Starting phenix.real_space_refine on Thu Jun 4 13:27:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijr_35493/06_2026/8ijr_35493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijr_35493/06_2026/8ijr_35493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ijr_35493/06_2026/8ijr_35493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijr_35493/06_2026/8ijr_35493.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijr_35493/06_2026/8ijr_35493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijr_35493/06_2026/8ijr_35493.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.107 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 C 9016 2.51 5 N 2126 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13420 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "B" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "D" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'OPE': 1, 'Z0P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'OPE': 1, 'Z0P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'Z0P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'Z0P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'Z0P': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'Z0P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.25, per 1000 atoms: 0.24 Number of scatterers: 13420 At special positions: 0 Unit cell: (159.5, 108.9, 80.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 2 15.00 O 2162 8.00 N 2126 7.00 C 9016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 493.5 milliseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 60.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 148 through 175 removed outlier: 4.014A pdb=" N THR A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 221 removed outlier: 3.993A pdb=" N MET A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 removed outlier: 3.767A pdb=" N CYS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.620A pdb=" N ARG A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 345 through 370 removed outlier: 3.519A pdb=" N VAL A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'B' and resid 148 through 175 removed outlier: 3.531A pdb=" N THR B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 219 removed outlier: 3.694A pdb=" N MET B 203 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 211 " --> pdb=" O CYS B 207 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 212 " --> pdb=" O GLY B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 4.124A pdb=" N THR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 240 " --> pdb=" O MET B 236 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 removed outlier: 3.520A pdb=" N ILE B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 315 Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.511A pdb=" N ILE B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 370 removed outlier: 3.519A pdb=" N VAL B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'C' and resid 148 through 175 removed outlier: 3.511A pdb=" N ILE C 153 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 222 removed outlier: 3.764A pdb=" N MET C 203 " --> pdb=" O TRP C 199 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 250 removed outlier: 3.672A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 237 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 299 through 308 removed outlier: 3.889A pdb=" N VAL C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.790A pdb=" N VAL C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 313' Processing helix chain 'C' and resid 322 through 341 removed outlier: 3.590A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 369 removed outlier: 3.564A pdb=" N VAL C 349 " --> pdb=" O TYR C 345 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 355 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 4.192A pdb=" N SER C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.097A pdb=" N PHE C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 175 removed outlier: 3.633A pdb=" N VAL D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 160 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 221 removed outlier: 3.544A pdb=" N THR D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 250 removed outlier: 3.526A pdb=" N CYS D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 Processing helix chain 'D' and resid 299 through 315 removed outlier: 3.848A pdb=" N VAL D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 341 Processing helix chain 'D' and resid 345 through 370 removed outlier: 3.628A pdb=" N VAL D 349 " --> pdb=" O TYR D 345 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 351 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.757A pdb=" N GLN D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 375' Processing helix chain 'D' and resid 384 through 389 removed outlier: 3.942A pdb=" N PHE D 388 " --> pdb=" O MET D 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 175 removed outlier: 3.514A pdb=" N LEU E 154 " --> pdb=" O TRP E 150 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 172 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 221 removed outlier: 3.762A pdb=" N GLU E 205 " --> pdb=" O PHE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 250 removed outlier: 4.411A pdb=" N THR E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 281 removed outlier: 3.616A pdb=" N HIS E 274 " --> pdb=" O TRP E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.834A pdb=" N VAL E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE E 311 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 341 Processing helix chain 'E' and resid 345 through 370 removed outlier: 3.650A pdb=" N VAL E 349 " --> pdb=" O TYR E 345 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 356 " --> pdb=" O ALA E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 389 removed outlier: 3.917A pdb=" N PHE E 388 " --> pdb=" O MET E 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 175 removed outlier: 3.845A pdb=" N LEU F 154 " --> pdb=" O TRP F 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 222 removed outlier: 3.781A pdb=" N MET F 203 " --> pdb=" O TRP F 199 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU F 205 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 250 removed outlier: 3.645A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 281 Processing helix chain 'F' and resid 299 through 308 removed outlier: 3.889A pdb=" N VAL F 303 " --> pdb=" O SER F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 removed outlier: 3.811A pdb=" N VAL F 312 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR F 313 " --> pdb=" O ASN F 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 308 through 313' Processing helix chain 'F' and resid 322 through 341 removed outlier: 3.624A pdb=" N VAL F 329 " --> pdb=" O THR F 325 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 369 removed outlier: 3.556A pdb=" N VAL F 349 " --> pdb=" O TYR F 345 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 363 " --> pdb=" O LEU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 375 removed outlier: 4.348A pdb=" N SER F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1890 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: 1.91 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 1670 1.25 - 1.39: 4143 1.39 - 1.53: 7329 1.53 - 1.68: 576 1.68 - 1.82: 174 Bond restraints: 13892 Sorted by residual: bond pdb=" C HIS B 344 " pdb=" O HIS B 344 " ideal model delta sigma weight residual 1.234 1.102 0.132 1.22e-02 6.72e+03 1.17e+02 bond pdb=" C HIS A 344 " pdb=" O HIS A 344 " ideal model delta sigma weight residual 1.234 1.105 0.129 1.22e-02 6.72e+03 1.12e+02 bond pdb=" C30 Z0P D 500 " pdb=" C31 Z0P D 500 " ideal model delta sigma weight residual 1.333 1.536 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C28 Z0P F 500 " pdb=" C29 Z0P F 500 " ideal model delta sigma weight residual 1.529 1.326 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C28 Z0P C 500 " pdb=" C29 Z0P C 500 " ideal model delta sigma weight residual 1.529 1.326 0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 13887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 18746 3.80 - 7.60: 84 7.60 - 11.40: 20 11.40 - 15.19: 4 15.19 - 18.99: 10 Bond angle restraints: 18864 Sorted by residual: angle pdb=" C29 Z0P F 500 " pdb=" C30 Z0P F 500 " pdb=" C31 Z0P F 500 " ideal model delta sigma weight residual 127.58 108.59 18.99 3.00e+00 1.11e-01 4.01e+01 angle pdb=" C29 Z0P D 500 " pdb=" C30 Z0P D 500 " pdb=" C31 Z0P D 500 " ideal model delta sigma weight residual 127.58 108.91 18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C29 Z0P A 500 " pdb=" C30 Z0P A 500 " pdb=" C31 Z0P A 500 " ideal model delta sigma weight residual 127.58 109.35 18.23 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C29 Z0P B 500 " pdb=" C30 Z0P B 500 " pdb=" C31 Z0P B 500 " ideal model delta sigma weight residual 127.58 109.38 18.20 3.00e+00 1.11e-01 3.68e+01 angle pdb=" C29 Z0P C 500 " pdb=" C30 Z0P C 500 " pdb=" C31 Z0P C 500 " ideal model delta sigma weight residual 127.58 109.49 18.09 3.00e+00 1.11e-01 3.64e+01 ... (remaining 18859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 7750 35.65 - 71.31: 164 71.31 - 106.96: 10 106.96 - 142.61: 9 142.61 - 178.27: 9 Dihedral angle restraints: 7942 sinusoidal: 3274 harmonic: 4668 Sorted by residual: dihedral pdb=" C27 Z0P B 500 " pdb=" C28 Z0P B 500 " pdb=" C29 Z0P B 500 " pdb=" C30 Z0P B 500 " ideal model delta sinusoidal sigma weight residual 177.88 -0.39 178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C27 Z0P A 500 " pdb=" C28 Z0P A 500 " pdb=" C29 Z0P A 500 " pdb=" C30 Z0P A 500 " ideal model delta sinusoidal sigma weight residual 177.88 -0.31 178.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C27 Z0P E 500 " pdb=" C28 Z0P E 500 " pdb=" C29 Z0P E 500 " pdb=" C30 Z0P E 500 " ideal model delta sinusoidal sigma weight residual 177.88 -0.26 178.14 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1575 0.043 - 0.087: 396 0.087 - 0.130: 61 0.130 - 0.173: 8 0.173 - 0.216: 6 Chirality restraints: 2046 Sorted by residual: chirality pdb=" C2 Z0P F 500 " pdb=" C1 Z0P F 500 " pdb=" C3 Z0P F 500 " pdb=" O3 Z0P F 500 " both_signs ideal model delta sigma weight residual False -2.30 -2.52 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C2 Z0P C 500 " pdb=" C1 Z0P C 500 " pdb=" C3 Z0P C 500 " pdb=" O3 Z0P C 500 " both_signs ideal model delta sigma weight residual False -2.30 -2.51 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C2 Z0P E 500 " pdb=" C1 Z0P E 500 " pdb=" C3 Z0P E 500 " pdb=" O3 Z0P E 500 " both_signs ideal model delta sigma weight residual False -2.30 -2.51 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2043 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 Z0P E 500 " 0.010 2.00e-02 2.50e+03 3.52e-01 1.24e+03 pdb=" C30 Z0P E 500 " -0.300 2.00e-02 2.50e+03 pdb=" C31 Z0P E 500 " 0.571 2.00e-02 2.50e+03 pdb=" C32 Z0P E 500 " -0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 Z0P B 500 " 0.232 2.00e-02 2.50e+03 3.49e-01 1.22e+03 pdb=" C30 Z0P B 500 " -0.077 2.00e-02 2.50e+03 pdb=" C31 Z0P B 500 " -0.534 2.00e-02 2.50e+03 pdb=" C32 Z0P B 500 " 0.379 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 Z0P A 500 " 0.300 2.00e-02 2.50e+03 3.34e-01 1.12e+03 pdb=" C30 Z0P A 500 " -0.236 2.00e-02 2.50e+03 pdb=" C31 Z0P A 500 " -0.419 2.00e-02 2.50e+03 pdb=" C32 Z0P A 500 " 0.355 2.00e-02 2.50e+03 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2503 2.77 - 3.30: 12589 3.30 - 3.84: 20313 3.84 - 4.37: 23426 4.37 - 4.90: 41975 Nonbonded interactions: 100806 Sorted by model distance: nonbonded pdb=" OH TYR B 372 " pdb=" O VAL B 392 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR A 372 " pdb=" O VAL A 392 " model vdw 2.257 3.040 nonbonded pdb=" O TYR B 266 " pdb=" NZ LYS B 272 " model vdw 2.305 3.120 nonbonded pdb=" OH TYR D 372 " pdb=" O VAL D 392 " model vdw 2.306 3.040 nonbonded pdb=" O TYR A 266 " pdb=" NZ LYS A 272 " model vdw 2.309 3.120 ... (remaining 100801 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 144 through 500) selection = (chain 'B' and resid 144 through 500) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.290 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.007 0.203 13898 Z= 0.384 Angle : 0.803 18.993 18876 Z= 0.350 Chirality : 0.040 0.216 2046 Planarity : 0.018 0.352 2268 Dihedral : 17.763 178.266 4912 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.20), residues: 1572 helix: -0.05 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -2.63 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 370 TYR 0.010 0.001 TYR B 296 PHE 0.014 0.001 PHE E 298 TRP 0.014 0.001 TRP D 270 HIS 0.005 0.001 HIS C 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.38 (13892) covalent geometry : angle 0.80290 / 0.35 (18864) SS BOND : bond 0.00268 / 0.14 ( 6) SS BOND : angle 1.00472 / 0.61 ( 12) hydrogen bonds : bond 0.26458 / 17.61 ( 630) hydrogen bonds : angle 6.36078 / 4.54 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.536 Fit side-chains REVERT: A 321 ASN cc_start: 0.8224 (p0) cc_final: 0.8016 (p0) REVERT: B 321 ASN cc_start: 0.8316 (p0) cc_final: 0.8092 (p0) REVERT: C 189 ILE cc_start: 0.8607 (tp) cc_final: 0.8369 (tp) REVERT: C 280 TRP cc_start: 0.7134 (t60) cc_final: 0.6809 (t60) REVERT: D 253 SER cc_start: 0.8496 (p) cc_final: 0.7944 (p) REVERT: F 189 ILE cc_start: 0.8740 (tp) cc_final: 0.8537 (tp) REVERT: F 280 TRP cc_start: 0.7142 (t60) cc_final: 0.6825 (t60) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1011 time to fit residues: 33.0523 Evaluate side-chains 197 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 181 GLN C 174 HIS C 301 HIS C 344 HIS D 224 HIS ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 HIS D 364 HIS E 224 HIS ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS E 364 HIS F 301 HIS F 344 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.218284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165303 restraints weight = 14417.708| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.79 r_work: 0.3518 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13898 Z= 0.148 Angle : 0.567 6.550 18876 Z= 0.300 Chirality : 0.040 0.168 2046 Planarity : 0.005 0.104 2268 Dihedral : 15.034 134.622 1972 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 0.76 % Allowed : 7.19 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1572 helix: 1.22 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.59 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.014 0.001 TYR B 296 PHE 0.018 0.001 PHE B 298 TRP 0.016 0.001 TRP B 150 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (13892) covalent geometry : angle 0.56654 / 0.30 (18864) SS BOND : bond 0.00298 / 0.15 ( 6) SS BOND : angle 0.90198 / 0.54 ( 12) hydrogen bonds : bond 0.06521 / 4.20 ( 630) hydrogen bonds : angle 3.60145 / 2.53 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.328 Fit side-chains REVERT: A 321 ASN cc_start: 0.8637 (p0) cc_final: 0.8339 (p0) REVERT: A 370 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7434 (ttp-110) REVERT: B 321 ASN cc_start: 0.8596 (p0) cc_final: 0.8292 (p0) REVERT: B 358 ARG cc_start: 0.8741 (tpt170) cc_final: 0.8303 (tpt170) REVERT: C 189 ILE cc_start: 0.8863 (tp) cc_final: 0.8610 (tp) REVERT: C 209 MET cc_start: 0.7245 (mmm) cc_final: 0.6782 (tpp) REVERT: C 280 TRP cc_start: 0.6993 (t60) cc_final: 0.6552 (t60) REVERT: D 180 MET cc_start: 0.5393 (tpp) cc_final: 0.5044 (mtm) REVERT: F 189 ILE cc_start: 0.8887 (tp) cc_final: 0.8575 (tp) REVERT: F 280 TRP cc_start: 0.7046 (t60) cc_final: 0.6611 (t60) outliers start: 11 outliers final: 10 residues processed: 213 average time/residue: 0.0978 time to fit residues: 31.6793 Evaluate side-chains 197 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 154 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 181 GLN C 174 HIS ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.220370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167025 restraints weight = 14522.704| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.78 r_work: 0.3541 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13898 Z= 0.116 Angle : 0.506 4.848 18876 Z= 0.268 Chirality : 0.039 0.168 2046 Planarity : 0.004 0.072 2268 Dihedral : 14.058 129.544 1972 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 1.04 % Allowed : 9.27 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1572 helix: 1.73 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.60 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.013 0.001 TYR B 296 PHE 0.015 0.001 PHE F 387 TRP 0.013 0.001 TRP B 402 HIS 0.004 0.001 HIS C 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (13892) covalent geometry : angle 0.50603 / 0.27 (18864) SS BOND : bond 0.00266 / 0.14 ( 6) SS BOND : angle 0.81490 / 0.48 ( 12) hydrogen bonds : bond 0.05133 / 3.29 ( 630) hydrogen bonds : angle 3.23727 / 2.27 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.365 Fit side-chains REVERT: A 321 ASN cc_start: 0.8531 (p0) cc_final: 0.8238 (p0) REVERT: B 321 ASN cc_start: 0.8497 (p0) cc_final: 0.8156 (p0) REVERT: B 358 ARG cc_start: 0.8721 (tpt170) cc_final: 0.8386 (tpt170) REVERT: C 189 ILE cc_start: 0.8891 (tp) cc_final: 0.8612 (tp) REVERT: C 209 MET cc_start: 0.7265 (mmm) cc_final: 0.6789 (tpp) REVERT: C 280 TRP cc_start: 0.7025 (t60) cc_final: 0.6634 (t60) REVERT: C 380 ILE cc_start: 0.7428 (mm) cc_final: 0.7148 (mm) REVERT: D 180 MET cc_start: 0.5545 (tpp) cc_final: 0.5262 (mtm) REVERT: D 345 TYR cc_start: 0.8017 (m-80) cc_final: 0.7701 (m-10) REVERT: F 189 ILE cc_start: 0.8942 (tp) cc_final: 0.8600 (tp) REVERT: F 280 TRP cc_start: 0.7003 (t60) cc_final: 0.6632 (t60) outliers start: 15 outliers final: 11 residues processed: 218 average time/residue: 0.1026 time to fit residues: 33.6857 Evaluate side-chains 215 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 0.0020 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 181 GLN C 181 GLN D 257 GLN D 393 ASN E 331 ASN F 181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.221778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167902 restraints weight = 14535.237| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.80 r_work: 0.3562 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13898 Z= 0.102 Angle : 0.483 6.267 18876 Z= 0.257 Chirality : 0.038 0.171 2046 Planarity : 0.003 0.049 2268 Dihedral : 13.668 133.974 1972 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 1.11 % Allowed : 10.58 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1572 helix: 2.01 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.54 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 196 TYR 0.012 0.001 TYR B 296 PHE 0.014 0.001 PHE C 387 TRP 0.009 0.001 TRP B 150 HIS 0.004 0.001 HIS F 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (13892) covalent geometry : angle 0.48291 / 0.26 (18864) SS BOND : bond 0.00242 / 0.13 ( 6) SS BOND : angle 0.78041 / 0.47 ( 12) hydrogen bonds : bond 0.04291 / 2.73 ( 630) hydrogen bonds : angle 3.07319 / 2.16 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.491 Fit side-chains REVERT: A 321 ASN cc_start: 0.8512 (p0) cc_final: 0.8195 (p0) REVERT: B 321 ASN cc_start: 0.8473 (p0) cc_final: 0.8128 (p0) REVERT: B 358 ARG cc_start: 0.8704 (tpt170) cc_final: 0.8349 (tpt170) REVERT: C 189 ILE cc_start: 0.8982 (tp) cc_final: 0.8688 (tp) REVERT: C 209 MET cc_start: 0.7253 (mmm) cc_final: 0.6809 (tpp) REVERT: C 280 TRP cc_start: 0.6872 (t60) cc_final: 0.6625 (t60) REVERT: C 380 ILE cc_start: 0.7441 (mm) cc_final: 0.7153 (mm) REVERT: D 180 MET cc_start: 0.5430 (tpp) cc_final: 0.5201 (mtm) REVERT: D 345 TYR cc_start: 0.7992 (m-80) cc_final: 0.7725 (m-10) REVERT: E 196 ARG cc_start: 0.8409 (ttt180) cc_final: 0.7666 (ttm-80) REVERT: E 307 MET cc_start: 0.6775 (tpp) cc_final: 0.6376 (tpp) REVERT: F 280 TRP cc_start: 0.6861 (t60) cc_final: 0.6582 (t60) REVERT: F 380 ILE cc_start: 0.7467 (mm) cc_final: 0.7181 (mm) outliers start: 16 outliers final: 10 residues processed: 229 average time/residue: 0.0992 time to fit residues: 34.8469 Evaluate side-chains 227 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 109 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.217714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.169564 restraints weight = 14699.134| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.94 r_work: 0.3481 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13898 Z= 0.152 Angle : 0.534 5.550 18876 Z= 0.282 Chirality : 0.040 0.170 2046 Planarity : 0.004 0.036 2268 Dihedral : 13.616 136.997 1972 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 1.80 % Allowed : 10.37 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.22), residues: 1572 helix: 1.99 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.53 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.019 0.002 TYR B 296 PHE 0.021 0.001 PHE A 298 TRP 0.012 0.001 TRP A 402 HIS 0.005 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (13892) covalent geometry : angle 0.53356 / 0.28 (18864) SS BOND : bond 0.00316 / 0.16 ( 6) SS BOND : angle 0.80807 / 0.48 ( 12) hydrogen bonds : bond 0.05453 / 3.47 ( 630) hydrogen bonds : angle 3.18258 / 2.23 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.514 Fit side-chains REVERT: A 321 ASN cc_start: 0.8692 (p0) cc_final: 0.8307 (p0) REVERT: B 321 ASN cc_start: 0.8673 (p0) cc_final: 0.8325 (p0) REVERT: C 189 ILE cc_start: 0.8991 (tp) cc_final: 0.8694 (tp) REVERT: C 209 MET cc_start: 0.7319 (mmm) cc_final: 0.6886 (tpp) REVERT: C 280 TRP cc_start: 0.6896 (t60) cc_final: 0.6624 (t60) REVERT: C 380 ILE cc_start: 0.7515 (mm) cc_final: 0.7237 (mm) REVERT: D 180 MET cc_start: 0.5701 (tpp) cc_final: 0.5391 (mtm) REVERT: D 297 MET cc_start: 0.7480 (tpp) cc_final: 0.7249 (tpp) REVERT: F 280 TRP cc_start: 0.6884 (t60) cc_final: 0.6618 (t60) outliers start: 26 outliers final: 21 residues processed: 231 average time/residue: 0.0992 time to fit residues: 35.1409 Evaluate side-chains 228 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 78 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.220348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.168006 restraints weight = 14565.842| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.85 r_work: 0.3529 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13898 Z= 0.104 Angle : 0.484 4.994 18876 Z= 0.257 Chirality : 0.039 0.173 2046 Planarity : 0.003 0.032 2268 Dihedral : 13.037 135.275 1972 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 1.11 % Allowed : 11.00 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.22), residues: 1572 helix: 2.19 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.60 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 225 TYR 0.012 0.001 TYR A 296 PHE 0.012 0.001 PHE C 387 TRP 0.009 0.001 TRP B 150 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (13892) covalent geometry : angle 0.48376 / 0.26 (18864) SS BOND : bond 0.00255 / 0.13 ( 6) SS BOND : angle 0.76245 / 0.46 ( 12) hydrogen bonds : bond 0.04208 / 2.68 ( 630) hydrogen bonds : angle 3.00263 / 2.10 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 0.483 Fit side-chains REVERT: A 188 ASP cc_start: 0.8671 (t0) cc_final: 0.8174 (t0) REVERT: A 321 ASN cc_start: 0.8436 (p0) cc_final: 0.8130 (p0) REVERT: B 321 ASN cc_start: 0.8461 (p0) cc_final: 0.8105 (p0) REVERT: C 180 MET cc_start: 0.6310 (ttm) cc_final: 0.5975 (ttp) REVERT: C 209 MET cc_start: 0.7294 (mmm) cc_final: 0.6864 (tpp) REVERT: C 280 TRP cc_start: 0.6926 (t60) cc_final: 0.6701 (t60) REVERT: C 380 ILE cc_start: 0.7456 (mm) cc_final: 0.7178 (mm) REVERT: D 180 MET cc_start: 0.5934 (tpp) cc_final: 0.5506 (mtm) REVERT: D 277 PHE cc_start: 0.6173 (m-80) cc_final: 0.5731 (t80) REVERT: D 297 MET cc_start: 0.7429 (tpp) cc_final: 0.7192 (tpp) REVERT: E 196 ARG cc_start: 0.8466 (ttt180) cc_final: 0.7805 (ttm-80) REVERT: F 180 MET cc_start: 0.6142 (ttm) cc_final: 0.5857 (ttp) REVERT: F 380 ILE cc_start: 0.7436 (mm) cc_final: 0.7142 (mm) outliers start: 16 outliers final: 16 residues processed: 230 average time/residue: 0.0993 time to fit residues: 35.1424 Evaluate side-chains 235 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 7.9990 chunk 57 optimal weight: 0.0570 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 152 optimal weight: 3.9990 chunk 49 optimal weight: 0.0000 chunk 100 optimal weight: 0.7980 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 181 GLN D 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.222972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.175294 restraints weight = 14465.711| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 3.66 r_work: 0.3433 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13898 Z= 0.091 Angle : 0.463 4.752 18876 Z= 0.245 Chirality : 0.038 0.183 2046 Planarity : 0.003 0.048 2268 Dihedral : 12.431 137.108 1972 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 0.97 % Allowed : 11.76 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.22), residues: 1572 helix: 2.33 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 225 TYR 0.010 0.001 TYR B 296 PHE 0.015 0.001 PHE F 387 TRP 0.008 0.001 TRP B 150 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 (13892) covalent geometry : angle 0.46238 / 0.25 (18864) SS BOND : bond 0.00223 / 0.12 ( 6) SS BOND : angle 0.72135 / 0.44 ( 12) hydrogen bonds : bond 0.03526 / 2.24 ( 630) hydrogen bonds : angle 2.87589 / 2.01 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.407 Fit side-chains REVERT: A 188 ASP cc_start: 0.8630 (t0) cc_final: 0.8155 (t0) REVERT: A 321 ASN cc_start: 0.8443 (p0) cc_final: 0.8079 (p0) REVERT: A 358 ARG cc_start: 0.8772 (tpt170) cc_final: 0.8423 (tpt170) REVERT: B 321 ASN cc_start: 0.8423 (p0) cc_final: 0.8100 (p0) REVERT: B 358 ARG cc_start: 0.8731 (tpt170) cc_final: 0.8391 (tpt170) REVERT: C 180 MET cc_start: 0.6413 (ttm) cc_final: 0.6128 (ttp) REVERT: C 209 MET cc_start: 0.7264 (mmm) cc_final: 0.6855 (tpp) REVERT: C 280 TRP cc_start: 0.6852 (t60) cc_final: 0.6650 (t60) REVERT: C 380 ILE cc_start: 0.7425 (mm) cc_final: 0.7172 (mm) REVERT: D 174 HIS cc_start: 0.8457 (t-90) cc_final: 0.8108 (t-90) REVERT: D 180 MET cc_start: 0.5944 (tpp) cc_final: 0.4918 (ppp) REVERT: D 196 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7280 (ttm-80) REVERT: D 277 PHE cc_start: 0.6115 (m-80) cc_final: 0.5660 (t80) REVERT: D 297 MET cc_start: 0.7411 (tpp) cc_final: 0.7159 (tpp) REVERT: D 345 TYR cc_start: 0.7874 (m-80) cc_final: 0.7577 (m-10) REVERT: E 196 ARG cc_start: 0.8465 (ttt180) cc_final: 0.7779 (ttm-80) REVERT: F 180 MET cc_start: 0.6391 (ttm) cc_final: 0.6023 (ttp) REVERT: F 380 ILE cc_start: 0.7438 (mm) cc_final: 0.7158 (mm) outliers start: 14 outliers final: 14 residues processed: 228 average time/residue: 0.0954 time to fit residues: 33.4994 Evaluate side-chains 232 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 0.0770 chunk 119 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 0.0070 chunk 151 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN E 393 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.221411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 141)---------------| | r_work = 0.3949 r_free = 0.3949 target = 0.169587 restraints weight = 14410.034| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.73 r_work: 0.3548 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13898 Z= 0.105 Angle : 0.475 5.030 18876 Z= 0.252 Chirality : 0.039 0.177 2046 Planarity : 0.003 0.039 2268 Dihedral : 12.399 136.602 1972 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 1.45 % Allowed : 11.76 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1572 helix: 2.08 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -2.43 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 176 TYR 0.013 0.001 TYR B 296 PHE 0.013 0.001 PHE C 387 TRP 0.007 0.001 TRP B 150 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (13892) covalent geometry : angle 0.47487 / 0.25 (18864) SS BOND : bond 0.00254 / 0.13 ( 6) SS BOND : angle 0.74225 / 0.44 ( 12) hydrogen bonds : bond 0.04056 / 2.57 ( 630) hydrogen bonds : angle 2.89700 / 2.03 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.524 Fit side-chains REVERT: A 188 ASP cc_start: 0.8689 (t0) cc_final: 0.8152 (t0) REVERT: A 321 ASN cc_start: 0.8460 (p0) cc_final: 0.8124 (p0) REVERT: B 321 ASN cc_start: 0.8484 (p0) cc_final: 0.8127 (p0) REVERT: B 358 ARG cc_start: 0.8700 (tpt170) cc_final: 0.8353 (tpt170) REVERT: C 180 MET cc_start: 0.6266 (ttm) cc_final: 0.5994 (ttp) REVERT: C 209 MET cc_start: 0.7342 (mmm) cc_final: 0.6902 (tpp) REVERT: C 380 ILE cc_start: 0.7335 (mm) cc_final: 0.7069 (mm) REVERT: D 174 HIS cc_start: 0.8424 (t-90) cc_final: 0.8113 (t-90) REVERT: D 180 MET cc_start: 0.5758 (tpp) cc_final: 0.4848 (ppp) REVERT: D 196 ARG cc_start: 0.8074 (ttt180) cc_final: 0.7333 (ttm-80) REVERT: D 277 PHE cc_start: 0.6184 (m-80) cc_final: 0.5722 (t80) REVERT: D 297 MET cc_start: 0.7396 (tpp) cc_final: 0.7149 (tpp) REVERT: D 345 TYR cc_start: 0.7898 (m-80) cc_final: 0.7583 (m-10) REVERT: E 196 ARG cc_start: 0.8485 (ttt180) cc_final: 0.7812 (ttm-80) REVERT: F 170 MET cc_start: 0.8430 (ttm) cc_final: 0.8134 (mtp) REVERT: F 180 MET cc_start: 0.6359 (ttm) cc_final: 0.6016 (ttp) REVERT: F 380 ILE cc_start: 0.7432 (mm) cc_final: 0.7146 (mm) outliers start: 21 outliers final: 20 residues processed: 228 average time/residue: 0.1041 time to fit residues: 36.0014 Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 100 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.219282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172290 restraints weight = 14779.152| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.85 r_work: 0.3514 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13898 Z= 0.128 Angle : 0.500 5.254 18876 Z= 0.264 Chirality : 0.039 0.182 2046 Planarity : 0.003 0.041 2268 Dihedral : 12.566 135.352 1972 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 1.59 % Allowed : 11.76 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1572 helix: 2.04 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.016 0.001 TYR B 296 PHE 0.016 0.001 PHE A 298 TRP 0.009 0.001 TRP D 280 HIS 0.004 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13892) covalent geometry : angle 0.49938 / 0.26 (18864) SS BOND : bond 0.00284 / 0.15 ( 6) SS BOND : angle 0.75599 / 0.43 ( 12) hydrogen bonds : bond 0.04681 / 2.97 ( 630) hydrogen bonds : angle 2.97580 / 2.08 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.421 Fit side-chains REVERT: A 188 ASP cc_start: 0.8714 (t0) cc_final: 0.8206 (t0) REVERT: A 321 ASN cc_start: 0.8539 (p0) cc_final: 0.8181 (p0) REVERT: B 321 ASN cc_start: 0.8527 (p0) cc_final: 0.8164 (p0) REVERT: C 180 MET cc_start: 0.6342 (ttm) cc_final: 0.5981 (ttp) REVERT: C 380 ILE cc_start: 0.7351 (mm) cc_final: 0.7091 (mm) REVERT: D 174 HIS cc_start: 0.8437 (t-90) cc_final: 0.8168 (t-90) REVERT: D 180 MET cc_start: 0.5784 (tpp) cc_final: 0.4885 (ppp) REVERT: D 196 ARG cc_start: 0.8099 (ttt180) cc_final: 0.7343 (ttm-80) REVERT: D 277 PHE cc_start: 0.6181 (m-80) cc_final: 0.5738 (t80) REVERT: D 297 MET cc_start: 0.7421 (tpp) cc_final: 0.7169 (tpp) REVERT: D 345 TYR cc_start: 0.7967 (m-80) cc_final: 0.7596 (m-10) REVERT: E 196 ARG cc_start: 0.8510 (ttt180) cc_final: 0.7827 (ttm-80) REVERT: F 170 MET cc_start: 0.8466 (ttm) cc_final: 0.8174 (mtp) REVERT: F 180 MET cc_start: 0.6350 (ttm) cc_final: 0.6018 (ttp) outliers start: 23 outliers final: 23 residues processed: 233 average time/residue: 0.0981 time to fit residues: 34.8007 Evaluate side-chains 243 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.220444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.172892 restraints weight = 14651.946| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.70 r_work: 0.3359 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13898 Z= 0.111 Angle : 0.486 5.274 18876 Z= 0.258 Chirality : 0.039 0.184 2046 Planarity : 0.003 0.041 2268 Dihedral : 12.435 135.935 1972 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 1.73 % Allowed : 11.96 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1572 helix: 2.08 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.013 0.001 TYR B 296 PHE 0.017 0.001 PHE C 387 TRP 0.009 0.001 TRP B 150 HIS 0.003 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13892) covalent geometry : angle 0.48581 / 0.26 (18864) SS BOND : bond 0.00265 / 0.14 ( 6) SS BOND : angle 0.76031 / 0.44 ( 12) hydrogen bonds : bond 0.04275 / 2.71 ( 630) hydrogen bonds : angle 2.93955 / 2.06 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.465 Fit side-chains REVERT: A 159 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 188 ASP cc_start: 0.8687 (t0) cc_final: 0.8198 (t0) REVERT: A 321 ASN cc_start: 0.8563 (p0) cc_final: 0.8225 (p0) REVERT: B 321 ASN cc_start: 0.8549 (p0) cc_final: 0.8191 (p0) REVERT: B 400 TYR cc_start: 0.8619 (m-80) cc_final: 0.8192 (m-80) REVERT: C 180 MET cc_start: 0.6270 (ttm) cc_final: 0.5970 (ttp) REVERT: C 380 ILE cc_start: 0.7362 (mm) cc_final: 0.7104 (mm) REVERT: D 174 HIS cc_start: 0.8450 (t-90) cc_final: 0.8182 (t-90) REVERT: D 180 MET cc_start: 0.5790 (tpp) cc_final: 0.4887 (ppp) REVERT: D 196 ARG cc_start: 0.8126 (ttt180) cc_final: 0.7411 (ttm-80) REVERT: D 277 PHE cc_start: 0.6144 (m-80) cc_final: 0.5717 (t80) REVERT: D 297 MET cc_start: 0.7465 (tpp) cc_final: 0.7212 (tpp) REVERT: D 345 TYR cc_start: 0.7988 (m-80) cc_final: 0.7620 (m-10) REVERT: E 196 ARG cc_start: 0.8491 (ttt180) cc_final: 0.7842 (ttm-80) REVERT: F 180 MET cc_start: 0.6282 (ttm) cc_final: 0.6018 (ttp) REVERT: F 380 ILE cc_start: 0.7444 (mm) cc_final: 0.7191 (mm) outliers start: 25 outliers final: 23 residues processed: 232 average time/residue: 0.1007 time to fit residues: 35.8856 Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.219859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.172474 restraints weight = 14691.955| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.76 r_work: 0.3345 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13898 Z= 0.117 Angle : 0.492 5.286 18876 Z= 0.261 Chirality : 0.039 0.181 2046 Planarity : 0.003 0.040 2268 Dihedral : 12.475 135.950 1972 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 1.73 % Allowed : 12.17 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1572 helix: 2.05 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.014 0.001 TYR B 296 PHE 0.018 0.001 PHE F 387 TRP 0.008 0.001 TRP B 150 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13892) covalent geometry : angle 0.49212 / 0.26 (18864) SS BOND : bond 0.00269 / 0.14 ( 6) SS BOND : angle 0.76041 / 0.44 ( 12) hydrogen bonds : bond 0.04397 / 2.79 ( 630) hydrogen bonds : angle 2.95086 / 2.06 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3738.89 seconds wall clock time: 64 minutes 38.19 seconds (3878.19 seconds total)