Starting phenix.real_space_refine on Fri Jul 3 16:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d46_46550/07_2026/9d46_46550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d46_46550/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9d46_46550/07_2026/9d46_46550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d46_46550/07_2026/9d46_46550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d46_46550/07_2026/9d46_46550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d46_46550/07_2026/9d46_46550.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.33, 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: 1.00 Conformation dependent library (CDL) restraints added in 613.4 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: 0.39 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: 2.37 Time building geometry restraints manager: 1.39 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 13.050 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- 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 : 0.502 10.025 20952 Z= 0.323 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 0.50217 / 0.32 (20952) hydrogen bonds : bond 0.17019 / 15.47 ( 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 : 0.506 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: 0.1191 time to fit residues: 21.8759 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 : 0.576 ------------------------------------------------------------------------------- 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: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 2.1302 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.075892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.055286 restraints weight = 38411.656| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.48 r_work: 0.2714 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15443 Z= 0.165 Angle : 0.526 9.667 20952 Z= 0.282 Chirality : 0.043 0.149 2380 Planarity : 0.004 0.048 2666 Dihedral : 14.112 83.712 2461 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.26 % Allowed : 3.27 % Favored : 96.47 % 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: 1.43 (0.20), residues: 1912 helix: 1.53 (0.18), residues: 896 sheet: 0.56 (0.30), residues: 308 loop : 0.56 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 287 TYR 0.010 0.001 TYR B 249 PHE 0.024 0.001 PHE A 187 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (15443) covalent geometry : angle 0.52587 / 0.28 (20952) hydrogen bonds : bond 0.03779 / 3.34 ( 799) hydrogen bonds : angle 4.77367 / 3.92 ( 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 120 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.629 Fit side-chains REVERT: C 134 ASN cc_start: 0.9345 (m110) cc_final: 0.9042 (m110) REVERT: C 388 TYR cc_start: 0.8411 (m-10) cc_final: 0.8145 (m-10) REVERT: F 89 ASN cc_start: 0.8973 (m110) cc_final: 0.8627 (m110) REVERT: F 159 CYS cc_start: 0.7953 (p) cc_final: 0.7542 (p) REVERT: F 166 ASN cc_start: 0.9434 (m-40) cc_final: 0.9144 (m110) REVERT: B 364 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8784 (ttpt) REVERT: E 120 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8847 (pp20) REVERT: E 126 GLU cc_start: 0.8627 (tp30) cc_final: 0.8174 (tp30) REVERT: E 134 ASN cc_start: 0.9377 (m110) cc_final: 0.9172 (m-40) REVERT: E 166 ASN cc_start: 0.9136 (m110) cc_final: 0.8813 (m110) REVERT: E 286 TYR cc_start: 0.9319 (m-80) cc_final: 0.9021 (m-80) REVERT: E 335 MET cc_start: 0.5137 (ppp) cc_final: 0.3902 (ppp) REVERT: A 142 MET cc_start: 0.7720 (mmm) cc_final: 0.7274 (tpt) REVERT: A 166 ASN cc_start: 0.9388 (m110) cc_final: 0.9147 (m110) REVERT: A 245 ASN cc_start: 0.9441 (m-40) cc_final: 0.9067 (m110) REVERT: D 301 MET cc_start: 0.9062 (tpp) cc_final: 0.8708 (tpp) outliers start: 4 outliers final: 4 residues processed: 120 average time/residue: 0.1275 time to fit residues: 23.0598 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 : 0.564 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.074452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.053836 restraints weight = 38381.031| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.44 r_work: 0.2678 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1379 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= 0.197 Angle : 0.521 10.993 20952 Z= 0.276 Chirality : 0.043 0.143 2380 Planarity : 0.004 0.048 2666 Dihedral : 13.546 87.425 2461 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.39 % Allowed : 4.88 % Favored : 94.74 % 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 : 0.42 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.016 0.001 TYR C 388 PHE 0.017 0.001 PHE B 187 HIS 0.003 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (15443) covalent geometry : angle 0.52073 / 0.28 (20952) hydrogen bonds : bond 0.03354 / 2.93 ( 799) hydrogen bonds : angle 4.42341 / 3.63 ( 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 116 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.608 Fit side-chains REVERT: C 134 ASN cc_start: 0.9360 (m110) cc_final: 0.9031 (m110) REVERT: C 152 MET cc_start: 0.9050 (tpt) cc_final: 0.8752 (tmm) REVERT: F 89 ASN cc_start: 0.8977 (m110) cc_final: 0.8638 (m110) REVERT: F 166 ASN cc_start: 0.9425 (m-40) cc_final: 0.9134 (m110) REVERT: F 285 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8261 (mp) REVERT: F 335 MET cc_start: 0.3097 (ppp) cc_final: 0.1453 (ptp) REVERT: B 364 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8812 (ttpt) REVERT: E 126 GLU cc_start: 0.8607 (tp30) cc_final: 0.8198 (tp30) REVERT: E 234 GLN cc_start: 0.9051 (mm110) cc_final: 0.8737 (mm110) REVERT: E 335 MET cc_start: 0.5295 (ppp) cc_final: 0.4139 (ppp) REVERT: A 142 MET cc_start: 0.7747 (mmm) cc_final: 0.7234 (tpt) REVERT: A 166 ASN cc_start: 0.9394 (m110) cc_final: 0.9134 (m110) REVERT: A 245 ASN cc_start: 0.9453 (m-40) cc_final: 0.9069 (m110) REVERT: D 301 MET cc_start: 0.9051 (tpp) cc_final: 0.8707 (tpp) outliers start: 6 outliers final: 3 residues processed: 116 average time/residue: 0.1150 time to fit residues: 20.5688 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 : 0.643 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 96 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 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 = 0.3278 r_free = 0.3278 target = 0.073184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.052810 restraints weight = 38773.008| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.44 r_work: 0.2633 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15443 Z= 0.247 Angle : 0.550 8.366 20952 Z= 0.289 Chirality : 0.043 0.147 2380 Planarity : 0.004 0.045 2666 Dihedral : 13.224 89.679 2461 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.51 % Allowed : 5.71 % Favored : 93.77 % 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: 1.47 (0.18), residues: 914 sheet: -0.23 (0.29), residues: 312 loop : 0.43 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.012 0.001 TYR B 249 PHE 0.013 0.001 PHE B 187 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (15443) covalent geometry : angle 0.55047 / 0.29 (20952) hydrogen bonds : bond 0.03300 / 2.91 ( 799) hydrogen bonds : angle 4.38184 / 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: 8 poor density : 100 time to evaluate : 0.585 Fit side-chains REVERT: C 134 ASN cc_start: 0.9383 (m110) cc_final: 0.9062 (m110) REVERT: C 152 MET cc_start: 0.9037 (tpt) cc_final: 0.8779 (tmm) REVERT: F 89 ASN cc_start: 0.8897 (m110) cc_final: 0.8540 (m110) REVERT: F 166 ASN cc_start: 0.9394 (m-40) cc_final: 0.9082 (m-40) REVERT: F 285 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 142 MET cc_start: 0.9164 (mmp) cc_final: 0.8958 (mmp) REVERT: E 126 GLU cc_start: 0.8551 (tp30) cc_final: 0.8136 (tp30) REVERT: E 234 GLN cc_start: 0.9034 (mm110) cc_final: 0.8698 (mm110) REVERT: E 335 MET cc_start: 0.5217 (ppp) cc_final: 0.3943 (ppp) REVERT: A 142 MET cc_start: 0.7789 (mmm) cc_final: 0.7250 (tpt) REVERT: A 166 ASN cc_start: 0.9395 (m110) cc_final: 0.9116 (m110) REVERT: A 188 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7300 (pmt-80) REVERT: A 234 GLN cc_start: 0.9025 (mm110) cc_final: 0.8746 (mm110) REVERT: A 245 ASN cc_start: 0.9484 (m-40) cc_final: 0.9128 (m110) REVERT: D 188 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8176 (pmt-80) REVERT: D 301 MET cc_start: 0.9060 (tpp) cc_final: 0.8735 (tpp) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.1291 time to fit residues: 20.7458 Evaluate side-chains 102 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 192 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 234 GLN E 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.054658 restraints weight = 39126.785| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.41 r_work: 0.2642 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15443 Z= 0.195 Angle : 0.522 12.858 20952 Z= 0.275 Chirality : 0.042 0.142 2380 Planarity : 0.003 0.039 2666 Dihedral : 13.069 89.536 2461 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.64 % Allowed : 6.42 % 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: 1.06 (0.19), residues: 1912 helix: 1.45 (0.18), residues: 910 sheet: -0.31 (0.29), residues: 312 loop : 0.36 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 312 TYR 0.012 0.001 TYR C 388 PHE 0.012 0.001 PHE A 187 HIS 0.002 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (15443) covalent geometry : angle 0.52163 / 0.27 (20952) hydrogen bonds : bond 0.03115 / 2.73 ( 799) hydrogen bonds : angle 4.25779 / 3.47 ( 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 111 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.533 Fit side-chains REVERT: C 93 MET cc_start: 0.9100 (tpp) cc_final: 0.8715 (tpp) REVERT: C 97 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9136 (mmmt) REVERT: C 134 ASN cc_start: 0.9388 (m110) cc_final: 0.9061 (m110) REVERT: C 152 MET cc_start: 0.9036 (tpt) cc_final: 0.8762 (tmm) REVERT: F 89 ASN cc_start: 0.8881 (m110) cc_final: 0.8527 (m110) REVERT: F 166 ASN cc_start: 0.9392 (m-40) cc_final: 0.9088 (m-40) REVERT: F 285 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8323 (mp) REVERT: F 335 MET cc_start: 0.3014 (ppp) cc_final: 0.1610 (pmm) REVERT: E 126 GLU cc_start: 0.8630 (tp30) cc_final: 0.8194 (tp30) REVERT: E 234 GLN cc_start: 0.9013 (mm110) cc_final: 0.8668 (mm110) REVERT: E 335 MET cc_start: 0.5233 (ppp) cc_final: 0.3920 (ppp) REVERT: A 142 MET cc_start: 0.7921 (mmm) cc_final: 0.7301 (tpt) REVERT: A 166 ASN cc_start: 0.9383 (m110) cc_final: 0.9104 (m110) REVERT: A 188 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7304 (pmt-80) REVERT: A 245 ASN cc_start: 0.9497 (m-40) cc_final: 0.9119 (m110) REVERT: D 188 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8121 (pmt-80) REVERT: D 301 MET cc_start: 0.9034 (tpp) cc_final: 0.8705 (tpp) outliers start: 10 outliers final: 3 residues processed: 111 average time/residue: 0.1060 time to fit residues: 17.9726 Evaluate side-chains 105 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 234 GLN C 330 GLN F 330 GLN D 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.054954 restraints weight = 38060.676| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.45 r_work: 0.2689 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15443 Z= 0.113 Angle : 0.481 10.205 20952 Z= 0.257 Chirality : 0.041 0.142 2380 Planarity : 0.003 0.032 2666 Dihedral : 12.860 89.794 2461 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.58 % Allowed : 7.32 % Favored : 92.11 % 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: 1.40 (0.17), residues: 918 sheet: -0.09 (0.30), residues: 308 loop : 0.37 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 115 TYR 0.014 0.001 TYR A 249 PHE 0.012 0.001 PHE A 187 HIS 0.002 0.000 HIS F 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15443) covalent geometry : angle 0.48102 / 0.26 (20952) hydrogen bonds : bond 0.02735 / 2.41 ( 799) hydrogen bonds : angle 4.03600 / 3.30 ( 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 120 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.605 Fit side-chains REVERT: C 134 ASN cc_start: 0.9385 (m110) cc_final: 0.9046 (m110) REVERT: C 152 MET cc_start: 0.8994 (tpt) cc_final: 0.8726 (tmm) REVERT: C 388 TYR cc_start: 0.8395 (m-10) cc_final: 0.8128 (m-10) REVERT: F 89 ASN cc_start: 0.8844 (m110) cc_final: 0.8474 (m110) REVERT: F 115 ARG cc_start: 0.8024 (ttt90) cc_final: 0.7640 (ttt90) REVERT: F 159 CYS cc_start: 0.7938 (p) cc_final: 0.7460 (p) REVERT: F 166 ASN cc_start: 0.9381 (m-40) cc_final: 0.9086 (m110) REVERT: F 285 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 188 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.6486 (pmt-80) REVERT: E 126 GLU cc_start: 0.8669 (tp30) cc_final: 0.8200 (tp30) REVERT: E 234 GLN cc_start: 0.9014 (mm110) cc_final: 0.8649 (mm110) REVERT: E 268 MET cc_start: 0.8907 (mtp) cc_final: 0.8700 (ptp) REVERT: E 335 MET cc_start: 0.5153 (ppp) cc_final: 0.3894 (ppp) REVERT: A 122 LYS cc_start: 0.9050 (pptt) cc_final: 0.8850 (pptt) REVERT: A 142 MET cc_start: 0.7901 (mmm) cc_final: 0.7296 (tpt) REVERT: A 166 ASN cc_start: 0.9381 (m110) cc_final: 0.9135 (m110) REVERT: A 188 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7268 (pmt-80) REVERT: A 245 ASN cc_start: 0.9496 (m-40) cc_final: 0.9180 (m110) REVERT: D 188 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8197 (pmt-80) REVERT: D 301 MET cc_start: 0.8999 (tpp) cc_final: 0.8645 (tpp) outliers start: 9 outliers final: 4 residues processed: 120 average time/residue: 0.1351 time to fit residues: 24.1747 Evaluate side-chains 110 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 147 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 26 optimal weight: 0.0070 chunk 123 optimal weight: 0.0670 chunk 142 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.076171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056101 restraints weight = 37739.788| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.44 r_work: 0.2720 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15443 Z= 0.098 Angle : 0.491 15.810 20952 Z= 0.258 Chirality : 0.040 0.137 2380 Planarity : 0.003 0.031 2666 Dihedral : 12.627 88.376 2461 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.58 % Allowed : 7.96 % 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: 1.09 (0.20), residues: 1912 helix: 1.35 (0.17), residues: 938 sheet: 0.01 (0.30), residues: 308 loop : 0.38 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.010 0.001 TYR C 388 PHE 0.013 0.001 PHE A 187 HIS 0.003 0.000 HIS F 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (15443) covalent geometry : angle 0.49121 / 0.26 (20952) hydrogen bonds : bond 0.02559 / 2.25 ( 799) hydrogen bonds : angle 3.92534 / 3.22 ( 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 120 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.665 Fit side-chains REVERT: C 134 ASN cc_start: 0.9386 (m110) cc_final: 0.9039 (m110) REVERT: C 152 MET cc_start: 0.8949 (tpt) cc_final: 0.8682 (tmm) REVERT: C 388 TYR cc_start: 0.8393 (m-10) cc_final: 0.8114 (m-10) REVERT: F 89 ASN cc_start: 0.8823 (m110) cc_final: 0.8450 (m110) REVERT: F 115 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7692 (ttt90) REVERT: F 159 CYS cc_start: 0.7835 (p) cc_final: 0.7357 (p) REVERT: F 166 ASN cc_start: 0.9381 (m-40) cc_final: 0.9125 (m110) REVERT: F 285 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8201 (mp) REVERT: F 335 MET cc_start: 0.3174 (ppp) cc_final: 0.1834 (pmm) REVERT: B 188 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.6404 (pmt-80) REVERT: E 126 GLU cc_start: 0.8669 (tp30) cc_final: 0.8138 (tp30) REVERT: E 234 GLN cc_start: 0.8993 (mm110) cc_final: 0.8634 (mm110) REVERT: E 286 TYR cc_start: 0.9294 (m-80) cc_final: 0.8793 (m-80) REVERT: E 335 MET cc_start: 0.5141 (ppp) cc_final: 0.3886 (ppp) REVERT: A 122 LYS cc_start: 0.9062 (pptt) cc_final: 0.8848 (pptt) REVERT: A 142 MET cc_start: 0.7892 (mmm) cc_final: 0.7304 (tpt) REVERT: A 166 ASN cc_start: 0.9380 (m110) cc_final: 0.9162 (m110) REVERT: A 188 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7317 (pmt-80) REVERT: A 245 ASN cc_start: 0.9494 (m-40) cc_final: 0.9186 (m110) REVERT: D 152 MET cc_start: 0.9149 (ttm) cc_final: 0.8916 (tmm) REVERT: D 188 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8233 (pmt-80) REVERT: D 301 MET cc_start: 0.9001 (tpp) cc_final: 0.8644 (tpp) REVERT: D 353 SER cc_start: 0.9481 (m) cc_final: 0.9276 (m) outliers start: 9 outliers final: 4 residues processed: 120 average time/residue: 0.1339 time to fit residues: 23.9516 Evaluate side-chains 113 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 188 ARG Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 345 ILE 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: 1.9990 chunk 177 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 157 optimal weight: 0.0040 chunk 150 optimal weight: 0.0470 chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.4096 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.074572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.054377 restraints weight = 38319.534| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.45 r_work: 0.2673 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15443 Z= 0.166 Angle : 0.514 12.636 20952 Z= 0.269 Chirality : 0.041 0.142 2380 Planarity : 0.003 0.051 2666 Dihedral : 12.542 89.887 2461 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.58 % Allowed : 8.02 % Favored : 91.40 % 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: 1.17 (0.20), residues: 1912 helix: 1.51 (0.18), residues: 914 sheet: -0.04 (0.30), residues: 308 loop : 0.35 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 115 TYR 0.022 0.001 TYR A 249 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 0.00368 / 0.17 (15443) covalent geometry : angle 0.51432 / 0.27 (20952) hydrogen bonds : bond 0.02797 / 2.45 ( 799) hydrogen bonds : angle 3.98685 / 3.26 ( 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 112 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.626 Fit side-chains REVERT: C 134 ASN cc_start: 0.9401 (m110) cc_final: 0.9068 (m110) REVERT: C 152 MET cc_start: 0.8980 (tpt) cc_final: 0.8706 (tmm) REVERT: C 335 MET cc_start: 0.3130 (ppp) cc_final: 0.2606 (ppp) REVERT: C 388 TYR cc_start: 0.8406 (m-10) cc_final: 0.8108 (m-10) REVERT: F 89 ASN cc_start: 0.8829 (m110) cc_final: 0.8461 (m110) REVERT: F 115 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7702 (ttt90) REVERT: F 159 CYS cc_start: 0.7964 (p) cc_final: 0.7474 (p) REVERT: F 166 ASN cc_start: 0.9384 (m-40) cc_final: 0.9099 (m110) REVERT: F 285 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8242 (mp) REVERT: F 335 MET cc_start: 0.3396 (ppp) cc_final: 0.1510 (ptp) REVERT: B 188 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.6507 (pmt-80) REVERT: E 126 GLU cc_start: 0.8655 (tp30) cc_final: 0.8194 (tp30) REVERT: E 234 GLN cc_start: 0.9009 (mm110) cc_final: 0.8624 (mm110) REVERT: E 286 TYR cc_start: 0.9332 (m-80) cc_final: 0.8877 (m-80) REVERT: E 335 MET cc_start: 0.5096 (ppp) cc_final: 0.3859 (ppp) REVERT: A 122 LYS cc_start: 0.9076 (pptt) cc_final: 0.8854 (pptt) REVERT: A 142 MET cc_start: 0.7915 (mmm) cc_final: 0.7344 (tpt) REVERT: A 166 ASN cc_start: 0.9393 (m110) cc_final: 0.9155 (m110) REVERT: A 188 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7220 (pmt-80) REVERT: A 245 ASN cc_start: 0.9506 (m-40) cc_final: 0.9198 (m110) REVERT: A 362 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8584 (tptp) REVERT: D 152 MET cc_start: 0.9157 (ttm) cc_final: 0.8925 (tmm) REVERT: D 188 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7872 (pmt-80) REVERT: D 301 MET cc_start: 0.9032 (tpp) cc_final: 0.8689 (tpp) outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 0.1441 time to fit residues: 23.9436 Evaluate side-chains 110 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 35 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.075903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.055800 restraints weight = 37984.689| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.46 r_work: 0.2712 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15443 Z= 0.108 Angle : 0.498 12.843 20952 Z= 0.260 Chirality : 0.041 0.140 2380 Planarity : 0.003 0.045 2666 Dihedral : 12.381 87.969 2461 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.51 % Allowed : 8.02 % 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: 1.16 (0.20), residues: 1912 helix: 1.49 (0.17), residues: 914 sheet: 0.03 (0.30), residues: 308 loop : 0.33 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 312 TYR 0.022 0.001 TYR A 249 PHE 0.011 0.001 PHE A 187 HIS 0.002 0.000 HIS F 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (15443) covalent geometry : angle 0.49777 / 0.26 (20952) hydrogen bonds : bond 0.02558 / 2.24 ( 799) hydrogen bonds : angle 3.87890 / 3.17 ( 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 112 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.619 Fit side-chains REVERT: C 134 ASN cc_start: 0.9398 (m110) cc_final: 0.9062 (m110) REVERT: C 152 MET cc_start: 0.8949 (tpt) cc_final: 0.8686 (tmm) REVERT: C 335 MET cc_start: 0.3133 (ppp) cc_final: 0.2696 (ppp) REVERT: F 89 ASN cc_start: 0.8794 (m110) cc_final: 0.8426 (m110) REVERT: F 115 ARG cc_start: 0.8089 (ttt90) cc_final: 0.7721 (ttt90) REVERT: F 159 CYS cc_start: 0.7834 (p) cc_final: 0.7342 (p) REVERT: F 166 ASN cc_start: 0.9380 (m-40) cc_final: 0.9148 (m110) REVERT: F 285 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8183 (mp) REVERT: F 335 MET cc_start: 0.3494 (ppp) cc_final: 0.2187 (pmm) REVERT: B 188 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.6461 (pmt-80) REVERT: B 350 MET cc_start: 0.9121 (tpt) cc_final: 0.8445 (tpt) REVERT: E 234 GLN cc_start: 0.8981 (mm110) cc_final: 0.8607 (mm110) REVERT: E 249 TYR cc_start: 0.8675 (t80) cc_final: 0.8177 (t80) REVERT: E 286 TYR cc_start: 0.9291 (m-80) cc_final: 0.8847 (m-80) REVERT: E 335 MET cc_start: 0.5022 (ppp) cc_final: 0.3811 (ppp) REVERT: A 122 LYS cc_start: 0.9061 (pptt) cc_final: 0.8845 (pptt) REVERT: A 142 MET cc_start: 0.8129 (mmm) cc_final: 0.7365 (tpt) REVERT: A 166 ASN cc_start: 0.9384 (m110) cc_final: 0.9163 (m110) REVERT: A 188 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7285 (pmt-80) REVERT: A 245 ASN cc_start: 0.9508 (m-40) cc_final: 0.9198 (m110) REVERT: D 152 MET cc_start: 0.9149 (ttm) cc_final: 0.8910 (tmm) REVERT: D 188 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8090 (pmt-80) REVERT: D 301 MET cc_start: 0.9005 (tpp) cc_final: 0.8641 (tpp) outliers start: 8 outliers final: 4 residues processed: 112 average time/residue: 0.1372 time to fit residues: 22.8690 Evaluate side-chains 110 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 167 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.055071 restraints weight = 38400.489| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.42 r_work: 0.2692 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15443 Z= 0.150 Angle : 0.525 12.061 20952 Z= 0.271 Chirality : 0.041 0.141 2380 Planarity : 0.003 0.047 2666 Dihedral : 12.294 88.639 2461 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.58 % Allowed : 8.15 % Favored : 91.27 % 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: 1.19 (0.20), residues: 1912 helix: 1.53 (0.18), residues: 914 sheet: 0.00 (0.30), residues: 308 loop : 0.34 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.040 0.001 TYR D 249 PHE 0.011 0.001 PHE E 150 HIS 0.003 0.000 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15443) covalent geometry : angle 0.52504 / 0.27 (20952) hydrogen bonds : bond 0.02681 / 2.32 ( 799) hydrogen bonds : angle 3.91317 / 3.20 ( 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 113 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.519 Fit side-chains REVERT: C 134 ASN cc_start: 0.9401 (m110) cc_final: 0.9067 (m110) REVERT: C 152 MET cc_start: 0.8950 (tpt) cc_final: 0.8684 (tmm) REVERT: C 335 MET cc_start: 0.3392 (ppp) cc_final: 0.3015 (ppp) REVERT: C 388 TYR cc_start: 0.8377 (m-10) cc_final: 0.8030 (m-10) REVERT: F 89 ASN cc_start: 0.8803 (m110) cc_final: 0.8436 (m110) REVERT: F 115 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7719 (ttt90) REVERT: F 159 CYS cc_start: 0.7900 (p) cc_final: 0.7401 (p) REVERT: F 166 ASN cc_start: 0.9379 (m-40) cc_final: 0.9128 (m110) REVERT: F 285 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8207 (mp) REVERT: F 335 MET cc_start: 0.3400 (ppp) cc_final: 0.1561 (ptp) REVERT: B 188 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.6468 (pmt-80) REVERT: E 126 GLU cc_start: 0.8794 (tp30) cc_final: 0.8288 (tp30) REVERT: E 234 GLN cc_start: 0.8989 (mm110) cc_final: 0.8620 (mm110) REVERT: E 286 TYR cc_start: 0.9331 (m-80) cc_final: 0.8898 (m-80) REVERT: E 335 MET cc_start: 0.5070 (ppp) cc_final: 0.3847 (ppp) REVERT: A 122 LYS cc_start: 0.9078 (pptt) cc_final: 0.8857 (pptt) REVERT: A 142 MET cc_start: 0.8168 (mmm) cc_final: 0.7394 (tpt) REVERT: A 166 ASN cc_start: 0.9392 (m110) cc_final: 0.9162 (m110) REVERT: A 188 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7281 (pmt-80) REVERT: A 245 ASN cc_start: 0.9510 (m-40) cc_final: 0.9202 (m110) REVERT: A 362 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8622 (tptp) REVERT: D 152 MET cc_start: 0.9157 (ttm) cc_final: 0.8926 (tmm) REVERT: D 188 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7823 (pmt-80) REVERT: D 301 MET cc_start: 0.9021 (tpp) cc_final: 0.8662 (tpp) outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.1412 time to fit residues: 23.6332 Evaluate side-chains 112 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054239 restraints weight = 38575.518| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.48 r_work: 0.2651 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2105 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= 0.184 Angle : 0.546 12.317 20952 Z= 0.281 Chirality : 0.042 0.161 2380 Planarity : 0.003 0.046 2666 Dihedral : 12.225 88.523 2461 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.58 % Allowed : 8.28 % Favored : 91.14 % 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: 1.52 (0.18), residues: 914 sheet: -0.11 (0.30), residues: 308 loop : 0.31 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.036 0.001 TYR D 249 PHE 0.010 0.001 PHE A 187 HIS 0.003 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (15443) covalent geometry : angle 0.54633 / 0.28 (20952) hydrogen bonds : bond 0.02863 / 2.49 ( 799) hydrogen bonds : angle 4.01592 / 3.28 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3366.31 seconds wall clock time: 58 minutes 41.91 seconds (3521.91 seconds total)