Starting phenix.real_space_refine on Thu Sep 18 07:45:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d46_46550/09_2025/9d46_46550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d46_46550/09_2025/9d46_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_46550/09_2025/9d46_46550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d46_46550/09_2025/9d46_46550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d46_46550/09_2025/9d46_46550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d46_46550/09_2025/9d46_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-2.0-5805/lib/python3.9/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: 3.94, per 1000 atoms: 0.26 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: 1.33 Conformation dependent library (CDL) restraints added in 618.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.56 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: 2.87 Time building geometry restraints manager: 1.76 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=" N ARG D 308 " pdb=" CA ARG D 308 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.19e-02 7.06e+03 3.63e+00 bond pdb=" N ARG E 188 " pdb=" CA ARG E 188 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.96e+00 bond pdb=" CA ARG B 188 " pdb=" CB ARG B 188 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.27e+00 bond pdb=" CB LYS E 122 " pdb=" CG LYS E 122 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" C1' DT X 17 " pdb=" N1 DT X 17 " ideal model delta sigma weight residual 1.490 1.521 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 15438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 20712 2.01 - 4.01: 217 4.01 - 6.02: 13 6.02 - 8.02: 7 8.02 - 10.03: 3 Bond angle restraints: 20952 Sorted by residual: angle pdb=" CA ARG B 188 " pdb=" CB ARG B 188 " pdb=" CG ARG B 188 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" N ARG D 308 " pdb=" CA ARG D 308 " pdb=" C ARG D 308 " ideal model delta sigma weight residual 111.07 107.35 3.72 1.07e+00 8.73e-01 1.21e+01 angle pdb=" CB MET C 335 " pdb=" CG MET C 335 " pdb=" SD MET C 335 " ideal model delta sigma weight residual 112.70 122.73 -10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB LYS E 122 " pdb=" CG LYS E 122 " pdb=" CD LYS E 122 " ideal model delta sigma weight residual 111.30 118.90 -7.60 2.30e+00 1.89e-01 1.09e+01 angle pdb=" CA ARG D 188 " pdb=" CB ARG D 188 " pdb=" CG ARG D 188 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+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: 1662 0.033 - 0.067: 461 0.067 - 0.100: 176 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: 1.500 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.740 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 0.032 15443 Z= 0.104 Angle : 0.482 10.025 20952 Z= 0.260 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 aren 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 covalent geometry : bond 0.00212 (15443) covalent geometry : angle 0.48229 (20952) hydrogen bonds : bond 0.17019 ( 799) hydrogen bonds : angle 6.53939 ( 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 : 0.581 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: 0.1427 time to fit residues: 26.1438 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 : 0.512 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.055059 restraints weight = 38350.194| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.49 r_work: 0.2707 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15443 Z= 0.167 Angle : 0.521 9.009 20952 Z= 0.278 Chirality : 0.042 0.145 2380 Planarity : 0.004 0.049 2666 Dihedral : 13.714 89.079 2461 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.26 % Allowed : 3.02 % Favored : 96.73 % 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 aren not related in a simple way. whole: 1.43 (0.20), residues: 1912 helix: 1.54 (0.18), residues: 896 sheet: 0.58 (0.30), residues: 308 loop : 0.53 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.012 0.001 TYR C 388 PHE 0.026 0.001 PHE B 187 HIS 0.001 0.000 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00368 (15443) covalent geometry : angle 0.52075 (20952) hydrogen bonds : bond 0.03410 ( 799) hydrogen bonds : angle 4.59696 ( 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 121 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 134 ASN cc_start: 0.9354 (m110) cc_final: 0.9039 (m110) REVERT: F 89 ASN cc_start: 0.8982 (m110) cc_final: 0.8635 (m110) REVERT: F 159 CYS cc_start: 0.7929 (p) cc_final: 0.7534 (p) REVERT: F 166 ASN cc_start: 0.9417 (m-40) cc_final: 0.9143 (m110) REVERT: B 234 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8811 (mm-40) REVERT: E 126 GLU cc_start: 0.8652 (tp30) cc_final: 0.8202 (tp30) REVERT: E 134 ASN cc_start: 0.9373 (m110) cc_final: 0.9154 (m-40) REVERT: E 166 ASN cc_start: 0.9136 (m110) cc_final: 0.8818 (m110) REVERT: E 234 GLN cc_start: 0.9079 (mm110) cc_final: 0.8783 (mm110) REVERT: E 286 TYR cc_start: 0.9314 (m-80) cc_final: 0.8940 (m-80) REVERT: E 335 MET cc_start: 0.5224 (ppp) cc_final: 0.4029 (ppp) REVERT: A 112 TYR cc_start: 0.8404 (m-10) cc_final: 0.7626 (m-80) REVERT: A 142 MET cc_start: 0.7749 (mmm) cc_final: 0.7245 (tpt) REVERT: A 166 ASN cc_start: 0.9384 (m110) cc_final: 0.9144 (m110) REVERT: A 234 GLN cc_start: 0.9106 (mm110) cc_final: 0.8832 (mm110) REVERT: D 301 MET cc_start: 0.9045 (tpp) cc_final: 0.8689 (tpp) outliers start: 4 outliers final: 4 residues processed: 121 average time/residue: 0.1318 time to fit residues: 23.8969 Evaluate side-chains 111 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 2.9990 chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 180 optimal weight: 0.0980 chunk 174 optimal weight: 4.9990 chunk 161 optimal weight: 0.0570 overall best weight: 2.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.054208 restraints weight = 38146.516| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.53 r_work: 0.2679 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15443 Z= 0.162 Angle : 0.501 10.036 20952 Z= 0.266 Chirality : 0.041 0.140 2380 Planarity : 0.004 0.041 2666 Dihedral : 13.190 87.385 2461 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.32 % Allowed : 4.24 % Favored : 95.44 % 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 aren not related in a simple way. whole: 1.35 (0.20), residues: 1912 helix: 1.58 (0.18), residues: 892 sheet: 0.28 (0.30), residues: 308 loop : 0.47 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 115 TYR 0.017 0.001 TYR C 388 PHE 0.018 0.001 PHE A 187 HIS 0.003 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00360 (15443) covalent geometry : angle 0.50105 (20952) hydrogen bonds : bond 0.03146 ( 799) hydrogen bonds : angle 4.27484 ( 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 121 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: C 134 ASN cc_start: 0.9389 (m110) cc_final: 0.9071 (m110) REVERT: C 388 TYR cc_start: 0.8393 (m-10) cc_final: 0.8082 (m-10) REVERT: F 89 ASN cc_start: 0.8912 (m110) cc_final: 0.8550 (m110) REVERT: F 159 CYS cc_start: 0.7941 (p) cc_final: 0.7520 (p) REVERT: F 166 ASN cc_start: 0.9400 (m-40) cc_final: 0.9122 (m110) REVERT: F 285 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8186 (mp) REVERT: B 307 MET cc_start: 0.9274 (mmm) cc_final: 0.8707 (mmt) REVERT: B 350 MET cc_start: 0.9150 (tpt) cc_final: 0.8654 (tpt) REVERT: E 126 GLU cc_start: 0.8731 (tp30) cc_final: 0.8292 (tp30) REVERT: E 234 GLN cc_start: 0.9025 (mm110) cc_final: 0.8698 (mm110) REVERT: E 286 TYR cc_start: 0.9295 (m-80) cc_final: 0.8863 (m-80) REVERT: E 335 MET cc_start: 0.5206 (ppp) cc_final: 0.3954 (ppp) REVERT: A 142 MET cc_start: 0.7736 (mmm) cc_final: 0.7258 (tpt) REVERT: A 166 ASN cc_start: 0.9373 (m110) cc_final: 0.9132 (m110) REVERT: A 245 ASN cc_start: 0.9455 (m-40) cc_final: 0.9083 (m110) REVERT: D 301 MET cc_start: 0.9032 (tpp) cc_final: 0.8668 (tpp) outliers start: 5 outliers final: 3 residues processed: 121 average time/residue: 0.1188 time to fit residues: 21.8489 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 : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 366 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 2 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 330 GLN D 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055750 restraints weight = 39113.065| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.32 r_work: 0.2657 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15443 Z= 0.214 Angle : 0.538 12.411 20952 Z= 0.280 Chirality : 0.042 0.160 2380 Planarity : 0.004 0.042 2666 Dihedral : 12.955 89.388 2461 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.64 % Allowed : 5.65 % Favored : 93.71 % 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 aren not related in a simple way. whole: 1.22 (0.20), residues: 1912 helix: 1.54 (0.18), residues: 898 sheet: -0.10 (0.29), residues: 312 loop : 0.47 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 115 TYR 0.018 0.001 TYR C 388 PHE 0.013 0.001 PHE A 187 HIS 0.002 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00478 (15443) covalent geometry : angle 0.53802 (20952) hydrogen bonds : bond 0.03128 ( 799) hydrogen bonds : angle 4.25015 ( 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 114 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.393 Fit side-chains REVERT: C 97 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9113 (mmmt) REVERT: C 134 ASN cc_start: 0.9384 (m110) cc_final: 0.9056 (m110) REVERT: F 89 ASN cc_start: 0.8873 (m110) cc_final: 0.8505 (m110) REVERT: F 166 ASN cc_start: 0.9397 (m-40) cc_final: 0.9080 (m-40) REVERT: F 285 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8282 (mp) REVERT: F 335 MET cc_start: 0.3465 (ppp) cc_final: 0.2052 (pmm) REVERT: E 115 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8629 (mmm160) REVERT: E 126 GLU cc_start: 0.8710 (tp30) cc_final: 0.8270 (tp30) REVERT: E 234 GLN cc_start: 0.9014 (mm110) cc_final: 0.8663 (mm110) REVERT: E 249 TYR cc_start: 0.9067 (t80) cc_final: 0.8846 (t80) REVERT: E 286 TYR cc_start: 0.9321 (m-80) cc_final: 0.8985 (m-80) REVERT: E 335 MET cc_start: 0.5224 (ppp) cc_final: 0.3925 (ppp) REVERT: A 142 MET cc_start: 0.7821 (mmm) cc_final: 0.7282 (tpt) REVERT: A 166 ASN cc_start: 0.9396 (m110) cc_final: 0.9126 (m110) REVERT: A 188 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7443 (pmt-80) REVERT: A 245 ASN cc_start: 0.9480 (m-40) cc_final: 0.9109 (m110) REVERT: D 188 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8127 (pmt-80) REVERT: D 301 MET cc_start: 0.9029 (tpp) cc_final: 0.8681 (tpp) outliers start: 10 outliers final: 3 residues processed: 113 average time/residue: 0.1406 time to fit residues: 23.4405 Evaluate side-chains 106 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 38 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.054092 restraints weight = 38453.533| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.43 r_work: 0.2667 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15443 Z= 0.164 Angle : 0.500 9.149 20952 Z= 0.263 Chirality : 0.041 0.142 2380 Planarity : 0.003 0.037 2666 Dihedral : 12.801 89.965 2461 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.64 % Allowed : 6.29 % Favored : 93.07 % 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 aren not related in a simple way. whole: 1.22 (0.20), residues: 1912 helix: 1.50 (0.17), residues: 910 sheet: -0.16 (0.30), residues: 312 loop : 0.55 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 115 TYR 0.011 0.001 TYR E 249 PHE 0.012 0.001 PHE A 187 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00366 (15443) covalent geometry : angle 0.49979 (20952) hydrogen bonds : bond 0.02885 ( 799) hydrogen bonds : angle 4.10312 ( 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 114 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.856 Fit side-chains REVERT: C 134 ASN cc_start: 0.9393 (m110) cc_final: 0.9058 (m110) REVERT: F 89 ASN cc_start: 0.8853 (m110) cc_final: 0.8477 (m110) REVERT: F 159 CYS cc_start: 0.7938 (p) cc_final: 0.7486 (p) REVERT: F 166 ASN cc_start: 0.9384 (m-40) cc_final: 0.9068 (m110) REVERT: F 285 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8261 (mp) REVERT: E 115 ARG cc_start: 0.8990 (mmm-85) cc_final: 0.8633 (mmm160) REVERT: E 126 GLU cc_start: 0.8641 (tp30) cc_final: 0.8183 (tp30) REVERT: E 234 GLN cc_start: 0.9017 (mm110) cc_final: 0.8656 (mm110) REVERT: E 249 TYR cc_start: 0.9093 (t80) cc_final: 0.8802 (t80) REVERT: E 286 TYR cc_start: 0.9321 (m-80) cc_final: 0.8894 (m-80) REVERT: E 335 MET cc_start: 0.5249 (ppp) cc_final: 0.3962 (ppp) REVERT: A 122 LYS cc_start: 0.9062 (pptt) cc_final: 0.8850 (pptt) REVERT: A 142 MET cc_start: 0.7913 (mmm) cc_final: 0.7291 (tpt) REVERT: A 166 ASN cc_start: 0.9389 (m110) cc_final: 0.9125 (m110) REVERT: A 188 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7438 (pmt-80) REVERT: A 245 ASN cc_start: 0.9494 (m-40) cc_final: 0.9131 (m110) REVERT: D 188 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8107 (pmt-80) REVERT: D 301 MET cc_start: 0.9004 (tpp) cc_final: 0.8649 (tpp) outliers start: 10 outliers final: 4 residues processed: 113 average time/residue: 0.1276 time to fit residues: 21.2214 Evaluate side-chains 108 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 106 optimal weight: 0.1980 chunk 18 optimal weight: 0.0060 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.055179 restraints weight = 37975.392| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.44 r_work: 0.2703 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15443 Z= 0.116 Angle : 0.483 14.252 20952 Z= 0.253 Chirality : 0.040 0.139 2380 Planarity : 0.003 0.031 2666 Dihedral : 12.375 88.729 2461 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.51 % Allowed : 7.12 % Favored : 92.36 % 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 aren not related in a simple way. whole: 1.28 (0.20), residues: 1912 helix: 1.55 (0.17), residues: 910 sheet: 0.01 (0.30), residues: 308 loop : 0.49 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.014 0.001 TYR C 388 PHE 0.012 0.001 PHE A 187 HIS 0.002 0.000 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00252 (15443) covalent geometry : angle 0.48270 (20952) hydrogen bonds : bond 0.02604 ( 799) hydrogen bonds : angle 3.92458 ( 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 123 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.540 Fit side-chains REVERT: C 134 ASN cc_start: 0.9398 (m110) cc_final: 0.9056 (m110) REVERT: C 234 GLN cc_start: 0.8764 (mt0) cc_final: 0.8483 (mt0) REVERT: C 388 TYR cc_start: 0.8344 (m-10) cc_final: 0.8138 (m-10) REVERT: F 89 ASN cc_start: 0.8824 (m110) cc_final: 0.8438 (m110) REVERT: F 115 ARG cc_start: 0.8069 (ttt90) cc_final: 0.7683 (ttt90) REVERT: F 159 CYS cc_start: 0.7836 (p) cc_final: 0.7383 (p) REVERT: F 166 ASN cc_start: 0.9388 (m-40) cc_final: 0.9119 (m110) REVERT: F 285 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8215 (mp) REVERT: F 335 MET cc_start: 0.3435 (ppp) cc_final: 0.2283 (pmm) REVERT: B 188 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.6430 (pmt-80) REVERT: E 115 ARG cc_start: 0.9011 (mmm-85) cc_final: 0.8781 (mmm160) REVERT: E 234 GLN cc_start: 0.8989 (mm110) cc_final: 0.8610 (mm110) REVERT: E 286 TYR cc_start: 0.9297 (m-80) cc_final: 0.8852 (m-80) REVERT: E 335 MET cc_start: 0.5106 (ppp) cc_final: 0.3869 (ppp) REVERT: A 122 LYS cc_start: 0.9068 (pptt) cc_final: 0.8838 (pptt) REVERT: A 142 MET cc_start: 0.7896 (mmm) cc_final: 0.7319 (tpt) REVERT: A 166 ASN cc_start: 0.9389 (m110) cc_final: 0.9160 (m110) REVERT: A 188 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7511 (pmt-80) REVERT: A 245 ASN cc_start: 0.9489 (m-40) cc_final: 0.9167 (m110) REVERT: D 188 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8082 (pmt-80) REVERT: D 301 MET cc_start: 0.9001 (tpp) cc_final: 0.8631 (tpp) outliers start: 8 outliers final: 4 residues processed: 122 average time/residue: 0.1457 time to fit residues: 25.9060 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 : 0.646 ------------------------------------------------------------------------------- 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 E residue 152 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 131 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 0.0000 chunk 123 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 GLN E 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.054330 restraints weight = 37876.425| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.41 r_work: 0.2684 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15443 Z= 0.150 Angle : 0.510 10.527 20952 Z= 0.266 Chirality : 0.041 0.142 2380 Planarity : 0.003 0.033 2666 Dihedral : 12.212 89.858 2461 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.58 % Allowed : 7.57 % Favored : 91.85 % 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 aren not related in a simple way. whole: 1.22 (0.20), residues: 1912 helix: 1.47 (0.17), residues: 934 sheet: -0.01 (0.30), residues: 308 loop : 0.48 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 115 TYR 0.020 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 covalent geometry : bond 0.00336 (15443) covalent geometry : angle 0.50972 (20952) hydrogen bonds : bond 0.02707 ( 799) hydrogen bonds : angle 3.94118 ( 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 116 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.613 Fit side-chains REVERT: C 134 ASN cc_start: 0.9402 (m110) cc_final: 0.9062 (m110) REVERT: C 234 GLN cc_start: 0.8773 (mt0) cc_final: 0.8486 (mt0) REVERT: C 388 TYR cc_start: 0.8327 (m-10) cc_final: 0.8098 (m-10) REVERT: F 89 ASN cc_start: 0.8807 (m110) cc_final: 0.8443 (m110) REVERT: F 115 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7713 (ttt90) REVERT: F 159 CYS cc_start: 0.7881 (p) cc_final: 0.7416 (p) REVERT: F 166 ASN cc_start: 0.9383 (m-40) cc_final: 0.9125 (m110) REVERT: F 285 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 188 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.6496 (pmt-80) REVERT: E 115 ARG cc_start: 0.9043 (mmm-85) cc_final: 0.8559 (tpp80) REVERT: E 126 GLU cc_start: 0.8381 (tp30) cc_final: 0.7838 (tp30) REVERT: E 134 ASN cc_start: 0.9060 (m110) cc_final: 0.8779 (m-40) REVERT: E 234 GLN cc_start: 0.8987 (mm110) cc_final: 0.8601 (mm110) REVERT: E 286 TYR cc_start: 0.9331 (m-80) cc_final: 0.8902 (m-80) REVERT: E 335 MET cc_start: 0.5079 (ppp) cc_final: 0.3873 (ppp) REVERT: A 122 LYS cc_start: 0.9080 (pptt) cc_final: 0.8848 (pptt) REVERT: A 142 MET cc_start: 0.7898 (mmm) cc_final: 0.7311 (tpt) REVERT: A 166 ASN cc_start: 0.9391 (m110) cc_final: 0.9152 (m110) REVERT: A 188 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7345 (pmt-80) REVERT: A 245 ASN cc_start: 0.9497 (m-40) cc_final: 0.9158 (m110) REVERT: D 188 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8064 (pmt-80) REVERT: D 301 MET cc_start: 0.9013 (tpp) cc_final: 0.8648 (tpp) outliers start: 9 outliers final: 4 residues processed: 115 average time/residue: 0.1414 time to fit residues: 23.7324 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 : 0.586 ------------------------------------------------------------------------------- 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 E residue 152 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain D residue 188 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 16 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 157 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 182 optimal weight: 0.0040 chunk 52 optimal weight: 8.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.056859 restraints weight = 38651.346| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.43 r_work: 0.2703 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15443 Z= 0.121 Angle : 0.514 16.390 20952 Z= 0.264 Chirality : 0.041 0.140 2380 Planarity : 0.003 0.045 2666 Dihedral : 12.035 89.691 2461 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.58 % Allowed : 7.70 % Favored : 91.72 % 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 aren not related in a simple way. whole: 1.30 (0.20), residues: 1912 helix: 1.58 (0.17), residues: 910 sheet: 0.06 (0.30), residues: 308 loop : 0.46 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.021 0.001 TYR A 249 PHE 0.011 0.001 PHE A 187 HIS 0.003 0.000 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00269 (15443) covalent geometry : angle 0.51371 (20952) hydrogen bonds : bond 0.02549 ( 799) hydrogen bonds : angle 3.86249 ( 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 118 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.652 Fit side-chains REVERT: C 134 ASN cc_start: 0.9406 (m110) cc_final: 0.9074 (m110) REVERT: C 234 GLN cc_start: 0.8764 (mt0) cc_final: 0.8482 (mt0) REVERT: F 89 ASN cc_start: 0.8745 (m110) cc_final: 0.8404 (m110) REVERT: F 115 ARG cc_start: 0.8106 (ttt90) cc_final: 0.7728 (ttt90) REVERT: F 159 CYS cc_start: 0.7805 (p) cc_final: 0.7347 (p) REVERT: F 166 ASN cc_start: 0.9386 (m-40) cc_final: 0.9150 (m110) REVERT: F 285 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8200 (mp) REVERT: F 335 MET cc_start: 0.3531 (ppp) cc_final: 0.2312 (pmm) REVERT: B 188 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.6504 (pmt-80) REVERT: E 234 GLN cc_start: 0.8981 (mm110) cc_final: 0.8607 (mm110) REVERT: E 249 TYR cc_start: 0.8946 (t80) cc_final: 0.8598 (t80) REVERT: E 286 TYR cc_start: 0.9292 (m-80) cc_final: 0.8783 (m-80) REVERT: E 335 MET cc_start: 0.5094 (ppp) cc_final: 0.3875 (ppp) REVERT: A 122 LYS cc_start: 0.9081 (pptt) cc_final: 0.8851 (pptt) REVERT: A 142 MET cc_start: 0.8191 (mmm) cc_final: 0.7381 (tpt) REVERT: A 166 ASN cc_start: 0.9392 (m110) cc_final: 0.9165 (m110) REVERT: A 188 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7471 (pmt-80) REVERT: A 245 ASN cc_start: 0.9504 (m-40) cc_final: 0.9194 (m110) REVERT: A 293 ARG cc_start: 0.7702 (ttt180) cc_final: 0.6405 (tpt170) REVERT: D 152 MET cc_start: 0.9147 (ttm) cc_final: 0.8924 (tmm) REVERT: D 188 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8072 (pmt-80) REVERT: D 301 MET cc_start: 0.9008 (tpp) cc_final: 0.8642 (tpp) outliers start: 9 outliers final: 3 residues processed: 116 average time/residue: 0.1401 time to fit residues: 23.6450 Evaluate side-chains 110 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 115 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.055430 restraints weight = 38704.386| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.40 r_work: 0.2659 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15443 Z= 0.188 Angle : 0.549 14.482 20952 Z= 0.281 Chirality : 0.042 0.143 2380 Planarity : 0.003 0.046 2666 Dihedral : 11.910 89.364 2461 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.51 % Allowed : 7.70 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.20), residues: 1912 helix: 1.59 (0.18), residues: 910 sheet: -0.07 (0.30), residues: 308 loop : 0.42 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 115 TYR 0.023 0.001 TYR A 249 PHE 0.009 0.001 PHE A 187 HIS 0.003 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00422 (15443) covalent geometry : angle 0.54884 (20952) hydrogen bonds : bond 0.02860 ( 799) hydrogen bonds : angle 4.00062 ( 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 113 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.437 Fit side-chains REVERT: C 134 ASN cc_start: 0.9413 (m110) cc_final: 0.9082 (m110) REVERT: C 234 GLN cc_start: 0.8795 (mt0) cc_final: 0.8508 (mt0) REVERT: C 335 MET cc_start: 0.3326 (ppp) cc_final: 0.2917 (ppp) REVERT: C 388 TYR cc_start: 0.8373 (m-10) cc_final: 0.8046 (m-10) REVERT: F 89 ASN cc_start: 0.8735 (m110) cc_final: 0.8412 (m-40) REVERT: F 115 ARG cc_start: 0.8089 (ttt90) cc_final: 0.7702 (ttt90) REVERT: F 159 CYS cc_start: 0.7963 (p) cc_final: 0.7486 (p) REVERT: F 166 ASN cc_start: 0.9382 (m-40) cc_final: 0.9094 (m110) REVERT: F 285 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8249 (mp) REVERT: F 335 MET cc_start: 0.3761 (ppp) cc_final: 0.2526 (pmm) REVERT: B 188 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.6577 (pmt-80) REVERT: E 234 GLN cc_start: 0.8995 (mm110) cc_final: 0.8605 (mm110) REVERT: E 286 TYR cc_start: 0.9363 (m-80) cc_final: 0.9006 (m-80) REVERT: E 335 MET cc_start: 0.5192 (ppp) cc_final: 0.3959 (ppp) REVERT: A 122 LYS cc_start: 0.9091 (pptt) cc_final: 0.8849 (pptt) REVERT: A 142 MET cc_start: 0.8218 (mmm) cc_final: 0.7375 (tpt) REVERT: A 166 ASN cc_start: 0.9399 (m110) cc_final: 0.9135 (m110) REVERT: A 188 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7403 (pmt-80) REVERT: A 245 ASN cc_start: 0.9507 (m-40) cc_final: 0.9163 (m110) REVERT: A 293 ARG cc_start: 0.7731 (ttt180) cc_final: 0.6413 (tpt170) REVERT: D 152 MET cc_start: 0.9174 (ttm) cc_final: 0.8967 (tmm) REVERT: D 188 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7851 (pmt-80) REVERT: D 301 MET cc_start: 0.9027 (tpp) cc_final: 0.8670 (tpp) outliers start: 8 outliers final: 3 residues processed: 112 average time/residue: 0.1375 time to fit residues: 22.2378 Evaluate side-chains 111 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 113 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055438 restraints weight = 38848.634| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.42 r_work: 0.2662 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2154 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= 0.178 Angle : 0.551 14.344 20952 Z= 0.281 Chirality : 0.041 0.143 2380 Planarity : 0.003 0.049 2666 Dihedral : 11.822 89.865 2461 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.45 % Allowed : 7.77 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.20), residues: 1912 helix: 1.55 (0.17), residues: 910 sheet: -0.08 (0.30), residues: 308 loop : 0.41 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 115 TYR 0.022 0.001 TYR A 249 PHE 0.010 0.001 PHE A 187 HIS 0.003 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00400 (15443) covalent geometry : angle 0.55105 (20952) hydrogen bonds : bond 0.02794 ( 799) hydrogen bonds : angle 4.00297 ( 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 115 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: C 134 ASN cc_start: 0.9412 (m110) cc_final: 0.9079 (m110) REVERT: C 234 GLN cc_start: 0.8785 (mt0) cc_final: 0.8492 (mt0) REVERT: C 335 MET cc_start: 0.3436 (ppp) cc_final: 0.3048 (ppp) REVERT: F 89 ASN cc_start: 0.8714 (m110) cc_final: 0.8399 (m-40) REVERT: F 115 ARG cc_start: 0.8055 (ttt90) cc_final: 0.7663 (ttt90) REVERT: F 159 CYS cc_start: 0.7985 (p) cc_final: 0.7507 (p) REVERT: F 166 ASN cc_start: 0.9378 (m-40) cc_final: 0.9085 (m110) REVERT: F 285 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8245 (mp) REVERT: F 335 MET cc_start: 0.3747 (ppp) cc_final: 0.2540 (pmm) REVERT: B 188 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.6602 (pmt-80) REVERT: E 115 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8658 (tpp80) REVERT: E 234 GLN cc_start: 0.8990 (mm110) cc_final: 0.8597 (mm110) REVERT: E 249 TYR cc_start: 0.8971 (t80) cc_final: 0.8607 (t80) REVERT: E 286 TYR cc_start: 0.9365 (m-80) cc_final: 0.9074 (m-80) REVERT: E 335 MET cc_start: 0.5172 (ppp) cc_final: 0.3954 (ppp) REVERT: A 122 LYS cc_start: 0.9074 (pptt) cc_final: 0.8830 (pptt) REVERT: A 142 MET cc_start: 0.8186 (mmm) cc_final: 0.7368 (tpt) REVERT: A 166 ASN cc_start: 0.9398 (m110) cc_final: 0.9127 (m110) REVERT: A 188 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7371 (pmt-80) REVERT: A 245 ASN cc_start: 0.9517 (m-40) cc_final: 0.9165 (m110) REVERT: A 293 ARG cc_start: 0.7724 (ttt180) cc_final: 0.6397 (tpt170) REVERT: D 152 MET cc_start: 0.9160 (ttm) cc_final: 0.8932 (tmm) REVERT: D 188 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7887 (pmt-80) REVERT: D 301 MET cc_start: 0.9023 (tpp) cc_final: 0.8671 (tpp) outliers start: 7 outliers final: 3 residues processed: 115 average time/residue: 0.1421 time to fit residues: 23.5856 Evaluate side-chains 112 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 190 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055818 restraints weight = 38502.834| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.39 r_work: 0.2671 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15443 Z= 0.160 Angle : 0.545 13.721 20952 Z= 0.279 Chirality : 0.041 0.142 2380 Planarity : 0.003 0.062 2666 Dihedral : 11.789 89.462 2461 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.58 % Allowed : 7.70 % Favored : 91.72 % 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 aren not related in a simple way. whole: 1.18 (0.20), residues: 1912 helix: 1.52 (0.17), residues: 914 sheet: -0.06 (0.30), residues: 308 loop : 0.37 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 115 TYR 0.022 0.001 TYR A 249 PHE 0.010 0.001 PHE A 187 HIS 0.003 0.000 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00359 (15443) covalent geometry : angle 0.54517 (20952) hydrogen bonds : bond 0.02734 ( 799) hydrogen bonds : angle 3.96104 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.93 seconds wall clock time: 54 minutes 39.36 seconds (3279.36 seconds total)