral : 14.031 84.560 2461 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.26 % Allowed : 3.59 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1912 helix: 1.52 (0.18), residues: 896 sheet: 0.55 (0.30), residues: 308 loop : 0.54 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.011 0.001 TYR C 388 PHE 0.024 0.001 PHE A 187 HIS 0.002 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (15443) covalent geometry : angle 0.53119 / 0.28 (20952) hydrogen bonds : bond 0.03777 / 3.35 ( 799) hydrogen bonds : angle 4.72007 / 3.87 ( 2235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.488 Fit side-chains REVERT: C 134 ASN cc_start: 0.9346 (m110) cc_final: 0.9044 (m110) REVERT: F 89 ASN cc_start: 0.8978 (m110) cc_final: 0.8632 (m110) REVERT: F 159 CYS cc_start: 0.7957 (p) cc_final: 0.7546 (p) REVERT: F 166 ASN cc_start: 0.9436 (m-40) cc_final: 0.9148 (m110) REVERT: B 364 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8776 (ttpt) REVERT: E 120 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8850 (pp20) REVERT: E 126 GLU cc_start: 0.8626 (tp30) cc_final: 0.8175 (tp30) REVERT: E 134 ASN cc_start: 0.9378 (m110) cc_final: 0.9173 (m-40) REVERT: E 166 ASN cc_start: 0.9139 (m110) cc_final: 0.8808 (m110) REVERT: E 286 TYR cc_start: 0.9306 (m-80) cc_final: 0.9002 (m-80) REVERT: E 335 MET cc_start: 0.5202 (ppp) cc_final: 0.4693 (ppp) REVERT: A 142 MET cc_start: 0.7731 (mmm) cc_final: 0.7243 (tpt) REVERT: A 166 ASN cc_start: 0.9392 (m110) cc_final: 0.9142 (m110) REVERT: A 245 ASN cc_start: 0.9442 (m-40) cc_final: 0.9064 (m110) REVERT: D 301 MET cc_start: 0.9068 (tpp) cc_final: 0.8718 (tpp) outliers start: 4 outliers final: 4 residues processed: 119 average time/residue: 0.1128 time to fit residues: 20.3537 Evaluate side-chains 107 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 366 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 48 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 161 optimal weight: 0.0470 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.074559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.053826 restraints weight = 38363.718| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.54 r_work: 0.2667 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15443 Z= 0.187 Angle : 0.515 10.536 20952 Z= 0.273 Chirality : 0.042 0.144 2380 Planarity : 0.004 0.045 2666 Dihedral : 13.517 87.137 2461 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.39 % Allowed : 5.20 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1912 helix: 1.60 (0.18), residues: 888 sheet: 0.18 (0.29), residues: 308 loop : 0.43 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 115 TYR 0.017 0.001 TYR C 388 PHE 0.017 0.001 PHE B 187 HIS 0.002 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (15443) covalent geometry : angle 0.51507 / 0.27 (20952) hydrogen bonds : bond 0.03297 / 2.90 ( 799) hydrogen bonds : angle 4.41870 / 3.62 ( 2235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.429 Fit side-chains REVERT: C 134 ASN cc_start: 0.9368 (m110) cc_final: 0.9044 (m110) REVERT: C 152 MET cc_start: 0.9054 (tpt) cc_final: 0.8736 (tmm) REVERT: C 388 TYR cc_start: 0.8385 (m-10) cc_final: 0.8185 (m-10) REVERT: F 89 ASN cc_start: 0.8940 (m110) cc_final: 0.8585 (m110) REVERT: F 166 ASN cc_start: 0.9409 (m-40) cc_final: 0.9120 (m110) REVERT: F 285 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8220 (mp) REVERT: F 335 MET cc_start: 0.3132 (ppp) cc_final: 0.1549 (ptp) REVERT: B 364 LYS cc_start: 0.9015 (ttpt) cc_final: 0.8815 (ttpt) REVERT: E 93 MET cc_start: 0.8565 (tpt) cc_final: 0.8364 (tpt) REVERT: E 126 GLU cc_start: 0.8596 (tp30) cc_final: 0.8168 (tp30) REVERT: E 234 GLN cc_start: 0.9045 (mm110) cc_final: 0.8718 (mm110) REVERT: E 335 MET cc_start: 0.5323 (ppp) cc_final: 0.4156 (ppp) REVERT: A 142 MET cc_start: 0.7726 (mmm) cc_final: 0.7249 (tpt) REVERT: A 166 ASN cc_start: 0.9379 (m110) cc_final: 0.9122 (m110) REVERT: A 245 ASN cc_start: 0.9448 (m-40) cc_final: 0.9062 (m110) REVERT: D 301 MET cc_start: 0.9040 (tpp) cc_final: 0.8687 (tpp) outliers start: 6 outliers final: 3 residues processed: 117 average time/residue: 0.0997 time to fit residues: 17.8899 Evaluate side-chains 101 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 366 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 2 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 234 GLN D 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.055179 restraints weight = 39345.219| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.33 r_work: 0.2640 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15443 Z= 0.246 Angle : 0.547 8.319 20952 Z= 0.287 Chirality : 0.043 0.145 2380 Planarity : 0.004 0.043 2666 Dihedral : 13.219 89.866 2461 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.58 % Allowed : 5.91 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1912 helix: 1.48 (0.18), residues: 914 sheet: -0.12 (0.29), residues: 308 loop : 0.39 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 115 TYR 0.017 0.001 TYR C 388 PHE 0.012 0.001 PHE B 187 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (15443) covalent geometry : angle 0.54689 / 0.29 (20952) hydrogen bonds : bond 0.03292 / 2.90 ( 799) hydrogen bonds : angle 4.37849 / 3.59 ( 2235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.369 Fit side-chains REVERT: C 134 ASN cc_start: 0.9377 (m110) cc_final: 0.9060 (m110) REVERT: C 152 MET cc_start: 0.9043 (tpt) cc_final: 0.8771 (tmm) REVERT: F 89 ASN cc_start: 0.8917 (m110) cc_final: 0.8575 (m110) REVERT: F 166 ASN cc_start: 0.9397 (m-40) cc_final: 0.9088 (m-40) REVERT: F 285 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8326 (mp) REVERT: E 93 MET cc_start: 0.8614 (tpt) cc_final: 0.8390 (tpt) REVERT: E 126 GLU cc_start: 0.8595 (tp30) cc_final: 0.8177 (tp30) REVERT: E 234 GLN cc_start: 0.9038 (mm110) cc_final: 0.8688 (mm110) REVERT: E 335 MET cc_start: 0.5220 (ppp) cc_final: 0.3913 (ppp) REVERT: A 142 MET cc_start: 0.7817 (mmm) cc_final: 0.7259 (tpt) REVERT: A 166 ASN cc_start: 0.9398 (m110) cc_final: 0.9121 (m110) REVERT: A 188 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7296 (pmt-80) REVERT: A 245 ASN cc_start: 0.9481 (m-40) cc_final: 0.9095 (m110) REVERT: D 188 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8158 (pmt-80) REVERT: D 301 MET cc_start: 0.9059 (tpp) cc_final: 0.8730 (tpp) outliers start: 9 outliers final: 4 residues processed: 107 average time/residue: 0.1161 time to fit residues: 18.8069 Evaluate side-chains 101 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 38 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054820 restraints weight = 39073.272| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.46 r_work: 0.2650 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15443 Z= 0.180 Angle : 0.513 13.583 20952 Z= 0.270 Chirality : 0.042 0.141 2380 Planarity : 0.003 0.038 2666 Dihedral : 13.025 89.789 2461 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.83 % Allowed : 6.23 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1912 helix: 1.47 (0.18), residues: 910 sheet: -0.18 (0.29), residues: 308 loop : 0.36 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 312 TYR 0.020 0.001 TYR C 388 PHE 0.012 0.001 PHE A 187 HIS 0.002 0.000 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (15443) covalent geometry : angle 0.51320 / 0.27 (20952) hydrogen bonds : bond 0.03018 / 2.65 ( 799) hydrogen bonds : angle 4.25458 / 3.48 ( 2235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.389 Fit side-chains REVERT: C 93 MET cc_start: 0.9125 (tpp) cc_final: 0.8736 (tpp) REVERT: C 97 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9128 (mmmt) REVERT: C 134 ASN cc_start: 0.9386 (m110) cc_final: 0.9061 (m110) REVERT: C 152 MET cc_start: 0.9033 (tpt) cc_final: 0.8749 (tmm) REVERT: F 89 ASN cc_start: 0.8873 (m110) cc_final: 0.8510 (m110) REVERT: F 159 CYS cc_start: 0.8016 (p) cc_final: 0.7525 (p) REVERT: F 166 ASN cc_start: 0.9381 (m-40) cc_final: 0.9070 (m-40) REVERT: F 285 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8249 (mp) REVERT: F 335 MET cc_start: 0.3086 (ppp) cc_final: 0.1679 (pmm) REVERT: E 93 MET cc_start: 0.8633 (tpt) cc_final: 0.8387 (tpt) REVERT: E 126 GLU cc_start: 0.8653 (tp30) cc_final: 0.8204 (tp30) REVERT: E 234 GLN cc_start: 0.9021 (mm110) cc_final: 0.8686 (mm110) REVERT: E 335 MET cc_start: 0.5268 (ppp) cc_final: 0.3943 (ppp) REVERT: A 142 MET cc_start: 0.7909 (mmm) cc_final: 0.7298 (tpt) REVERT: A 166 ASN cc_start: 0.9379 (m110) cc_final: 0.9109 (m110) REVERT: A 188 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7348 (pmt-80) REVERT: A 245 ASN cc_start: 0.9483 (m-40) cc_final: 0.9094 (m110) REVERT: D 188 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8092 (pmt-80) REVERT: D 301 MET cc_start: 0.9022 (tpp) cc_final: 0.8687 (tpp) outliers start: 13 outliers final: 5 residues processed: 113 average time/residue: 0.1232 time to fit residues: 20.7138 Evaluate side-chains 108 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 10 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 330 GLN D 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.053614 restraints weight = 38776.486| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.39 r_work: 0.2643 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15443 Z= 0.194 Angle : 0.514 10.221 20952 Z= 0.271 Chirality : 0.042 0.144 2380 Planarity : 0.003 0.036 2666 Dihedral : 12.880 89.303 2461 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.83 % Allowed : 7.12 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 1912 helix: 1.46 (0.17), residues: 914 sheet: -0.18 (0.30), residues: 296 loop : 0.31 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 312 TYR 0.021 0.001 TYR C 388 PHE 0.010 0.001 PHE A 187 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (15443) covalent geometry : angle 0.51392 / 0.27 (20952) hydrogen bonds : bond 0.03014 / 2.64 ( 799) hydrogen bonds : angle 4.18823 / 3.43 ( 2235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.598 Fit side-chains REVERT: C 134 ASN cc_start: 0.9388 (m110) cc_final: 0.9055 (m110) REVERT: C 152 MET cc_start: 0.9030 (tpt) cc_final: 0.8751 (tmm) REVERT: F 89 ASN cc_start: 0.8864 (m110) cc_final: 0.8511 (m110) REVERT: F 159 CYS cc_start: 0.8036 (p) cc_final: 0.7530 (p) REVERT: F 166 ASN cc_start: 0.9384 (m-40) cc_final: 0.9076 (m-40) REVERT: F 285 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8306 (mp) REVERT: B 188 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.6508 (pmt-80) REVERT: E 93 MET cc_start: 0.8650 (tpt) cc_final: 0.8397 (tpt) REVERT: E 126 GLU cc_start: 0.8636 (tp30) cc_final: 0.8197 (tp30) REVERT: E 134 ASN cc_start: 0.9337 (m110) cc_final: 0.9119 (m-40) REVERT: E 234 GLN cc_start: 0.9025 (mm110) cc_final: 0.8668 (mm110) REVERT: E 335 MET cc_start: 0.5174 (ppp) cc_final: 0.3903 (ppp) REVERT: A 142 MET cc_start: 0.7919 (mmm) cc_final: 0.7297 (tpt) REVERT: A 166 ASN cc_start: 0.9387 (m110) cc_final: 0.9118 (m110) REVERT: A 188 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7256 (pmt-80) REVERT: A 245 ASN cc_start: 0.9492 (m-40) cc_final: 0.9114 (m110) REVERT: D 188 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8071 (pmt-80) REVERT: D 301 MET cc_start: 0.9037 (tpp) cc_final: 0.8707 (tpp) outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.1290 time to fit residues: 22.2710 Evaluate side-chains 110 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 131 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 0.0670 chunk 142 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 234 GLN C 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.055597 restraints weight = 38382.499| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.42 r_work: 0.2663 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15443 Z= 0.140 Angle : 0.508 16.038 20952 Z= 0.266 Chirality : 0.041 0.144 2380 Planarity : 0.003 0.046 2666 Dihedral : 12.698 89.942 2461 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.71 % Allowed : 7.51 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1912 helix: 1.45 (0.17), residues: 914 sheet: -0.14 (0.30), residues: 308 loop : 0.37 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 312 TYR 0.021 0.001 TYR C 388 PHE 0.011 0.001 PHE A 187 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (15443) covalent geometry : angle 0.50819 / 0.27 (20952) hydrogen bonds : bond 0.02815 / 2.48 ( 799) hydrogen bonds : angle 4.08740 / 3.35 ( 2235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.559 Fit side-chains REVERT: C 134 ASN cc_start: 0.9392 (m110) cc_final: 0.9064 (m110) REVERT: C 152 MET cc_start: 0.9018 (tpt) cc_final: 0.8729 (tmm) REVERT: C 388 TYR cc_start: 0.8378 (m-10) cc_final: 0.8143 (m-10) REVERT: F 89 ASN cc_start: 0.8837 (m110) cc_final: 0.8483 (m110) REVERT: F 115 ARG cc_start: 0.8035 (ttt90) cc_final: 0.7640 (ttt90) REVERT: F 159 CYS cc_start: 0.7973 (p) cc_final: 0.7463 (p) REVERT: F 166 ASN cc_start: 0.9381 (m-40) cc_final: 0.9073 (m-40) REVERT: F 285 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8270 (mp) REVERT: F 335 MET cc_start: 0.3241 (ppp) cc_final: 0.1879 (pmm) REVERT: B 188 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.6495 (pmt-80) REVERT: E 93 MET cc_start: 0.8657 (tpt) cc_final: 0.8397 (tpt) REVERT: E 126 GLU cc_start: 0.8650 (tp30) cc_final: 0.8203 (tp30) REVERT: E 234 GLN cc_start: 0.9020 (mm110) cc_final: 0.8653 (mm110) REVERT: E 335 MET cc_start: 0.5147 (ppp) cc_final: 0.3900 (ppp) REVERT: A 142 MET cc_start: 0.7921 (mmm) cc_final: 0.7308 (tpt) REVERT: A 166 ASN cc_start: 0.9389 (m110) cc_final: 0.9127 (m110) REVERT: A 188 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7230 (pmt-80) REVERT: A 245 ASN cc_start: 0.9503 (m-40) cc_final: 0.9141 (m110) REVERT: A 362 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8559 (tptp) REVERT: D 188 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8174 (pmt-80) REVERT: D 301 MET cc_start: 0.9010 (tpp) cc_final: 0.8666 (tpp) outliers start: 11 outliers final: 5 residues processed: 117 average time/residue: 0.1356 time to fit residues: 23.5434 Evaluate side-chains 110 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 16 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 182 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.054537 restraints weight = 38264.880| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.44 r_work: 0.2675 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15443 Z= 0.137 Angle : 0.505 12.903 20952 Z= 0.264 Chirality : 0.041 0.143 2380 Planarity : 0.003 0.048 2666 Dihedral : 12.569 88.982 2461 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.77 % Allowed : 7.57 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1912 helix: 1.46 (0.17), residues: 914 sheet: -0.10 (0.30), residues: 308 loop : 0.37 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 115 TYR 0.028 0.001 TYR C 388 PHE 0.011 0.001 PHE A 187 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (15443) covalent geometry : angle 0.50544 / 0.26 (20952) hydrogen bonds : bond 0.02751 / 2.40 ( 799) hydrogen bonds : angle 4.03883 / 3.30 ( 2235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.533 Fit side-chains REVERT: C 134 ASN cc_start: 0.9394 (m110) cc_final: 0.9061 (m110) REVERT: C 152 MET cc_start: 0.8996 (tpt) cc_final: 0.8715 (tmm) REVERT: C 335 MET cc_start: 0.3104 (ppp) cc_final: 0.2628 (ppp) REVERT: F 89 ASN cc_start: 0.8826 (m110) cc_final: 0.8469 (m110) REVERT: F 115 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7653 (ttt90) REVERT: F 159 CYS cc_start: 0.7946 (p) cc_final: 0.7431 (p) REVERT: F 166 ASN cc_start: 0.9380 (m-40) cc_final: 0.9085 (m-40) REVERT: F 285 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8263 (mp) REVERT: F 335 MET cc_start: 0.3291 (ppp) cc_final: 0.1473 (ptp) REVERT: B 188 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.6507 (pmt-80) REVERT: E 93 MET cc_start: 0.8660 (tpt) cc_final: 0.8394 (tpt) REVERT: E 115 ARG cc_start: 0.8961 (mmm-85) cc_final: 0.8562 (mmm160) REVERT: E 126 GLU cc_start: 0.8666 (tp30) cc_final: 0.8277 (tp30) REVERT: E 234 GLN cc_start: 0.9017 (mm110) cc_final: 0.8639 (mm110) REVERT: E 286 TYR cc_start: 0.9305 (m-80) cc_final: 0.8842 (m-80) REVERT: E 335 MET cc_start: 0.5099 (ppp) cc_final: 0.3888 (ppp) REVERT: A 142 MET cc_start: 0.7917 (mmm) cc_final: 0.7321 (tpt) REVERT: A 166 ASN cc_start: 0.9386 (m110) cc_final: 0.9133 (m110) REVERT: A 188 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7166 (pmt-80) REVERT: A 245 ASN cc_start: 0.9503 (m-40) cc_final: 0.9144 (m110) REVERT: A 362 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8589 (tptp) REVERT: D 188 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8078 (pmt-80) REVERT: D 301 MET cc_start: 0.9005 (tpp) cc_final: 0.8658 (tpp) outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.1416 time to fit residues: 24.1204 Evaluate side-chains 114 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.055063 restraints weight = 38015.654| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.45 r_work: 0.2694 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15443 Z= 0.120 Angle : 0.502 13.125 20952 Z= 0.262 Chirality : 0.041 0.145 2380 Planarity : 0.003 0.045 2666 Dihedral : 12.369 89.368 2461 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.77 % Allowed : 7.77 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1912 helix: 1.37 (0.17), residues: 938 sheet: -0.01 (0.30), residues: 308 loop : 0.37 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.011 0.001 TYR C 388 PHE 0.011 0.001 PHE A 187 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (15443) covalent geometry : angle 0.50234 / 0.26 (20952) hydrogen bonds : bond 0.02648 / 2.32 ( 799) hydrogen bonds : angle 3.95218 / 3.23 ( 2235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.594 Fit side-chains REVERT: C 134 ASN cc_start: 0.9393 (m110) cc_final: 0.9057 (m110) REVERT: C 152 MET cc_start: 0.8957 (tpt) cc_final: 0.8676 (tmm) REVERT: C 335 MET cc_start: 0.3199 (ppp) cc_final: 0.2774 (ppp) REVERT: F 89 ASN cc_start: 0.8811 (m110) cc_final: 0.8450 (m110) REVERT: F 115 ARG cc_start: 0.8066 (ttt90) cc_final: 0.7691 (ttt90) REVERT: F 159 CYS cc_start: 0.7897 (p) cc_final: 0.7386 (p) REVERT: F 166 ASN cc_start: 0.9381 (m-40) cc_final: 0.9101 (m110) REVERT: F 285 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8232 (mp) REVERT: F 335 MET cc_start: 0.3520 (ppp) cc_final: 0.2226 (pmm) REVERT: B 188 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6482 (pmt-80) REVERT: E 93 MET cc_start: 0.8673 (tpt) cc_final: 0.8404 (tpt) REVERT: E 126 GLU cc_start: 0.8665 (tp30) cc_final: 0.8227 (tp30) REVERT: E 234 GLN cc_start: 0.8996 (mm110) cc_final: 0.8621 (mm110) REVERT: E 286 TYR cc_start: 0.9296 (m-80) cc_final: 0.8851 (m-80) REVERT: E 335 MET cc_start: 0.5086 (ppp) cc_final: 0.3874 (ppp) REVERT: A 142 MET cc_start: 0.7918 (mmm) cc_final: 0.7330 (tpt) REVERT: A 166 ASN cc_start: 0.9390 (m110) cc_final: 0.9153 (m110) REVERT: A 188 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7189 (pmt-80) REVERT: A 245 ASN cc_start: 0.9497 (m-40) cc_final: 0.9166 (m110) REVERT: A 362 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8584 (tptp) REVERT: D 188 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8090 (pmt-80) REVERT: D 301 MET cc_start: 0.9008 (tpp) cc_final: 0.8655 (tpp) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 0.1286 time to fit residues: 22.3690 Evaluate side-chains 113 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 167 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 234 GLN F 87 GLN F 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.074280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.054171 restraints weight = 38425.719| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.43 r_work: 0.2665 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15443 Z= 0.177 Angle : 0.543 11.665 20952 Z= 0.279 Chirality : 0.041 0.161 2380 Planarity : 0.003 0.045 2666 Dihedral : 12.301 88.650 2461 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.77 % Allowed : 7.89 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1912 helix: 1.49 (0.18), residues: 914 sheet: -0.05 (0.31), residues: 296 loop : 0.26 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 115 TYR 0.012 0.001 TYR C 388 PHE 0.010 0.001 PHE A 187 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (15443) covalent geometry : angle 0.54336 / 0.28 (20952) hydrogen bonds : bond 0.02823 / 2.46 ( 799) hydrogen bonds : angle 4.02476 / 3.31 ( 2235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.612 Fit side-chains REVERT: C 134 ASN cc_start: 0.9399 (m110) cc_final: 0.9062 (m110) REVERT: C 152 MET cc_start: 0.8985 (tpt) cc_final: 0.8692 (tmm) REVERT: C 335 MET cc_start: 0.3470 (ppp) cc_final: 0.3077 (ppp) REVERT: F 89 ASN cc_start: 0.8816 (m110) cc_final: 0.8464 (m110) REVERT: F 115 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7684 (ttt90) REVERT: F 159 CYS cc_start: 0.7962 (p) cc_final: 0.7442 (p) REVERT: F 166 ASN cc_start: 0.9388 (m110) cc_final: 0.9150 (m110) REVERT: F 285 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8270 (mp) REVERT: F 335 MET cc_start: 0.3396 (ppp) cc_final: 0.1587 (ptp) REVERT: B 188 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.6527 (pmt-80) REVERT: E 93 MET cc_start: 0.8691 (tpt) cc_final: 0.8432 (tpt) REVERT: E 126 GLU cc_start: 0.8683 (tp30) cc_final: 0.8236 (tp30) REVERT: E 234 GLN cc_start: 0.9013 (mm110) cc_final: 0.8653 (mm110) REVERT: E 286 TYR cc_start: 0.9334 (m-80) cc_final: 0.8960 (m-80) REVERT: E 335 MET cc_start: 0.5126 (ppp) cc_final: 0.3891 (ppp) REVERT: A 142 MET cc_start: 0.7929 (mmm) cc_final: 0.7336 (tpt) REVERT: A 166 ASN cc_start: 0.9394 (m110) cc_final: 0.9139 (m110) REVERT: A 188 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7250 (pmt-80) REVERT: A 245 ASN cc_start: 0.9498 (m-40) cc_final: 0.9152 (m110) REVERT: A 362 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8559 (tptp) REVERT: D 188 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7844 (pmt-80) REVERT: D 301 MET cc_start: 0.9015 (tpp) cc_final: 0.8665 (tpp) outliers start: 12 outliers final: 7 residues processed: 111 average time/residue: 0.1340 time to fit residues: 22.0127 Evaluate side-chains 112 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 96 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.054562 restraints weight = 38045.018| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.43 r_work: 0.2679 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15443 Z= 0.148 Angle : 0.524 12.136 20952 Z= 0.270 Chirality : 0.041 0.154 2380 Planarity : 0.003 0.044 2666 Dihedral : 12.242 88.026 2461 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.77 % Allowed : 7.70 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1912 helix: 1.37 (0.17), residues: 938 sheet: -0.03 (0.30), residues: 308 loop : 0.33 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.014 0.001 TYR C 388 PHE 0.010 0.001 PHE A 187 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15443) covalent geometry : angle 0.52440 / 0.27 (20952) hydrogen bonds : bond 0.02725 / 2.38 ( 799) hydrogen bonds : angle 3.97605 / 3.26 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3027.39 seconds wall clock time: 52 minutes 52.93 seconds (3172.93 seconds total)