Starting phenix.real_space_refine on Fri Feb 6 10:25:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wy8_66366/02_2026/9wy8_66366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wy8_66366/02_2026/9wy8_66366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wy8_66366/02_2026/9wy8_66366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wy8_66366/02_2026/9wy8_66366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wy8_66366/02_2026/9wy8_66366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wy8_66366/02_2026/9wy8_66366.map" } resolution = 2.69 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= 0.002 sd= 0.077 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 15894 2.51 5 N 4122 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24462 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4077 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 17, 'TRANS': 477} Chain: "B" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4077 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 17, 'TRANS': 477} Chain: "C" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4077 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 17, 'TRANS': 477} Chain: "D" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4077 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 17, 'TRANS': 477} Chain: "E" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4077 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 17, 'TRANS': 477} Chain: "F" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4077 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 17, 'TRANS': 477} Time building chain proxies: 5.90, per 1000 atoms: 0.24 Number of scatterers: 24462 At special positions: 0 Unit cell: (144.4, 133.95, 95.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 4392 8.00 N 4122 7.00 C 15894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 17 sheets defined 64.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.857A pdb=" N TYR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.966A pdb=" N TYR A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.633A pdb=" N ILE A 141 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 143 No H-bonds generated for 'chain 'A' and resid 142 through 143' Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.888A pdb=" N TRP A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.805A pdb=" N HIS A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 249 removed outlier: 3.669A pdb=" N PHE A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.859A pdb=" N SER A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 306 removed outlier: 3.859A pdb=" N ASP A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 4.215A pdb=" N LYS A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.244A pdb=" N ASN A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP A 329 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 364 through 382 removed outlier: 3.958A pdb=" N LYS A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 382 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.545A pdb=" N GLY A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 453 through 462 Processing helix chain 'A' and resid 471 through 476 removed outlier: 3.646A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 486 removed outlier: 3.881A pdb=" N LEU A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 23 through 29 Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.793A pdb=" N TYR B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 80 through 89 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.984A pdb=" N TYR B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 removed outlier: 3.601A pdb=" N ILE B 141 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 143 No H-bonds generated for 'chain 'B' and resid 142 through 143' Processing helix chain 'B' and resid 144 through 152 removed outlier: 3.921A pdb=" N TRP B 148 " --> pdb=" O HIS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 190 through 213 removed outlier: 3.779A pdb=" N HIS B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 249 removed outlier: 3.743A pdb=" N PHE B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.952A pdb=" N SER B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 306 removed outlier: 3.820A pdb=" N ASP B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 removed outlier: 4.143A pdb=" N LYS B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 342 removed outlier: 4.243A pdb=" N ASN B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 329 " --> pdb=" O MET B 325 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'B' and resid 364 through 382 removed outlier: 4.030A pdb=" N LYS B 377 " --> pdb=" O ASN B 373 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 399 Processing helix chain 'B' and resid 403 through 412 removed outlier: 3.550A pdb=" N GLY B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 471 through 476 removed outlier: 3.592A pdb=" N GLN B 475 " --> pdb=" O HIS B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 486 removed outlier: 3.669A pdb=" N LEU B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 23 through 29 Processing helix chain 'C' and resid 29 through 40 removed outlier: 3.870A pdb=" N TYR C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Proline residue: C 35 - end of helix Processing helix chain 'C' and resid 66 through 80 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 111 through 123 removed outlier: 4.088A pdb=" N TYR C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.612A pdb=" N ILE C 141 " --> pdb=" O PHE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 143 No H-bonds generated for 'chain 'C' and resid 142 through 143' Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.952A pdb=" N TRP C 148 " --> pdb=" O HIS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 190 through 213 removed outlier: 3.743A pdb=" N HIS C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 249 removed outlier: 3.718A pdb=" N PHE C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.850A pdb=" N SER C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 306 removed outlier: 3.783A pdb=" N ASP C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 removed outlier: 4.086A pdb=" N LYS C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 323 through 342 removed outlier: 4.204A pdb=" N ASN C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP C 329 " --> pdb=" O MET C 325 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 359 Processing helix chain 'C' and resid 364 through 382 removed outlier: 3.993A pdb=" N LYS C 377 " --> pdb=" O ASN C 373 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 382 " --> pdb=" O ILE C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 403 through 412 removed outlier: 3.616A pdb=" N GLY C 412 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 446 through 451 Processing helix chain 'C' and resid 453 through 462 Processing helix chain 'C' and resid 471 through 476 removed outlier: 3.698A pdb=" N GLN C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 486 removed outlier: 3.810A pdb=" N LEU C 483 " --> pdb=" O PHE C 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 23 through 29 Processing helix chain 'D' and resid 29 through 40 removed outlier: 3.857A pdb=" N TYR D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Proline residue: D 35 - end of helix Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.983A pdb=" N TYR D 116 " --> pdb=" O PHE D 112 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 141 removed outlier: 3.629A pdb=" N ILE D 141 " --> pdb=" O PHE D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 143 No H-bonds generated for 'chain 'D' and resid 142 through 143' Processing helix chain 'D' and resid 144 through 152 removed outlier: 3.890A pdb=" N TRP D 148 " --> pdb=" O HIS D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 167 through 178 Processing helix chain 'D' and resid 190 through 213 removed outlier: 3.804A pdb=" N HIS D 194 " --> pdb=" O PRO D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 249 removed outlier: 3.727A pdb=" N PHE D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 270 through 278 removed outlier: 3.810A pdb=" N SER D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 306 removed outlier: 3.997A pdb=" N ASP D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 4.184A pdb=" N LYS D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 342 removed outlier: 4.056A pdb=" N ASN D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP D 329 " --> pdb=" O MET D 325 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 364 through 382 removed outlier: 3.939A pdb=" N LYS D 377 " --> pdb=" O ASN D 373 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 382 " --> pdb=" O ILE D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.550A pdb=" N GLY D 412 " --> pdb=" O ARG D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 436 through 441 Processing helix chain 'D' and resid 446 through 451 Processing helix chain 'D' and resid 453 through 462 Processing helix chain 'D' and resid 471 through 476 removed outlier: 3.636A pdb=" N GLN D 475 " --> pdb=" O HIS D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 486 removed outlier: 3.883A pdb=" N LEU D 483 " --> pdb=" O PHE D 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 23 through 29 Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.843A pdb=" N TYR E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Proline residue: E 35 - end of helix Processing helix chain 'E' and resid 66 through 80 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 111 through 123 removed outlier: 3.980A pdb=" N TYR E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 141 removed outlier: 3.599A pdb=" N ILE E 141 " --> pdb=" O PHE E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 143 No H-bonds generated for 'chain 'E' and resid 142 through 143' Processing helix chain 'E' and resid 144 through 152 removed outlier: 3.924A pdb=" N TRP E 148 " --> pdb=" O HIS E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 167 through 178 Processing helix chain 'E' and resid 190 through 213 removed outlier: 3.769A pdb=" N HIS E 194 " --> pdb=" O PRO E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 249 removed outlier: 3.673A pdb=" N PHE E 249 " --> pdb=" O ALA E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 270 through 278 removed outlier: 3.959A pdb=" N SER E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU E 278 " --> pdb=" O SER E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 306 removed outlier: 3.792A pdb=" N ASP E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 292 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 315 removed outlier: 4.146A pdb=" N LYS E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 342 removed outlier: 4.257A pdb=" N ASN E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP E 328 " --> pdb=" O LYS E 324 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP E 329 " --> pdb=" O MET E 325 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 359 Processing helix chain 'E' and resid 364 through 382 removed outlier: 4.029A pdb=" N LYS E 377 " --> pdb=" O ASN E 373 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER E 382 " --> pdb=" O ILE E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 399 Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.513A pdb=" N GLY E 412 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 428 Processing helix chain 'E' and resid 436 through 441 Processing helix chain 'E' and resid 446 through 451 Processing helix chain 'E' and resid 453 through 462 Processing helix chain 'E' and resid 471 through 476 removed outlier: 3.640A pdb=" N GLN E 475 " --> pdb=" O HIS E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 486 removed outlier: 4.021A pdb=" N LEU E 483 " --> pdb=" O PHE E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 23 through 29 Processing helix chain 'F' and resid 29 through 40 removed outlier: 3.866A pdb=" N TYR F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Proline residue: F 35 - end of helix Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 111 through 123 removed outlier: 4.063A pdb=" N TYR F 116 " --> pdb=" O PHE F 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 removed outlier: 3.611A pdb=" N ILE F 141 " --> pdb=" O PHE F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 143 No H-bonds generated for 'chain 'F' and resid 142 through 143' Processing helix chain 'F' and resid 144 through 152 removed outlier: 3.923A pdb=" N TRP F 148 " --> pdb=" O HIS F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 167 through 178 Processing helix chain 'F' and resid 190 through 213 removed outlier: 3.750A pdb=" N HIS F 194 " --> pdb=" O PRO F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 249 removed outlier: 3.721A pdb=" N PHE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 270 through 278 removed outlier: 3.805A pdb=" N SER F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 278 " --> pdb=" O SER F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 306 removed outlier: 3.771A pdb=" N ASP F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 315 removed outlier: 4.082A pdb=" N LYS F 312 " --> pdb=" O GLU F 308 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 323 through 342 removed outlier: 4.218A pdb=" N ASN F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP F 329 " --> pdb=" O MET F 325 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 359 Processing helix chain 'F' and resid 364 through 382 removed outlier: 3.989A pdb=" N LYS F 377 " --> pdb=" O ASN F 373 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER F 382 " --> pdb=" O ILE F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 399 Processing helix chain 'F' and resid 403 through 412 removed outlier: 3.602A pdb=" N GLY F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 428 Processing helix chain 'F' and resid 436 through 441 Processing helix chain 'F' and resid 446 through 451 Processing helix chain 'F' and resid 453 through 462 Processing helix chain 'F' and resid 471 through 476 removed outlier: 3.696A pdb=" N GLN F 475 " --> pdb=" O HIS F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 486 removed outlier: 3.805A pdb=" N LEU F 483 " --> pdb=" O PHE F 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.803A pdb=" N ASN A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 221 removed outlier: 4.236A pdb=" N SER A 217 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 11.103A pdb=" N VAL A 129 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N THR A 258 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N ILE A 131 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER A 256 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP A 133 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 55 removed outlier: 6.782A pdb=" N ASN B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA6, first strand: chain 'B' and resid 217 through 221 removed outlier: 4.247A pdb=" N SER B 217 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP B 133 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS B 257 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.830A pdb=" N ASN C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AA9, first strand: chain 'C' and resid 217 through 221 removed outlier: 4.313A pdb=" N SER C 217 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP C 133 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS C 257 " --> pdb=" O ASP C 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 55 removed outlier: 6.810A pdb=" N ASN D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB3, first strand: chain 'D' and resid 217 through 221 removed outlier: 4.245A pdb=" N SER D 217 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP D 133 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS D 257 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 48 through 55 removed outlier: 6.819A pdb=" N ASN E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AB6, first strand: chain 'E' and resid 217 through 221 removed outlier: 4.222A pdb=" N SER E 217 " --> pdb=" O PHE E 228 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP E 133 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS E 257 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 48 through 55 removed outlier: 6.786A pdb=" N ASN F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 217 through 221 removed outlier: 4.260A pdb=" N SER F 217 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP F 133 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS F 257 " --> pdb=" O ASP F 133 " (cutoff:3.500A) 1254 hydrogen bonds defined for protein. 3597 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: 5.04 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3827 1.30 - 1.43: 6984 1.43 - 1.55: 14184 1.55 - 1.68: 1 1.68 - 1.80: 84 Bond restraints: 25080 Sorted by residual: bond pdb=" C TYR C 226 " pdb=" O TYR C 226 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.14e-02 7.69e+03 2.59e+01 bond pdb=" C VAL D 222 " pdb=" O VAL D 222 " ideal model delta sigma weight residual 1.236 1.178 0.059 1.19e-02 7.06e+03 2.42e+01 bond pdb=" C VAL A 222 " pdb=" O VAL A 222 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.19e-02 7.06e+03 2.36e+01 bond pdb=" C TYR F 226 " pdb=" O TYR F 226 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.14e-02 7.69e+03 2.08e+01 bond pdb=" C ARG A 220 " pdb=" O ARG A 220 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.14e-02 7.69e+03 1.92e+01 ... (remaining 25075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 33430 2.83 - 5.65: 380 5.65 - 8.48: 62 8.48 - 11.31: 12 11.31 - 14.13: 4 Bond angle restraints: 33888 Sorted by residual: angle pdb=" C ASP E 224 " pdb=" CA ASP E 224 " pdb=" CB ASP E 224 " ideal model delta sigma weight residual 109.84 97.96 11.88 1.63e+00 3.76e-01 5.31e+01 angle pdb=" C ASP B 224 " pdb=" CA ASP B 224 " pdb=" CB ASP B 224 " ideal model delta sigma weight residual 109.84 98.65 11.19 1.63e+00 3.76e-01 4.72e+01 angle pdb=" C ASP C 224 " pdb=" CA ASP C 224 " pdb=" CB ASP C 224 " ideal model delta sigma weight residual 109.65 99.44 10.21 1.71e+00 3.42e-01 3.56e+01 angle pdb=" C ASP F 224 " pdb=" CA ASP F 224 " pdb=" CB ASP F 224 " ideal model delta sigma weight residual 109.65 99.56 10.09 1.71e+00 3.42e-01 3.48e+01 angle pdb=" C ASP D 224 " pdb=" CA ASP D 224 " pdb=" CB ASP D 224 " ideal model delta sigma weight residual 109.65 99.92 9.73 1.71e+00 3.42e-01 3.24e+01 ... (remaining 33883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12772 17.92 - 35.85: 1670 35.85 - 53.77: 514 53.77 - 71.69: 34 71.69 - 89.61: 22 Dihedral angle restraints: 15012 sinusoidal: 6192 harmonic: 8820 Sorted by residual: dihedral pdb=" C ASP E 224 " pdb=" N ASP E 224 " pdb=" CA ASP E 224 " pdb=" CB ASP E 224 " ideal model delta harmonic sigma weight residual -122.60 -108.50 -14.10 0 2.50e+00 1.60e-01 3.18e+01 dihedral pdb=" C ASP B 224 " pdb=" N ASP B 224 " pdb=" CA ASP B 224 " pdb=" CB ASP B 224 " ideal model delta harmonic sigma weight residual -122.60 -109.39 -13.21 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C ASP C 224 " pdb=" N ASP C 224 " pdb=" CA ASP C 224 " pdb=" CB ASP C 224 " ideal model delta harmonic sigma weight residual -122.60 -111.39 -11.21 0 2.50e+00 1.60e-01 2.01e+01 ... (remaining 15009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2812 0.058 - 0.116: 717 0.116 - 0.175: 95 0.175 - 0.233: 25 0.233 - 0.291: 17 Chirality restraints: 3666 Sorted by residual: chirality pdb=" CA ASP C 223 " pdb=" N ASP C 223 " pdb=" C ASP C 223 " pdb=" CB ASP C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ASP D 223 " pdb=" N ASP D 223 " pdb=" C ASP D 223 " pdb=" CB ASP D 223 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ASP F 223 " pdb=" N ASP F 223 " pdb=" C ASP F 223 " pdb=" CB ASP F 223 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3663 not shown) Planarity restraints: 4212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 101 " -0.084 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO F 102 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO F 102 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 102 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 101 " -0.064 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO D 102 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 296 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" CD GLU E 296 " 0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU E 296 " -0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU E 296 " -0.024 2.00e-02 2.50e+03 ... (remaining 4209 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4679 2.77 - 3.30: 23172 3.30 - 3.83: 45917 3.83 - 4.37: 56379 4.37 - 4.90: 93156 Nonbonded interactions: 223303 Sorted by model distance: nonbonded pdb=" OG SER B 96 " pdb=" OE1 GLU B 198 " model vdw 2.231 3.040 nonbonded pdb=" OG SER E 96 " pdb=" OE1 GLU E 198 " model vdw 2.240 3.040 nonbonded pdb=" O LYS F 337 " pdb=" OG SER F 341 " model vdw 2.245 3.040 nonbonded pdb=" OG SER C 96 " pdb=" OE1 GLU C 198 " model vdw 2.254 3.040 nonbonded pdb=" OG SER F 96 " pdb=" OE1 GLU F 198 " model vdw 2.256 3.040 ... (remaining 223298 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.110 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.006 0.079 25080 Z= 0.297 Angle : 0.823 14.135 33888 Z= 0.455 Chirality : 0.055 0.291 3666 Planarity : 0.007 0.127 4212 Dihedral : 17.063 89.614 9336 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.89 % Favored : 95.91 % Rotamer: Outliers : 0.37 % Allowed : 20.67 % Favored : 78.96 % Cbeta Deviations : 0.21 % 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: -1.40 (0.14), residues: 2958 helix: -0.81 (0.11), residues: 1620 sheet: -0.65 (0.41), residues: 156 loop : -0.91 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 436 TYR 0.023 0.002 TYR B 361 PHE 0.037 0.003 PHE E 101 TRP 0.018 0.002 TRP E 393 HIS 0.006 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00590 (25080) covalent geometry : angle 0.82333 (33888) hydrogen bonds : bond 0.13588 ( 1254) hydrogen bonds : angle 6.96023 ( 3597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 259 time to evaluate : 0.978 Fit side-chains REVERT: C 495 MET cc_start: 0.7492 (mtp) cc_final: 0.7226 (ptp) REVERT: F 495 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7296 (ptp) outliers start: 10 outliers final: 0 residues processed: 267 average time/residue: 0.7087 time to fit residues: 214.7455 Evaluate side-chains 234 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 495 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0470 chunk 111 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.160922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132994 restraints weight = 25797.244| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.56 r_work: 0.3353 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25080 Z= 0.138 Angle : 0.556 12.229 33888 Z= 0.292 Chirality : 0.042 0.143 3666 Planarity : 0.005 0.089 4212 Dihedral : 4.782 22.739 3303 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.92 % Rotamer: Outliers : 2.99 % Allowed : 21.45 % Favored : 75.56 % 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: -0.57 (0.15), residues: 2958 helix: 0.01 (0.12), residues: 1668 sheet: -0.66 (0.38), residues: 168 loop : -0.74 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 436 TYR 0.013 0.001 TYR E 70 PHE 0.020 0.002 PHE B 101 TRP 0.011 0.001 TRP C 328 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00304 (25080) covalent geometry : angle 0.55641 (33888) hydrogen bonds : bond 0.04453 ( 1254) hydrogen bonds : angle 5.30392 ( 3597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 277 time to evaluate : 0.977 Fit side-chains REVERT: A 342 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: A 381 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 492 ASP cc_start: 0.8399 (t0) cc_final: 0.8153 (t0) REVERT: A 495 MET cc_start: 0.7628 (mtp) cc_final: 0.7215 (ptm) REVERT: B 60 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8261 (ttm170) REVERT: B 124 THR cc_start: 0.6230 (OUTLIER) cc_final: 0.5899 (t) REVERT: B 262 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7296 (mm-30) REVERT: C 9 GLU cc_start: 0.8023 (tt0) cc_final: 0.7735 (tt0) REVERT: C 36 ILE cc_start: 0.7953 (mt) cc_final: 0.7744 (mp) REVERT: C 40 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7892 (mmtp) REVERT: C 262 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7269 (mm-30) REVERT: C 296 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: C 441 LYS cc_start: 0.8445 (mttp) cc_final: 0.8215 (mttm) REVERT: C 492 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7849 (t0) REVERT: C 495 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7397 (mtp) REVERT: D 172 ASP cc_start: 0.8258 (t70) cc_final: 0.8053 (t70) REVERT: E 124 THR cc_start: 0.6191 (OUTLIER) cc_final: 0.5844 (t) REVERT: F 9 GLU cc_start: 0.7939 (tt0) cc_final: 0.7672 (tt0) REVERT: F 36 ILE cc_start: 0.7974 (mt) cc_final: 0.7759 (mp) REVERT: F 40 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7960 (mmtp) REVERT: F 104 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6755 (tm) REVERT: F 492 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7724 (t0) REVERT: F 495 MET cc_start: 0.7611 (mtp) cc_final: 0.7160 (mtt) outliers start: 80 outliers final: 30 residues processed: 331 average time/residue: 0.7048 time to fit residues: 267.8796 Evaluate side-chains 280 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 492 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 155 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 HIS F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.161080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133187 restraints weight = 25802.629| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.56 r_work: 0.3347 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25080 Z= 0.127 Angle : 0.519 9.430 33888 Z= 0.272 Chirality : 0.041 0.140 3666 Planarity : 0.005 0.073 4212 Dihedral : 4.547 17.853 3300 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.38 % Favored : 96.42 % Rotamer: Outliers : 3.33 % Allowed : 22.01 % Favored : 74.66 % 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: -0.13 (0.15), residues: 2958 helix: 0.55 (0.12), residues: 1602 sheet: -1.39 (0.33), residues: 198 loop : -0.59 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 60 TYR 0.013 0.001 TYR C 70 PHE 0.028 0.002 PHE F 101 TRP 0.010 0.001 TRP C 328 HIS 0.004 0.001 HIS F 321 Details of bonding type rmsd covalent geometry : bond 0.00282 (25080) covalent geometry : angle 0.51937 (33888) hydrogen bonds : bond 0.03997 ( 1254) hydrogen bonds : angle 5.02835 ( 3597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 285 time to evaluate : 0.972 Fit side-chains REVERT: A 40 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7876 (mptt) REVERT: A 124 THR cc_start: 0.6231 (OUTLIER) cc_final: 0.6030 (t) REVERT: A 325 MET cc_start: 0.4345 (OUTLIER) cc_final: 0.4054 (tmm) REVERT: A 381 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8255 (mt) REVERT: A 492 ASP cc_start: 0.8414 (t0) cc_final: 0.8147 (t0) REVERT: A 495 MET cc_start: 0.7702 (mtp) cc_final: 0.7393 (ptm) REVERT: B 60 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8145 (ttm170) REVERT: B 114 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5703 (pt0) REVERT: B 262 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7300 (mm-30) REVERT: B 283 ASP cc_start: 0.5523 (m-30) cc_final: 0.5020 (t0) REVERT: B 495 MET cc_start: 0.7402 (mtp) cc_final: 0.6859 (ptp) REVERT: C 262 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7399 (mm-30) REVERT: C 296 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: C 315 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.4871 (mt) REVERT: C 495 MET cc_start: 0.7674 (mtp) cc_final: 0.7003 (ptp) REVERT: D 40 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7868 (mptt) REVERT: D 124 THR cc_start: 0.6167 (OUTLIER) cc_final: 0.5930 (t) REVERT: D 257 LYS cc_start: 0.7734 (mmtp) cc_final: 0.7509 (mmtm) REVERT: D 495 MET cc_start: 0.7429 (mtp) cc_final: 0.7007 (ptp) REVERT: E 40 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7765 (mmtp) REVERT: E 103 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6617 (mm-30) REVERT: E 495 MET cc_start: 0.7323 (mtp) cc_final: 0.6826 (ptp) REVERT: F 104 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6763 (tm) REVERT: F 262 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7409 (mm-30) REVERT: F 495 MET cc_start: 0.7644 (mtp) cc_final: 0.7413 (mtt) outliers start: 89 outliers final: 33 residues processed: 348 average time/residue: 0.6693 time to fit residues: 267.1661 Evaluate side-chains 295 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 344 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 170 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 181 optimal weight: 0.1980 chunk 160 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 284 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 224 optimal weight: 0.4980 chunk 239 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.161976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134261 restraints weight = 25640.367| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.56 r_work: 0.3359 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25080 Z= 0.119 Angle : 0.505 9.001 33888 Z= 0.264 Chirality : 0.041 0.142 3666 Planarity : 0.005 0.066 4212 Dihedral : 4.413 16.941 3300 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.01 % Favored : 96.79 % Rotamer: Outliers : 3.81 % Allowed : 21.82 % Favored : 74.36 % 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: -0.03 (0.15), residues: 2958 helix: 0.68 (0.12), residues: 1644 sheet: -1.57 (0.32), residues: 198 loop : -0.64 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 49 TYR 0.013 0.001 TYR C 70 PHE 0.024 0.002 PHE E 101 TRP 0.009 0.001 TRP C 328 HIS 0.004 0.001 HIS F 321 Details of bonding type rmsd covalent geometry : bond 0.00264 (25080) covalent geometry : angle 0.50458 (33888) hydrogen bonds : bond 0.03774 ( 1254) hydrogen bonds : angle 4.87067 ( 3597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 288 time to evaluate : 0.993 Fit side-chains REVERT: A 40 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7922 (mptt) REVERT: A 124 THR cc_start: 0.6184 (OUTLIER) cc_final: 0.5971 (t) REVERT: A 381 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 492 ASP cc_start: 0.8477 (t0) cc_final: 0.8203 (t0) REVERT: A 495 MET cc_start: 0.7691 (mtp) cc_final: 0.7418 (ptm) REVERT: B 40 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7843 (mmtp) REVERT: B 60 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8212 (ttm170) REVERT: B 104 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6568 (tm) REVERT: B 214 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8564 (pttm) REVERT: B 262 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7317 (mm-30) REVERT: B 283 ASP cc_start: 0.5564 (m-30) cc_final: 0.5026 (t0) REVERT: B 495 MET cc_start: 0.7264 (mtp) cc_final: 0.6732 (ptp) REVERT: C 9 GLU cc_start: 0.7943 (tt0) cc_final: 0.7662 (tt0) REVERT: C 40 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7905 (mmtp) REVERT: C 262 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7407 (mm-30) REVERT: C 296 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 315 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4881 (mt) REVERT: C 441 LYS cc_start: 0.8355 (mttp) cc_final: 0.8095 (mttm) REVERT: C 492 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7682 (t0) REVERT: C 495 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7390 (mtp) REVERT: D 40 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7907 (mptt) REVERT: D 124 THR cc_start: 0.6131 (OUTLIER) cc_final: 0.5928 (t) REVERT: D 214 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8544 (pttm) REVERT: D 257 LYS cc_start: 0.7735 (mmtp) cc_final: 0.7497 (mmtm) REVERT: D 495 MET cc_start: 0.7451 (mtp) cc_final: 0.7018 (ptp) REVERT: E 40 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7763 (mmtp) REVERT: E 103 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6546 (mm-30) REVERT: E 214 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8493 (pttm) REVERT: E 495 MET cc_start: 0.7214 (mtp) cc_final: 0.6804 (ptp) REVERT: F 40 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7996 (mmtp) REVERT: F 262 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7392 (mm-30) REVERT: F 441 LYS cc_start: 0.8326 (mttp) cc_final: 0.8084 (mttm) REVERT: F 492 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7636 (t0) REVERT: F 495 MET cc_start: 0.7648 (mtp) cc_final: 0.7223 (mtt) outliers start: 102 outliers final: 32 residues processed: 368 average time/residue: 0.6426 time to fit residues: 272.5983 Evaluate side-chains 310 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 492 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 292 optimal weight: 0.0010 chunk 185 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 267 optimal weight: 0.9980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131223 restraints weight = 25685.435| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.55 r_work: 0.3329 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25080 Z= 0.147 Angle : 0.525 8.728 33888 Z= 0.276 Chirality : 0.042 0.146 3666 Planarity : 0.005 0.060 4212 Dihedral : 4.443 16.824 3300 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.38 % Favored : 96.42 % Rotamer: Outliers : 3.70 % Allowed : 23.28 % Favored : 73.02 % 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: 0.05 (0.15), residues: 2958 helix: 0.74 (0.12), residues: 1638 sheet: -1.68 (0.32), residues: 198 loop : -0.54 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 49 TYR 0.012 0.001 TYR C 70 PHE 0.027 0.002 PHE F 101 TRP 0.009 0.001 TRP A 393 HIS 0.004 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00335 (25080) covalent geometry : angle 0.52545 (33888) hydrogen bonds : bond 0.03970 ( 1254) hydrogen bonds : angle 4.89924 ( 3597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 275 time to evaluate : 0.974 Fit side-chains REVERT: A 40 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7949 (mmtp) REVERT: A 124 THR cc_start: 0.6384 (OUTLIER) cc_final: 0.6132 (t) REVERT: A 200 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 283 ASP cc_start: 0.5867 (m-30) cc_final: 0.5333 (t0) REVERT: A 325 MET cc_start: 0.4667 (mtp) cc_final: 0.4442 (tmm) REVERT: A 381 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8081 (mt) REVERT: A 492 ASP cc_start: 0.8496 (t0) cc_final: 0.8201 (t0) REVERT: A 495 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7389 (ptm) REVERT: B 40 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7753 (mmtp) REVERT: B 49 ARG cc_start: 0.8492 (mtp-110) cc_final: 0.8238 (mtp-110) REVERT: B 60 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.8222 (ttm170) REVERT: B 114 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5748 (pt0) REVERT: B 214 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8514 (pttm) REVERT: B 262 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7470 (mm-30) REVERT: B 467 LYS cc_start: 0.8318 (mmmt) cc_final: 0.8106 (mmmt) REVERT: B 495 MET cc_start: 0.7268 (mtp) cc_final: 0.6689 (ptp) REVERT: C 40 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7889 (mmtp) REVERT: C 158 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8164 (mmtm) REVERT: C 262 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7453 (mm-30) REVERT: C 296 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: C 315 LEU cc_start: 0.5429 (OUTLIER) cc_final: 0.4877 (mt) REVERT: C 478 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: C 492 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7796 (t0) REVERT: C 495 MET cc_start: 0.7582 (mtp) cc_final: 0.7313 (mtp) REVERT: D 40 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7838 (mptt) REVERT: D 124 THR cc_start: 0.6374 (OUTLIER) cc_final: 0.6116 (t) REVERT: D 172 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8062 (t0) REVERT: D 200 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8024 (mp) REVERT: D 214 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8554 (pttm) REVERT: D 257 LYS cc_start: 0.7796 (mmtp) cc_final: 0.7516 (mmtm) REVERT: D 495 MET cc_start: 0.7521 (mtp) cc_final: 0.7095 (ptp) REVERT: E 40 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7705 (mmtp) REVERT: E 103 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6682 (mm-30) REVERT: E 114 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5803 (pt0) REVERT: E 214 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8528 (pttm) REVERT: E 495 MET cc_start: 0.7203 (mtp) cc_final: 0.6709 (ptp) REVERT: F 40 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8051 (mmtp) REVERT: F 262 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7431 (mm-30) REVERT: F 441 LYS cc_start: 0.8336 (mttp) cc_final: 0.8086 (mttm) REVERT: F 492 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7684 (t0) REVERT: F 495 MET cc_start: 0.7556 (mtp) cc_final: 0.7177 (mtt) outliers start: 99 outliers final: 34 residues processed: 350 average time/residue: 0.6357 time to fit residues: 257.0338 Evaluate side-chains 311 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 344 ASN Chi-restraints excluded: chain F residue 492 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 231 optimal weight: 3.9990 chunk 108 optimal weight: 0.0030 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 225 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN C 252 GLN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.160289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132527 restraints weight = 25550.545| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.56 r_work: 0.3349 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25080 Z= 0.128 Angle : 0.513 8.912 33888 Z= 0.268 Chirality : 0.041 0.142 3666 Planarity : 0.005 0.056 4212 Dihedral : 4.385 16.965 3300 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.21 % Favored : 96.59 % Rotamer: Outliers : 3.25 % Allowed : 24.22 % Favored : 72.53 % 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: 0.20 (0.15), residues: 2958 helix: 0.90 (0.12), residues: 1620 sheet: -1.72 (0.32), residues: 198 loop : -0.51 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 60 TYR 0.012 0.001 TYR C 70 PHE 0.027 0.002 PHE B 101 TRP 0.010 0.001 TRP D 393 HIS 0.003 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00288 (25080) covalent geometry : angle 0.51252 (33888) hydrogen bonds : bond 0.03796 ( 1254) hydrogen bonds : angle 4.83115 ( 3597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 283 time to evaluate : 0.989 Fit side-chains REVERT: A 40 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7876 (mptt) REVERT: A 124 THR cc_start: 0.6369 (OUTLIER) cc_final: 0.6119 (t) REVERT: A 283 ASP cc_start: 0.5899 (m-30) cc_final: 0.5362 (t0) REVERT: A 492 ASP cc_start: 0.8497 (t0) cc_final: 0.8253 (t0) REVERT: A 495 MET cc_start: 0.7667 (mtp) cc_final: 0.7393 (ptm) REVERT: B 40 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7758 (mmtp) REVERT: B 60 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8281 (ttm170) REVERT: B 103 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6584 (mm-30) REVERT: B 111 LYS cc_start: 0.7203 (mmpt) cc_final: 0.6873 (mmmt) REVERT: B 114 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5777 (pt0) REVERT: B 262 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7474 (mm-30) REVERT: B 467 LYS cc_start: 0.8288 (mmmt) cc_final: 0.8081 (mmmt) REVERT: B 495 MET cc_start: 0.7248 (mtp) cc_final: 0.6675 (ptp) REVERT: C 40 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7878 (mmtp) REVERT: C 155 ILE cc_start: 0.8749 (mp) cc_final: 0.8544 (mm) REVERT: C 158 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8130 (mmtm) REVERT: C 262 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7441 (mm-30) REVERT: C 296 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: C 315 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.4867 (mt) REVERT: C 441 LYS cc_start: 0.8425 (mttp) cc_final: 0.8175 (mttm) REVERT: C 492 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7677 (t0) REVERT: C 495 MET cc_start: 0.7644 (mtp) cc_final: 0.7363 (mtp) REVERT: D 40 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7851 (mptt) REVERT: D 124 THR cc_start: 0.6302 (OUTLIER) cc_final: 0.6081 (t) REVERT: D 214 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8553 (pttm) REVERT: D 257 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7516 (mmtm) REVERT: D 495 MET cc_start: 0.7532 (mtp) cc_final: 0.7108 (ptp) REVERT: E 40 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7755 (mmtp) REVERT: E 114 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5737 (pt0) REVERT: E 214 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8511 (pttm) REVERT: E 250 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8340 (mt-10) REVERT: E 262 GLU cc_start: 0.7807 (mm-30) cc_final: 0.6978 (mp0) REVERT: E 495 MET cc_start: 0.7200 (mtp) cc_final: 0.6701 (ptp) REVERT: F 40 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8035 (mmtp) REVERT: F 262 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7427 (mm-30) REVERT: F 441 LYS cc_start: 0.8308 (mttp) cc_final: 0.8105 (mttm) REVERT: F 492 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7663 (t0) REVERT: F 495 MET cc_start: 0.7532 (mtp) cc_final: 0.7144 (mtt) outliers start: 87 outliers final: 37 residues processed: 354 average time/residue: 0.6511 time to fit residues: 265.1784 Evaluate side-chains 314 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 344 ASN Chi-restraints excluded: chain F residue 492 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 107 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 281 optimal weight: 0.2980 chunk 240 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.160402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132691 restraints weight = 25640.750| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.56 r_work: 0.3352 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25080 Z= 0.129 Angle : 0.526 15.616 33888 Z= 0.273 Chirality : 0.041 0.176 3666 Planarity : 0.005 0.059 4212 Dihedral : 4.367 16.929 3300 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.35 % Favored : 96.45 % Rotamer: Outliers : 3.25 % Allowed : 24.59 % Favored : 72.16 % 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: 0.26 (0.15), residues: 2958 helix: 0.95 (0.12), residues: 1620 sheet: -1.70 (0.32), residues: 198 loop : -0.47 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 49 TYR 0.014 0.001 TYR E 361 PHE 0.030 0.002 PHE F 101 TRP 0.010 0.001 TRP D 393 HIS 0.003 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00291 (25080) covalent geometry : angle 0.52584 (33888) hydrogen bonds : bond 0.03754 ( 1254) hydrogen bonds : angle 4.81668 ( 3597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 0.957 Fit side-chains REVERT: A 40 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7900 (mptt) REVERT: A 124 THR cc_start: 0.6394 (OUTLIER) cc_final: 0.6157 (t) REVERT: A 283 ASP cc_start: 0.5891 (m-30) cc_final: 0.5341 (t0) REVERT: A 492 ASP cc_start: 0.8496 (t0) cc_final: 0.8201 (t0) REVERT: A 495 MET cc_start: 0.7664 (mtp) cc_final: 0.7378 (ptm) REVERT: B 40 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7778 (mmtp) REVERT: B 60 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8266 (ttm170) REVERT: B 104 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6597 (tm) REVERT: B 111 LYS cc_start: 0.7176 (mmpt) cc_final: 0.6841 (mmmt) REVERT: B 114 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5719 (pt0) REVERT: B 262 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7474 (mm-30) REVERT: B 467 LYS cc_start: 0.8251 (mmmt) cc_final: 0.8036 (mmmt) REVERT: B 495 MET cc_start: 0.7250 (mtp) cc_final: 0.6661 (ptp) REVERT: C 40 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7871 (mmtp) REVERT: C 158 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8119 (mmtm) REVERT: C 262 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7448 (mm-30) REVERT: C 315 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.4931 (mt) REVERT: C 441 LYS cc_start: 0.8423 (mttp) cc_final: 0.8167 (mttm) REVERT: C 478 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: C 492 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7684 (t0) REVERT: C 495 MET cc_start: 0.7639 (mtp) cc_final: 0.7355 (mtp) REVERT: D 40 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7816 (mptt) REVERT: D 124 THR cc_start: 0.6326 (OUTLIER) cc_final: 0.6121 (t) REVERT: D 214 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8549 (pttm) REVERT: D 257 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7528 (mmtm) REVERT: D 495 MET cc_start: 0.7478 (mtp) cc_final: 0.7057 (ptp) REVERT: E 40 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7752 (mmtp) REVERT: E 60 ARG cc_start: 0.8645 (ttm170) cc_final: 0.8351 (ttm-80) REVERT: E 114 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5727 (pt0) REVERT: E 250 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8284 (mt-10) REVERT: E 262 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7037 (mp0) REVERT: E 495 MET cc_start: 0.7189 (mtp) cc_final: 0.6574 (ptp) REVERT: F 40 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8064 (mmtp) REVERT: F 158 LYS cc_start: 0.8391 (mmpt) cc_final: 0.8141 (mmtm) REVERT: F 262 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7346 (mm-30) REVERT: F 441 LYS cc_start: 0.8350 (mttp) cc_final: 0.8144 (mttm) REVERT: F 492 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7641 (t0) REVERT: F 495 MET cc_start: 0.7473 (mtp) cc_final: 0.7086 (mtt) outliers start: 87 outliers final: 38 residues processed: 351 average time/residue: 0.6540 time to fit residues: 264.0512 Evaluate side-chains 315 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 344 ASN Chi-restraints excluded: chain F residue 492 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 4.9990 chunk 281 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.156797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129041 restraints weight = 25743.825| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.55 r_work: 0.3307 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25080 Z= 0.173 Angle : 0.552 8.857 33888 Z= 0.290 Chirality : 0.043 0.192 3666 Planarity : 0.005 0.067 4212 Dihedral : 4.522 17.967 3300 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.68 % Favored : 96.11 % Rotamer: Outliers : 2.91 % Allowed : 25.04 % Favored : 72.05 % 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: 0.08 (0.15), residues: 2958 helix: 0.75 (0.12), residues: 1638 sheet: -1.70 (0.32), residues: 198 loop : -0.50 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 60 TYR 0.017 0.001 TYR B 361 PHE 0.029 0.002 PHE B 101 TRP 0.011 0.001 TRP D 393 HIS 0.004 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00402 (25080) covalent geometry : angle 0.55225 (33888) hydrogen bonds : bond 0.04117 ( 1254) hydrogen bonds : angle 4.96973 ( 3597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 269 time to evaluate : 1.015 Fit side-chains REVERT: A 40 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7932 (mptt) REVERT: A 124 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6309 (t) REVERT: A 283 ASP cc_start: 0.5913 (m-30) cc_final: 0.5258 (t0) REVERT: A 492 ASP cc_start: 0.8493 (t0) cc_final: 0.8210 (t0) REVERT: A 495 MET cc_start: 0.7604 (mtp) cc_final: 0.7374 (OUTLIER) REVERT: B 40 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7683 (mmtp) REVERT: B 103 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6660 (mm-30) REVERT: B 111 LYS cc_start: 0.7220 (mmpt) cc_final: 0.6880 (mmmt) REVERT: B 114 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5822 (pt0) REVERT: B 262 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7399 (mm-30) REVERT: B 495 MET cc_start: 0.7221 (mtp) cc_final: 0.6677 (ptp) REVERT: C 40 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7951 (mmtp) REVERT: C 155 ILE cc_start: 0.8841 (mp) cc_final: 0.8612 (mm) REVERT: C 158 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8237 (mmtm) REVERT: C 262 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7410 (mm-30) REVERT: C 315 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.4923 (mt) REVERT: C 478 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: C 492 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7732 (t0) REVERT: C 495 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7330 (mtp) REVERT: D 40 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7862 (mptt) REVERT: D 124 THR cc_start: 0.6578 (OUTLIER) cc_final: 0.6296 (t) REVERT: D 214 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8571 (pttm) REVERT: D 257 LYS cc_start: 0.7936 (mmtp) cc_final: 0.7627 (mmtm) REVERT: D 495 MET cc_start: 0.7477 (mtp) cc_final: 0.7078 (ptp) REVERT: E 40 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7660 (mmtp) REVERT: E 114 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5838 (pt0) REVERT: E 469 ASN cc_start: 0.8041 (p0) cc_final: 0.7442 (p0) REVERT: E 495 MET cc_start: 0.7199 (mtp) cc_final: 0.6618 (ptp) REVERT: F 40 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8034 (mmtp) REVERT: F 158 LYS cc_start: 0.8398 (mmpt) cc_final: 0.8153 (mmtm) REVERT: F 262 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7479 (mm-30) REVERT: F 436 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7133 (mtt-85) REVERT: F 492 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7629 (t0) REVERT: F 495 MET cc_start: 0.7457 (mtp) cc_final: 0.7021 (mtt) outliers start: 78 outliers final: 44 residues processed: 329 average time/residue: 0.6217 time to fit residues: 236.5914 Evaluate side-chains 316 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 492 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 196 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 233 optimal weight: 0.7980 chunk 274 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN B 476 ASN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.158079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130464 restraints weight = 25770.749| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.55 r_work: 0.3319 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25080 Z= 0.146 Angle : 0.539 8.894 33888 Z= 0.282 Chirality : 0.042 0.187 3666 Planarity : 0.005 0.065 4212 Dihedral : 4.478 17.785 3300 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.62 % Favored : 96.18 % Rotamer: Outliers : 2.80 % Allowed : 25.37 % Favored : 71.82 % 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: 0.18 (0.15), residues: 2958 helix: 0.86 (0.12), residues: 1620 sheet: -1.75 (0.32), residues: 198 loop : -0.48 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 60 TYR 0.018 0.001 TYR B 361 PHE 0.028 0.002 PHE B 101 TRP 0.011 0.001 TRP D 393 HIS 0.003 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00334 (25080) covalent geometry : angle 0.53859 (33888) hydrogen bonds : bond 0.03906 ( 1254) hydrogen bonds : angle 4.93218 ( 3597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 1.017 Fit side-chains REVERT: A 40 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7949 (mptt) REVERT: A 124 THR cc_start: 0.6538 (OUTLIER) cc_final: 0.6284 (t) REVERT: A 492 ASP cc_start: 0.8498 (t0) cc_final: 0.8217 (t0) REVERT: A 495 MET cc_start: 0.7604 (mtp) cc_final: 0.7383 (OUTLIER) REVERT: B 40 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7698 (mmtp) REVERT: B 60 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8191 (ttm170) REVERT: B 103 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: B 111 LYS cc_start: 0.7185 (mmpt) cc_final: 0.6853 (mmmt) REVERT: B 114 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5804 (pt0) REVERT: B 262 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7360 (mm-30) REVERT: B 495 MET cc_start: 0.7207 (mtp) cc_final: 0.6663 (ptp) REVERT: C 40 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7950 (mmtp) REVERT: C 155 ILE cc_start: 0.8804 (mp) cc_final: 0.8588 (mm) REVERT: C 158 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8211 (mmtm) REVERT: C 262 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7459 (mm-30) REVERT: C 315 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.4884 (mt) REVERT: C 495 MET cc_start: 0.7630 (mtp) cc_final: 0.6828 (ptp) REVERT: D 1 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.4737 (tpp) REVERT: D 40 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7872 (mptt) REVERT: D 124 THR cc_start: 0.6492 (OUTLIER) cc_final: 0.6229 (t) REVERT: D 214 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8559 (pttm) REVERT: D 257 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7617 (mmtm) REVERT: D 495 MET cc_start: 0.7472 (mtp) cc_final: 0.7080 (ptp) REVERT: E 40 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7666 (mmtp) REVERT: E 114 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5884 (pt0) REVERT: E 262 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7171 (mt-10) REVERT: E 469 ASN cc_start: 0.8018 (p0) cc_final: 0.7355 (p0) REVERT: E 495 MET cc_start: 0.7215 (mtp) cc_final: 0.6636 (ptp) REVERT: F 40 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8045 (mmtp) REVERT: F 158 LYS cc_start: 0.8407 (mmpt) cc_final: 0.8159 (mmtm) REVERT: F 262 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7453 (mm-30) REVERT: F 436 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7212 (mtt-85) REVERT: F 492 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7619 (t0) REVERT: F 495 MET cc_start: 0.7423 (mtp) cc_final: 0.6988 (mtt) outliers start: 75 outliers final: 45 residues processed: 325 average time/residue: 0.6147 time to fit residues: 230.8519 Evaluate side-chains 316 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 257 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 492 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 247 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 292 optimal weight: 0.5980 chunk 250 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 124 optimal weight: 0.0060 chunk 153 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN B 476 ASN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.159284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131787 restraints weight = 25709.717| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.54 r_work: 0.3341 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25080 Z= 0.128 Angle : 0.528 9.073 33888 Z= 0.276 Chirality : 0.042 0.185 3666 Planarity : 0.005 0.066 4212 Dihedral : 4.414 18.482 3300 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.45 % Favored : 96.35 % Rotamer: Outliers : 2.39 % Allowed : 25.86 % Favored : 71.75 % 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 (0.15), residues: 2958 helix: 0.94 (0.13), residues: 1620 sheet: -1.76 (0.32), residues: 198 loop : -0.48 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 60 TYR 0.016 0.001 TYR B 361 PHE 0.029 0.002 PHE B 101 TRP 0.011 0.001 TRP D 393 HIS 0.003 0.001 HIS C 471 Details of bonding type rmsd covalent geometry : bond 0.00289 (25080) covalent geometry : angle 0.52805 (33888) hydrogen bonds : bond 0.03760 ( 1254) hydrogen bonds : angle 4.87798 ( 3597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 277 time to evaluate : 0.936 Fit side-chains REVERT: A 40 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7893 (mptt) REVERT: A 124 THR cc_start: 0.6457 (OUTLIER) cc_final: 0.6214 (t) REVERT: A 492 ASP cc_start: 0.8503 (t0) cc_final: 0.8168 (t0) REVERT: A 495 MET cc_start: 0.7608 (mtp) cc_final: 0.7309 (ptm) REVERT: B 40 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7775 (mmtp) REVERT: B 60 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8151 (ttm170) REVERT: B 103 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6611 (mm-30) REVERT: B 111 LYS cc_start: 0.7173 (mmpt) cc_final: 0.6864 (mmmt) REVERT: B 114 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5769 (pt0) REVERT: B 250 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8310 (mt-10) REVERT: B 262 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7353 (mm-30) REVERT: B 495 MET cc_start: 0.7219 (mtp) cc_final: 0.6631 (ptp) REVERT: C 40 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7944 (mmtp) REVERT: C 158 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8155 (mmtm) REVERT: C 262 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7447 (mm-30) REVERT: C 315 LEU cc_start: 0.5463 (OUTLIER) cc_final: 0.4908 (mt) REVERT: C 441 LYS cc_start: 0.8472 (mttp) cc_final: 0.8219 (mttm) REVERT: C 495 MET cc_start: 0.7620 (mtp) cc_final: 0.6844 (ptp) REVERT: D 40 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7837 (mptt) REVERT: D 124 THR cc_start: 0.6429 (OUTLIER) cc_final: 0.6186 (t) REVERT: D 214 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8498 (pttm) REVERT: D 257 LYS cc_start: 0.7898 (mmtp) cc_final: 0.7599 (mmtm) REVERT: D 495 MET cc_start: 0.7520 (mtp) cc_final: 0.7138 (ptp) REVERT: E 40 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7655 (mmtp) REVERT: E 60 ARG cc_start: 0.8599 (ttm170) cc_final: 0.8371 (ttm-80) REVERT: E 103 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6658 (mm-30) REVERT: E 114 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5880 (pt0) REVERT: E 262 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7173 (mt-10) REVERT: E 469 ASN cc_start: 0.7944 (p0) cc_final: 0.7324 (p0) REVERT: E 495 MET cc_start: 0.7231 (mtp) cc_final: 0.6579 (ptp) REVERT: F 158 LYS cc_start: 0.8360 (mmpt) cc_final: 0.8123 (mmtm) REVERT: F 262 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7437 (mm-30) REVERT: F 492 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7641 (t0) REVERT: F 495 MET cc_start: 0.7415 (mtp) cc_final: 0.6997 (mtt) outliers start: 64 outliers final: 39 residues processed: 325 average time/residue: 0.6304 time to fit residues: 236.2956 Evaluate side-chains 316 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 492 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 156 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 255 optimal weight: 0.0170 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN C 293 ASN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN E 476 ASN F 252 GLN F 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.157094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129408 restraints weight = 25788.714| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.55 r_work: 0.3313 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25080 Z= 0.163 Angle : 0.555 8.987 33888 Z= 0.291 Chirality : 0.043 0.190 3666 Planarity : 0.005 0.067 4212 Dihedral : 4.517 18.245 3300 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.75 % Favored : 96.04 % Rotamer: Outliers : 2.32 % Allowed : 25.67 % Favored : 72.01 % 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: 0.13 (0.15), residues: 2958 helix: 0.82 (0.12), residues: 1620 sheet: -1.77 (0.32), residues: 198 loop : -0.49 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 60 TYR 0.020 0.001 TYR E 361 PHE 0.028 0.002 PHE B 101 TRP 0.010 0.001 TRP D 393 HIS 0.003 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00379 (25080) covalent geometry : angle 0.55496 (33888) hydrogen bonds : bond 0.04029 ( 1254) hydrogen bonds : angle 4.96857 ( 3597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7693.93 seconds wall clock time: 132 minutes 43.90 seconds (7963.90 seconds total)