Starting phenix.real_space_refine on Fri Jun 13 14:56:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d46_46550/06_2025/9d46_46550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d46_46550/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d46_46550/06_2025/9d46_46550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d46_46550/06_2025/9d46_46550.map" model { file = "/net/cci-nas-00/data/ceres_data/9d46_46550/06_2025/9d46_46550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d46_46550/06_2025/9d46_46550.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.46, per 1000 atoms: 0.62 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: 4.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.74 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: 5.13 Time building geometry restraints manager: 4.65 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 400 or resid 501 through 502)) selection = (chain 'B' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'C' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'D' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'E' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'F' and (resid 81 through 400 or resid 501 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: 0.010 Normalize map: mean=0, sd=1: 1.650 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 36.510 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (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 HIS 0.002 0.000 HIS B 352 PHE 0.043 0.001 PHE A 187 TYR 0.012 0.001 TYR B 217 ARG 0.009 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.17019 ( 799) hydrogen bonds : angle 6.53939 ( 2235) covalent geometry : bond 0.00212 (15443) covalent geometry : angle 0.48229 (20952) *********************** 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 : 1.800 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: 0.3202 time to fit residues: 58.5058 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 : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.075269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.054567 restraints weight = 38360.669| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.47 r_work: 0.2692 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15443 Z= 0.186 Angle : 0.528 8.946 20952 Z= 0.281 Chirality : 0.042 0.144 2380 Planarity : 0.004 0.048 2666 Dihedral : 13.737 89.849 2461 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.26 % Allowed : 3.08 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1912 helix: 1.54 (0.18), residues: 896 sheet: 0.53 (0.30), residues: 308 loop : 0.53 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 105 PHE 0.025 0.001 PHE B 187 TYR 0.012 0.001 TYR C 388 ARG 0.006 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 799) hydrogen bonds : angle 4.62568 ( 2235) covalent geometry : bond 0.00414 (15443) covalent geometry : angle 0.52800 (20952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 1.835 Fit side-chains revert: symmetry clash REVERT: C 134 ASN cc_start: 0.9354 (m110) cc_final: 0.9041 (m110) REVERT: F 89 ASN cc_start: 0.8985 (m110) cc_final: 0.8646 (m110) REVERT: F 159 CYS cc_start: 0.7955 (p) cc_final: 0.7551 (p) REVERT: F 166 ASN cc_start: 0.9428 (m-40) cc_final: 0.9137 (m110) REVERT: B 234 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8815 (mm-40) REVERT: B 364 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8804 (ttpt) REVERT: E 120 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8853 (pp20) REVERT: E 126 GLU cc_start: 0.8662 (tp30) cc_final: 0.8218 (tp30) REVERT: E 134 ASN cc_start: 0.9375 (m110) cc_final: 0.9162 (m-40) REVERT: E 166 ASN cc_start: 0.9145 (m110) cc_final: 0.8808 (m110) REVERT: E 234 GLN cc_start: 0.9086 (mm110) cc_final: 0.8793 (mm110) REVERT: E 286 TYR cc_start: 0.9313 (m-80) cc_final: 0.9012 (m-80) REVERT: E 335 MET cc_start: 0.5276 (ppp) cc_final: 0.4046 (ppp) REVERT: A 112 TYR cc_start: 0.8415 (m-10) cc_final: 0.7640 (m-80) REVERT: A 142 MET cc_start: 0.7761 (mmm) cc_final: 0.7246 (tpt) REVERT: A 166 ASN cc_start: 0.9387 (m110) cc_final: 0.9135 (m110) REVERT: A 234 GLN cc_start: 0.9108 (mm110) cc_final: 0.8825 (mm110) REVERT: D 301 MET cc_start: 0.9055 (tpp) cc_final: 0.8709 (tpp) outliers start: 4 outliers final: 4 residues processed: 120 average time/residue: 0.2962 time to fit residues: 53.6615 Evaluate side-chains 109 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 181 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 106 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.074551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.053655 restraints weight = 38168.946| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.53 r_work: 0.2671 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1484 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= 0.181 Angle : 0.511 9.783 20952 Z= 0.271 Chirality : 0.042 0.140 2380 Planarity : 0.004 0.044 2666 Dihedral : 13.166 88.300 2461 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.32 % Allowed : 4.36 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1912 helix: 1.59 (0.18), residues: 890 sheet: 0.19 (0.29), residues: 308 loop : 0.45 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 105 PHE 0.018 0.001 PHE A 187 TYR 0.016 0.001 TYR C 388 ARG 0.006 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 799) hydrogen bonds : angle 4.30037 ( 2235) covalent geometry : bond 0.00402 (15443) covalent geometry : angle 0.51080 (20952) *********************** 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 119 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.750 Fit side-chains REVERT: C 134 ASN cc_start: 0.9379 (m110) cc_final: 0.9046 (m110) REVERT: C 388 TYR cc_start: 0.8416 (m-10) cc_final: 0.8158 (m-10) REVERT: F 89 ASN cc_start: 0.8912 (m110) cc_final: 0.8557 (m110) REVERT: F 159 CYS cc_start: 0.7977 (p) cc_final: 0.7551 (p) REVERT: F 166 ASN cc_start: 0.9402 (m-40) cc_final: 0.9121 (m110) REVERT: F 285 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8233 (mp) REVERT: B 350 MET cc_start: 0.9232 (tpt) cc_final: 0.8620 (tpt) REVERT: E 120 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8854 (tm-30) REVERT: E 126 GLU cc_start: 0.8729 (tp30) cc_final: 0.8298 (tp30) REVERT: E 234 GLN cc_start: 0.9024 (mm110) cc_final: 0.8677 (mm110) REVERT: E 286 TYR cc_start: 0.9304 (m-80) cc_final: 0.8872 (m-80) REVERT: E 335 MET cc_start: 0.5209 (ppp) cc_final: 0.3926 (ppp) REVERT: A 142 MET cc_start: 0.7753 (mmm) cc_final: 0.7249 (tpt) REVERT: A 166 ASN cc_start: 0.9382 (m110) cc_final: 0.9129 (m110) REVERT: A 245 ASN cc_start: 0.9450 (m-40) cc_final: 0.9076 (m110) REVERT: D 301 MET cc_start: 0.9018 (tpp) cc_final: 0.8660 (tpp) outliers start: 5 outliers final: 3 residues processed: 119 average time/residue: 0.2759 time to fit residues: 50.1736 Evaluate side-chains 104 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 106 optimal weight: 0.0070 chunk 13 optimal weight: 0.4980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.076400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.056314 restraints weight = 38079.192| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.43 r_work: 0.2730 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15443 Z= 0.103 Angle : 0.491 11.935 20952 Z= 0.257 Chirality : 0.041 0.163 2380 Planarity : 0.003 0.033 2666 Dihedral : 12.913 89.571 2461 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.51 % Allowed : 5.71 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1912 helix: 1.46 (0.18), residues: 914 sheet: 0.19 (0.30), residues: 308 loop : 0.48 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 196 PHE 0.015 0.001 PHE A 187 TYR 0.017 0.001 TYR C 388 ARG 0.006 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 799) hydrogen bonds : angle 4.04715 ( 2235) covalent geometry : bond 0.00219 (15443) covalent geometry : angle 0.49061 (20952) *********************** 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 125 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 1.541 Fit side-chains REVERT: C 97 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9115 (mmmt) REVERT: C 134 ASN cc_start: 0.9391 (m110) cc_final: 0.9059 (m110) REVERT: F 89 ASN cc_start: 0.8844 (m110) cc_final: 0.8464 (m110) REVERT: F 159 CYS cc_start: 0.7817 (p) cc_final: 0.7403 (p) REVERT: F 166 ASN cc_start: 0.9389 (m-40) cc_final: 0.9126 (m110) REVERT: F 285 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8195 (mp) REVERT: F 335 MET cc_start: 0.3552 (ppp) cc_final: 0.2369 (pmm) REVERT: E 234 GLN cc_start: 0.9006 (mm110) cc_final: 0.8655 (mm110) REVERT: E 286 TYR cc_start: 0.9297 (m-80) cc_final: 0.8857 (m-80) REVERT: E 335 MET cc_start: 0.5073 (ppp) cc_final: 0.3831 (ppp) REVERT: A 142 MET cc_start: 0.7770 (mmm) cc_final: 0.7258 (tpt) REVERT: A 166 ASN cc_start: 0.9377 (m110) cc_final: 0.9166 (m110) REVERT: A 188 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7347 (pmt-80) REVERT: A 245 ASN cc_start: 0.9477 (m-40) cc_final: 0.9149 (m110) REVERT: D 301 MET cc_start: 0.9006 (tpp) cc_final: 0.8619 (tpp) outliers start: 8 outliers final: 3 residues processed: 125 average time/residue: 0.3146 time to fit residues: 57.7936 Evaluate side-chains 107 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 185 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 187 optimal weight: 0.0050 chunk 126 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 overall best weight: 2.5198 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.074816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.054681 restraints weight = 38438.853| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.42 r_work: 0.2677 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15443 Z= 0.174 Angle : 0.509 9.010 20952 Z= 0.267 Chirality : 0.041 0.173 2380 Planarity : 0.003 0.034 2666 Dihedral : 12.769 89.040 2461 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.71 % Allowed : 6.48 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1912 helix: 1.40 (0.17), residues: 936 sheet: 0.06 (0.30), residues: 308 loop : 0.46 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 352 PHE 0.013 0.001 PHE A 187 TYR 0.018 0.001 TYR C 388 ARG 0.008 0.000 ARG D 287 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 799) hydrogen bonds : angle 4.07144 ( 2235) covalent geometry : bond 0.00390 (15443) covalent geometry : angle 0.50923 (20952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.565 Fit side-chains REVERT: C 134 ASN cc_start: 0.9397 (m110) cc_final: 0.9063 (m110) REVERT: F 89 ASN cc_start: 0.8848 (m110) cc_final: 0.8472 (m110) REVERT: F 115 ARG cc_start: 0.8103 (ttt90) cc_final: 0.7718 (ttt90) REVERT: F 159 CYS cc_start: 0.7902 (p) cc_final: 0.7461 (p) REVERT: F 166 ASN cc_start: 0.9394 (m-40) cc_final: 0.9123 (m110) REVERT: F 285 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8241 (mp) REVERT: E 234 GLN cc_start: 0.9027 (mm110) cc_final: 0.8665 (mm110) REVERT: E 286 TYR cc_start: 0.9328 (m-80) cc_final: 0.8937 (m-80) REVERT: E 335 MET cc_start: 0.5167 (ppp) cc_final: 0.3912 (ppp) REVERT: A 142 MET cc_start: 0.7788 (mmm) cc_final: 0.7268 (tpt) REVERT: A 166 ASN cc_start: 0.9393 (m110) cc_final: 0.9154 (m110) REVERT: A 188 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7539 (pmt-80) REVERT: A 245 ASN cc_start: 0.9488 (m-40) cc_final: 0.9127 (m110) REVERT: A 249 TYR cc_start: 0.9335 (t80) cc_final: 0.9132 (t80) REVERT: D 188 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7833 (pmt-80) REVERT: D 301 MET cc_start: 0.9024 (tpp) cc_final: 0.8653 (tpp) outliers start: 11 outliers final: 4 residues processed: 114 average time/residue: 0.2762 time to fit residues: 47.5771 Evaluate side-chains 107 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 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 185 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 165 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 GLN E 134 ASN D 134 ASN D 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.077891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.058277 restraints weight = 38699.051| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.45 r_work: 0.2748 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15443 Z= 0.099 Angle : 0.488 14.125 20952 Z= 0.254 Chirality : 0.040 0.137 2380 Planarity : 0.003 0.030 2666 Dihedral : 12.401 87.637 2461 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.45 % Allowed : 7.57 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1912 helix: 1.51 (0.17), residues: 910 sheet: 0.17 (0.30), residues: 308 loop : 0.44 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 196 PHE 0.012 0.001 PHE A 187 TYR 0.012 0.001 TYR C 388 ARG 0.008 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02488 ( 799) hydrogen bonds : angle 3.86453 ( 2235) covalent geometry : bond 0.00211 (15443) covalent geometry : angle 0.48827 (20952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.688 Fit side-chains REVERT: C 134 ASN cc_start: 0.9396 (m110) cc_final: 0.9048 (m110) REVERT: C 152 MET cc_start: 0.8633 (tmm) cc_final: 0.8415 (tmm) REVERT: F 89 ASN cc_start: 0.8808 (m110) cc_final: 0.8413 (m110) REVERT: F 115 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7546 (ttt90) REVERT: F 159 CYS cc_start: 0.7706 (p) cc_final: 0.7282 (p) REVERT: F 166 ASN cc_start: 0.9389 (m-40) cc_final: 0.9147 (m110) REVERT: F 285 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8162 (mp) REVERT: F 335 MET cc_start: 0.3229 (ppp) cc_final: 0.2117 (pmm) REVERT: B 188 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.6415 (pmt-80) REVERT: B 350 MET cc_start: 0.8936 (mmm) cc_final: 0.8472 (tpt) REVERT: E 234 GLN cc_start: 0.8975 (mm110) cc_final: 0.8602 (mm110) REVERT: E 286 TYR cc_start: 0.9295 (m-80) cc_final: 0.8793 (m-80) REVERT: E 335 MET cc_start: 0.5041 (ppp) cc_final: 0.3817 (ppp) REVERT: A 142 MET cc_start: 0.7724 (mmm) cc_final: 0.7287 (tpt) REVERT: A 188 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7459 (pmt-80) REVERT: A 245 ASN cc_start: 0.9492 (m-40) cc_final: 0.9178 (m110) REVERT: A 249 TYR cc_start: 0.9326 (t80) cc_final: 0.9027 (t80) REVERT: D 166 ASN cc_start: 0.9126 (m-40) cc_final: 0.8804 (m-40) REVERT: D 188 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7974 (pmt-80) REVERT: D 301 MET cc_start: 0.8994 (tpp) cc_final: 0.8605 (tpp) outliers start: 7 outliers final: 2 residues processed: 119 average time/residue: 0.2898 time to fit residues: 51.3112 Evaluate side-chains 109 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 158 optimal weight: 0.1980 chunk 156 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.058050 restraints weight = 38762.597| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.45 r_work: 0.2729 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15443 Z= 0.109 Angle : 0.482 9.879 20952 Z= 0.253 Chirality : 0.040 0.148 2380 Planarity : 0.003 0.030 2666 Dihedral : 12.096 88.844 2461 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.45 % Allowed : 7.64 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1912 helix: 1.55 (0.18), residues: 914 sheet: 0.19 (0.31), residues: 308 loop : 0.43 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 196 PHE 0.011 0.001 PHE A 187 TYR 0.024 0.001 TYR E 249 ARG 0.007 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02478 ( 799) hydrogen bonds : angle 3.81997 ( 2235) covalent geometry : bond 0.00238 (15443) covalent geometry : angle 0.48178 (20952) *********************** 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 113 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.522 Fit side-chains REVERT: C 134 ASN cc_start: 0.9407 (m110) cc_final: 0.9067 (m110) REVERT: C 152 MET cc_start: 0.8659 (tmm) cc_final: 0.8403 (tmm) REVERT: C 388 TYR cc_start: 0.8390 (m-10) cc_final: 0.8003 (m-10) REVERT: F 89 ASN cc_start: 0.8798 (m110) cc_final: 0.8424 (m110) REVERT: F 115 ARG cc_start: 0.8147 (ttt90) cc_final: 0.7618 (ttt90) REVERT: F 159 CYS cc_start: 0.7746 (p) cc_final: 0.7316 (p) REVERT: F 166 ASN cc_start: 0.9370 (m-40) cc_final: 0.9157 (m110) REVERT: F 285 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 188 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.6471 (pmt-80) REVERT: E 126 GLU cc_start: 0.8844 (tp30) cc_final: 0.8349 (tp30) REVERT: E 234 GLN cc_start: 0.8979 (mm110) cc_final: 0.8589 (mm110) REVERT: E 286 TYR cc_start: 0.9302 (m-80) cc_final: 0.8762 (m-80) REVERT: E 335 MET cc_start: 0.5107 (ppp) cc_final: 0.3878 (ppp) REVERT: A 142 MET cc_start: 0.7772 (mmm) cc_final: 0.7313 (tpt) REVERT: A 188 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7441 (pmt-80) REVERT: A 245 ASN cc_start: 0.9501 (m-40) cc_final: 0.9188 (m110) REVERT: A 249 TYR cc_start: 0.9333 (t80) cc_final: 0.8983 (t80) REVERT: D 166 ASN cc_start: 0.9124 (m-40) cc_final: 0.8817 (m-40) REVERT: D 188 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7513 (pmt-80) REVERT: D 249 TYR cc_start: 0.9144 (t80) cc_final: 0.8937 (t80) REVERT: D 301 MET cc_start: 0.9016 (tpp) cc_final: 0.8635 (tpp) outliers start: 7 outliers final: 3 residues processed: 113 average time/residue: 0.3181 time to fit residues: 53.4074 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 : 1.712 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 124 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 GLN E 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.073923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.053701 restraints weight = 38319.381| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.42 r_work: 0.2665 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15443 Z= 0.195 Angle : 0.543 16.413 20952 Z= 0.279 Chirality : 0.042 0.192 2380 Planarity : 0.003 0.031 2666 Dihedral : 12.064 89.995 2461 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.51 % Allowed : 7.83 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1912 helix: 1.54 (0.18), residues: 910 sheet: -0.11 (0.30), residues: 312 loop : 0.43 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 352 PHE 0.009 0.001 PHE A 187 TYR 0.020 0.001 TYR C 388 ARG 0.008 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.02880 ( 799) hydrogen bonds : angle 4.00362 ( 2235) covalent geometry : bond 0.00437 (15443) covalent geometry : angle 0.54348 (20952) *********************** 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 113 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.692 Fit side-chains REVERT: C 134 ASN cc_start: 0.9417 (m110) cc_final: 0.9089 (m110) REVERT: C 152 MET cc_start: 0.8727 (tmm) cc_final: 0.8450 (tmm) REVERT: C 388 TYR cc_start: 0.8394 (m-10) cc_final: 0.8089 (m-10) REVERT: F 89 ASN cc_start: 0.8792 (m110) cc_final: 0.8434 (m110) REVERT: F 115 ARG cc_start: 0.8130 (ttt90) cc_final: 0.7750 (ttt90) REVERT: F 159 CYS cc_start: 0.7941 (p) cc_final: 0.7486 (p) REVERT: F 166 ASN cc_start: 0.9385 (m-40) cc_final: 0.9103 (m110) REVERT: F 285 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8249 (mp) REVERT: F 335 MET cc_start: 0.3558 (ppp) cc_final: 0.2295 (pmm) REVERT: B 188 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6575 (pmt-80) REVERT: E 234 GLN cc_start: 0.8993 (mm110) cc_final: 0.8610 (mm110) REVERT: E 286 TYR cc_start: 0.9350 (m-80) cc_final: 0.8935 (m-80) REVERT: E 335 MET cc_start: 0.5137 (ppp) cc_final: 0.3910 (ppp) REVERT: A 142 MET cc_start: 0.8178 (mmm) cc_final: 0.7358 (tpt) REVERT: A 188 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7395 (pmt-80) REVERT: A 245 ASN cc_start: 0.9505 (m-40) cc_final: 0.9162 (m110) REVERT: A 293 ARG cc_start: 0.7623 (ttt180) cc_final: 0.6367 (tpt170) REVERT: D 188 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7379 (pmt-80) REVERT: D 249 TYR cc_start: 0.9162 (t80) cc_final: 0.8919 (t80) REVERT: D 286 TYR cc_start: 0.9534 (m-80) cc_final: 0.9308 (m-80) REVERT: D 301 MET cc_start: 0.9023 (tpp) cc_final: 0.8650 (tpp) outliers start: 8 outliers final: 3 residues processed: 113 average time/residue: 0.2953 time to fit residues: 49.3264 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 : 1.788 ------------------------------------------------------------------------------- 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 172 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 159 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.076070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.056147 restraints weight = 38092.158| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.42 r_work: 0.2719 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15443 Z= 0.111 Angle : 0.509 14.363 20952 Z= 0.263 Chirality : 0.041 0.159 2380 Planarity : 0.003 0.045 2666 Dihedral : 11.847 89.914 2461 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.51 % Allowed : 7.83 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1912 helix: 1.51 (0.17), residues: 914 sheet: 0.08 (0.31), residues: 308 loop : 0.41 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 352 PHE 0.011 0.001 PHE A 187 TYR 0.017 0.001 TYR C 388 ARG 0.008 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02488 ( 799) hydrogen bonds : angle 3.84334 ( 2235) covalent geometry : bond 0.00245 (15443) covalent geometry : angle 0.50857 (20952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.612 Fit side-chains REVERT: C 134 ASN cc_start: 0.9409 (m110) cc_final: 0.9065 (m110) REVERT: C 152 MET cc_start: 0.8708 (tmm) cc_final: 0.8416 (tmm) REVERT: C 388 TYR cc_start: 0.8393 (m-10) cc_final: 0.8131 (m-10) REVERT: F 89 ASN cc_start: 0.8726 (m110) cc_final: 0.8394 (m-40) REVERT: F 115 ARG cc_start: 0.8097 (ttt90) cc_final: 0.7730 (ttt90) REVERT: F 159 CYS cc_start: 0.7794 (p) cc_final: 0.7337 (p) REVERT: F 166 ASN cc_start: 0.9376 (m-40) cc_final: 0.9128 (m110) REVERT: F 285 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8164 (mp) REVERT: F 335 MET cc_start: 0.3837 (ppp) cc_final: 0.2614 (pmm) REVERT: B 188 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.6465 (pmt-80) REVERT: E 234 GLN cc_start: 0.8970 (mm110) cc_final: 0.8586 (mm110) REVERT: E 249 TYR cc_start: 0.8632 (t80) cc_final: 0.8288 (t80) REVERT: E 286 TYR cc_start: 0.9312 (m-80) cc_final: 0.8857 (m-80) REVERT: E 335 MET cc_start: 0.5071 (ppp) cc_final: 0.3859 (ppp) REVERT: A 122 LYS cc_start: 0.9152 (pptt) cc_final: 0.8892 (pptt) REVERT: A 142 MET cc_start: 0.8135 (mmm) cc_final: 0.7404 (tpt) REVERT: A 188 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7490 (pmt-80) REVERT: A 245 ASN cc_start: 0.9500 (m-40) cc_final: 0.9173 (m110) REVERT: A 293 ARG cc_start: 0.7593 (ttt180) cc_final: 0.6193 (tpt170) REVERT: D 152 MET cc_start: 0.9156 (ttm) cc_final: 0.8945 (tmm) REVERT: D 188 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7681 (pmt-80) REVERT: D 249 TYR cc_start: 0.9130 (t80) cc_final: 0.8899 (t80) REVERT: D 286 TYR cc_start: 0.9509 (m-80) cc_final: 0.9213 (m-80) REVERT: D 301 MET cc_start: 0.8999 (tpp) cc_final: 0.8612 (tpp) outliers start: 8 outliers final: 2 residues processed: 116 average time/residue: 0.3002 time to fit residues: 51.2472 Evaluate side-chains 112 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 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 150 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 1 optimal weight: 0.0050 chunk 63 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.076810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056795 restraints weight = 38280.414| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.49 r_work: 0.2734 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15443 Z= 0.105 Angle : 0.509 14.330 20952 Z= 0.261 Chirality : 0.040 0.139 2380 Planarity : 0.003 0.045 2666 Dihedral : 11.644 89.100 2461 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.39 % Allowed : 8.34 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1912 helix: 1.55 (0.18), residues: 914 sheet: 0.17 (0.31), residues: 308 loop : 0.40 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 352 PHE 0.011 0.001 PHE A 187 TYR 0.015 0.001 TYR C 388 ARG 0.009 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02397 ( 799) hydrogen bonds : angle 3.76889 ( 2235) covalent geometry : bond 0.00230 (15443) covalent geometry : angle 0.50892 (20952) ********************** 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 118 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 1.634 Fit side-chains REVERT: C 134 ASN cc_start: 0.9420 (m110) cc_final: 0.9085 (m110) REVERT: C 152 MET cc_start: 0.8686 (tmm) cc_final: 0.8364 (tmm) REVERT: F 89 ASN cc_start: 0.8676 (m110) cc_final: 0.8345 (m-40) REVERT: F 115 ARG cc_start: 0.8116 (ttt90) cc_final: 0.7573 (ttt90) REVERT: F 159 CYS cc_start: 0.7762 (p) cc_final: 0.7308 (p) REVERT: F 166 ASN cc_start: 0.9377 (m-40) cc_final: 0.9163 (m110) REVERT: F 335 MET cc_start: 0.3664 (ppp) cc_final: 0.2426 (pmm) REVERT: B 188 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.6523 (pmt-80) REVERT: E 234 GLN cc_start: 0.8976 (mm110) cc_final: 0.8580 (mm110) REVERT: E 249 TYR cc_start: 0.8596 (t80) cc_final: 0.8306 (t80) REVERT: E 286 TYR cc_start: 0.9334 (m-80) cc_final: 0.8950 (m-80) REVERT: E 335 MET cc_start: 0.5054 (ppp) cc_final: 0.3890 (ppp) REVERT: A 122 LYS cc_start: 0.9165 (pptt) cc_final: 0.8931 (pptt) REVERT: A 142 MET cc_start: 0.8065 (mmm) cc_final: 0.7420 (tpt) REVERT: A 188 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7442 (pmt-80) REVERT: A 245 ASN cc_start: 0.9517 (m-40) cc_final: 0.9201 (m110) REVERT: A 249 TYR cc_start: 0.9359 (t80) cc_final: 0.9039 (t80) REVERT: A 293 ARG cc_start: 0.7492 (ttt180) cc_final: 0.6244 (tpt170) REVERT: D 152 MET cc_start: 0.9138 (ttm) cc_final: 0.8904 (tmm) REVERT: D 166 ASN cc_start: 0.9124 (m-40) cc_final: 0.8800 (m-40) REVERT: D 188 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7746 (pmt-80) REVERT: D 249 TYR cc_start: 0.9130 (t80) cc_final: 0.8901 (t80) REVERT: D 286 TYR cc_start: 0.9511 (m-80) cc_final: 0.9246 (m-80) REVERT: D 301 MET cc_start: 0.8996 (tpp) cc_final: 0.8602 (tpp) outliers start: 6 outliers final: 1 residues processed: 118 average time/residue: 0.3070 time to fit residues: 53.4465 Evaluate side-chains 113 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain A residue 188 ARG 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 117 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 169 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 187 optimal weight: 0.2980 chunk 179 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.057942 restraints weight = 38374.342| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.44 r_work: 0.2752 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 15443 Z= 0.107 Angle : 0.535 13.715 20952 Z= 0.270 Chirality : 0.040 0.156 2380 Planarity : 0.003 0.056 2666 Dihedral : 11.616 89.564 2461 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.26 % Allowed : 8.66 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1912 helix: 1.56 (0.17), residues: 914 sheet: 0.20 (0.31), residues: 308 loop : 0.38 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 196 PHE 0.012 0.001 PHE A 187 TYR 0.022 0.001 TYR C 388 ARG 0.008 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02357 ( 799) hydrogen bonds : angle 3.74334 ( 2235) covalent geometry : bond 0.00242 (15443) covalent geometry : angle 0.53468 (20952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6842.11 seconds wall clock time: 118 minutes 31.22 seconds (7111.22 seconds total)