Starting phenix.real_space_refine on Mon Oct 26 05:35:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38lb_78900/10_2026/38lb_78900.cif Found real_map, /net/cci-nas-00/data/ceres_data/38lb_78900/10_2026/38lb_78900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/38lb_78900/10_2026/38lb_78900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38lb_78900/10_2026/38lb_78900.map" model { file = "/net/cci-nas-00/data/ceres_data/38lb_78900/10_2026/38lb_78900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38lb_78900/10_2026/38lb_78900.cif" } resolution = 3.18 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= -0.000 sd= 0.020 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 108 5.16 5 C 12204 2.51 5 N 3316 2.21 5 O 3640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19268 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4817 Classifications: {'peptide': 599} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 578} Chain breaks: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 4.63, per 1000 atoms: 0.24 Number of scatterers: 19268 At special positions: 0 Unit cell: (114.46, 123.9, 130.98, 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 108 16.00 O 3640 8.00 N 3316 7.00 C 12204 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: 1.24 Conformation dependent library (CDL) restraints added in 807.8 milliseconds 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 51.6% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 Processing helix chain 'A' and resid 41 through 62 removed outlier: 3.503A pdb=" N THR A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.932A pdb=" N TYR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.633A pdb=" N THR A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.565A pdb=" N PHE A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 175 through 181 removed outlier: 4.266A pdb=" N ALA A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.604A pdb=" N ALA A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 229 removed outlier: 3.690A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 229 " --> pdb=" O MET A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 258 removed outlier: 3.616A pdb=" N SER A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.779A pdb=" N ILE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 303 removed outlier: 3.681A pdb=" N MET A 303 " --> pdb=" O MET A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.853A pdb=" N PHE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.997A pdb=" N VAL A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.612A pdb=" N LEU A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 493 Processing helix chain 'A' and resid 495 through 501 removed outlier: 3.788A pdb=" N PHE A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.524A pdb=" N ARG A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.638A pdb=" N ASN A 584 " --> pdb=" O CYS A 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 27 Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.503A pdb=" N THR B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.932A pdb=" N TYR B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 removed outlier: 3.632A pdb=" N THR B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.564A pdb=" N PHE B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 175 through 181 removed outlier: 4.265A pdb=" N ALA B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.604A pdb=" N ALA B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 229 removed outlier: 3.690A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 229 " --> pdb=" O MET B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 258 removed outlier: 3.617A pdb=" N SER B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 283 removed outlier: 3.778A pdb=" N ILE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR B 275 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 303 removed outlier: 3.682A pdb=" N MET B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.853A pdb=" N PHE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.998A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.611A pdb=" N LEU B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 493 Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.789A pdb=" N PHE B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 530 Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.524A pdb=" N ARG B 577 " --> pdb=" O MET B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.637A pdb=" N ASN B 584 " --> pdb=" O CYS B 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 27 Processing helix chain 'C' and resid 41 through 62 removed outlier: 3.503A pdb=" N THR C 45 " --> pdb=" O THR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.932A pdb=" N TYR C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.633A pdb=" N THR C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.565A pdb=" N PHE C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 175 through 181 removed outlier: 4.265A pdb=" N ALA C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.604A pdb=" N ALA C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 229 removed outlier: 3.691A pdb=" N ASN C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 229 " --> pdb=" O MET C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 258 removed outlier: 3.617A pdb=" N SER C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.778A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR C 275 " --> pdb=" O PHE C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 303 removed outlier: 3.682A pdb=" N MET C 303 " --> pdb=" O MET C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 353 removed outlier: 3.853A pdb=" N PHE C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.997A pdb=" N VAL C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 removed outlier: 3.612A pdb=" N LEU C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 493 Processing helix chain 'C' and resid 495 through 501 removed outlier: 3.788A pdb=" N PHE C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 530 Processing helix chain 'C' and resid 558 through 577 removed outlier: 3.524A pdb=" N ARG C 577 " --> pdb=" O MET C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 removed outlier: 3.639A pdb=" N ASN C 584 " --> pdb=" O CYS C 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 27 Processing helix chain 'D' and resid 41 through 62 removed outlier: 3.503A pdb=" N THR D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.933A pdb=" N TYR D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.633A pdb=" N THR D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.564A pdb=" N PHE D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 175 through 181 removed outlier: 4.266A pdb=" N ALA D 179 " --> pdb=" O TYR D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.604A pdb=" N ALA D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 229 removed outlier: 3.691A pdb=" N ASN D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 258 removed outlier: 3.615A pdb=" N SER D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.779A pdb=" N ILE D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR D 275 " --> pdb=" O PHE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 303 removed outlier: 3.682A pdb=" N MET D 303 " --> pdb=" O MET D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 353 removed outlier: 3.853A pdb=" N PHE D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 348 " --> pdb=" O ARG D 344 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU D 349 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.997A pdb=" N VAL D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 436 removed outlier: 3.612A pdb=" N LEU D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 493 Processing helix chain 'D' and resid 495 through 501 removed outlier: 3.788A pdb=" N PHE D 501 " --> pdb=" O ILE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 530 Processing helix chain 'D' and resid 558 through 577 removed outlier: 3.525A pdb=" N ARG D 577 " --> pdb=" O MET D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 removed outlier: 3.638A pdb=" N ASN D 584 " --> pdb=" O CYS D 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 72 removed outlier: 6.687A pdb=" N ASP A 66 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU A 103 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASP A 68 " --> pdb=" O LEU A 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160 removed outlier: 6.261A pdb=" N ALA A 424 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 160 removed outlier: 6.261A pdb=" N ALA A 424 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 514 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 536 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 72 removed outlier: 6.687A pdb=" N ASP B 66 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU B 103 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASP B 68 " --> pdb=" O LEU B 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 removed outlier: 6.260A pdb=" N ALA B 424 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 160 removed outlier: 6.260A pdb=" N ALA B 424 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 514 " --> pdb=" O SER B 590 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 324 through 327 Processing sheet with id=AB2, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AB3, first strand: chain 'B' and resid 531 through 536 Processing sheet with id=AB4, first strand: chain 'C' and resid 66 through 72 removed outlier: 6.686A pdb=" N ASP C 66 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU C 103 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASP C 68 " --> pdb=" O LEU C 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 159 through 160 removed outlier: 6.260A pdb=" N ALA C 424 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 159 through 160 removed outlier: 6.260A pdb=" N ALA C 424 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 514 " --> pdb=" O SER C 590 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 324 through 327 Processing sheet with id=AB8, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB9, first strand: chain 'C' and resid 531 through 536 Processing sheet with id=AC1, first strand: chain 'D' and resid 66 through 72 removed outlier: 6.688A pdb=" N ASP D 66 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU D 103 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASP D 68 " --> pdb=" O LEU D 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.261A pdb=" N ALA D 424 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.261A pdb=" N ALA D 424 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 514 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 324 through 327 Processing sheet with id=AC5, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC6, first strand: chain 'D' and resid 531 through 536 916 hydrogen bonds defined for protein. 2676 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: 3.27 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6364 1.35 - 1.46: 4764 1.46 - 1.58: 8380 1.58 - 1.70: 0 1.70 - 1.82: 188 Bond restraints: 19696 Sorted by residual: bond pdb=" CB PHE B 130 " pdb=" CG PHE B 130 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.31e+00 bond pdb=" CB PHE D 130 " pdb=" CG PHE D 130 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.26e+00 bond pdb=" CB PHE C 130 " pdb=" CG PHE C 130 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.23e+00 bond pdb=" CB PHE A 130 " pdb=" CG PHE A 130 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.23e+00 bond pdb=" CA VAL A 408 " pdb=" CB VAL A 408 " ideal model delta sigma weight residual 1.536 1.550 -0.014 1.37e-02 5.33e+03 1.07e+00 ... (remaining 19691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 25571 0.94 - 1.87: 806 1.87 - 2.81: 161 2.81 - 3.75: 62 3.75 - 4.68: 12 Bond angle restraints: 26612 Sorted by residual: angle pdb=" N GLY B 328 " pdb=" CA GLY B 328 " pdb=" C GLY B 328 " ideal model delta sigma weight residual 112.33 116.19 -3.86 1.10e+00 8.26e-01 1.23e+01 angle pdb=" N GLY A 328 " pdb=" CA GLY A 328 " pdb=" C GLY A 328 " ideal model delta sigma weight residual 112.33 116.18 -3.85 1.10e+00 8.26e-01 1.23e+01 angle pdb=" N GLY D 328 " pdb=" CA GLY D 328 " pdb=" C GLY D 328 " ideal model delta sigma weight residual 112.33 116.18 -3.85 1.10e+00 8.26e-01 1.23e+01 angle pdb=" N GLY C 328 " pdb=" CA GLY C 328 " pdb=" C GLY C 328 " ideal model delta sigma weight residual 112.33 116.17 -3.84 1.10e+00 8.26e-01 1.22e+01 angle pdb=" CA GLY A 329 " pdb=" C GLY A 329 " pdb=" N ILE A 330 " ideal model delta sigma weight residual 114.96 117.48 -2.52 1.34e+00 5.57e-01 3.55e+00 ... (remaining 26607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 9844 16.26 - 32.52: 1241 32.52 - 48.78: 511 48.78 - 65.03: 124 65.03 - 81.29: 20 Dihedral angle restraints: 11740 sinusoidal: 4788 harmonic: 6952 Sorted by residual: dihedral pdb=" CA PHE D 130 " pdb=" C PHE D 130 " pdb=" N TYR D 131 " pdb=" CA TYR D 131 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PHE B 130 " pdb=" C PHE B 130 " pdb=" N TYR B 131 " pdb=" CA TYR B 131 " ideal model delta harmonic sigma weight residual -180.00 -156.20 -23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PHE C 130 " pdb=" C PHE C 130 " pdb=" N TYR C 131 " pdb=" CA TYR C 131 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 11737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1672 0.025 - 0.050: 696 0.050 - 0.075: 293 0.075 - 0.099: 107 0.099 - 0.124: 80 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA ILE D 159 " pdb=" N ILE D 159 " pdb=" C ILE D 159 " pdb=" CB ILE D 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 159 " pdb=" N ILE A 159 " pdb=" C ILE A 159 " pdb=" CB ILE A 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE B 159 " pdb=" N ILE B 159 " pdb=" C ILE B 159 " pdb=" CB ILE B 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 2845 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 607 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO C 608 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 608 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 608 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 607 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 608 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 608 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 608 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 607 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 608 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 608 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 608 " -0.023 5.00e-02 4.00e+02 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 9427 3.01 - 3.49: 17930 3.49 - 3.96: 30650 3.96 - 4.43: 36057 4.43 - 4.90: 59020 Nonbonded interactions: 153084 Sorted by model distance: nonbonded pdb=" O ASP A 18 " pdb=" OD1 ASP A 18 " model vdw 2.542 3.040 nonbonded pdb=" O ASP B 18 " pdb=" OD1 ASP B 18 " model vdw 2.542 3.040 nonbonded pdb=" O ASP D 18 " pdb=" OD1 ASP D 18 " model vdw 2.542 3.040 nonbonded pdb=" O ASP C 18 " pdb=" OD1 ASP C 18 " model vdw 2.543 3.040 nonbonded pdb=" O ASN C 196 " pdb=" OD1 ASN C 196 " model vdw 2.587 3.040 ... (remaining 153079 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.240 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.003 0.030 19696 Z= 0.114 Angle : 0.434 4.682 26612 Z= 0.255 Chirality : 0.038 0.124 2848 Planarity : 0.003 0.042 3440 Dihedral : 17.352 81.293 7308 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.81 % Allowed : 21.19 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.27 (0.15), residues: 2372 helix: -0.78 (0.13), residues: 1144 sheet: -0.71 (0.41), residues: 144 loop : -0.77 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 134 TYR 0.010 0.001 TYR C 82 PHE 0.019 0.001 PHE D 130 TRP 0.010 0.001 TRP A 246 HIS 0.002 0.000 HIS C 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (19696) covalent geometry : angle 0.43395 / 0.26 (26612) hydrogen bonds : bond 0.25262 / 16.80 ( 908) hydrogen bonds : angle 7.13842 / 5.14 ( 2676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7321 (t80) REVERT: C 510 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7343 (t80) REVERT: D 510 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7329 (t80) outliers start: 37 outliers final: 19 residues processed: 238 average time/residue: 0.1651 time to fit residues: 56.9380 Evaluate side-chains 151 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 510 PHE Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 146 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 510 PHE Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 553 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.073562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.052107 restraints weight = 60028.179| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 4.59 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19696 Z= 0.176 Angle : 0.520 8.659 26612 Z= 0.283 Chirality : 0.039 0.126 2848 Planarity : 0.004 0.045 3440 Dihedral : 5.299 55.966 2724 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.98 % Allowed : 18.60 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.97 (0.16), residues: 2372 helix: 1.92 (0.15), residues: 1128 sheet: -0.62 (0.39), residues: 148 loop : -0.51 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 577 TYR 0.017 0.001 TYR C 467 PHE 0.015 0.001 PHE D 130 TRP 0.010 0.001 TRP D 246 HIS 0.005 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (19696) covalent geometry : angle 0.51994 / 0.28 (26612) hydrogen bonds : bond 0.06032 / 4.04 ( 908) hydrogen bonds : angle 4.44823 / 3.19 ( 2676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 137 time to evaluate : 0.722 Fit side-chains REVERT: A 52 MET cc_start: 0.9709 (mtm) cc_final: 0.9256 (mpp) REVERT: A 59 ARG cc_start: 0.9299 (ptp-170) cc_final: 0.9063 (ptt-90) REVERT: A 361 THR cc_start: 0.8697 (m) cc_final: 0.8397 (p) REVERT: A 499 MET cc_start: 0.9086 (mmm) cc_final: 0.8737 (mmm) REVERT: B 52 MET cc_start: 0.9705 (mtm) cc_final: 0.9258 (mpp) REVERT: B 59 ARG cc_start: 0.9292 (ptp-170) cc_final: 0.9068 (ptt-90) REVERT: B 189 GLU cc_start: 0.8873 (tp30) cc_final: 0.8312 (tp30) REVERT: B 499 MET cc_start: 0.9103 (mmm) cc_final: 0.8728 (mmm) REVERT: C 52 MET cc_start: 0.9715 (mtm) cc_final: 0.9114 (mpp) REVERT: C 56 LYS cc_start: 0.9721 (ttpt) cc_final: 0.9497 (ptpp) REVERT: C 129 LYS cc_start: 0.9281 (mttt) cc_final: 0.9034 (tptm) REVERT: C 499 MET cc_start: 0.9097 (mmm) cc_final: 0.8788 (mmt) REVERT: D 52 MET cc_start: 0.9707 (mtm) cc_final: 0.9266 (mpp) REVERT: D 59 ARG cc_start: 0.9288 (ptp-170) cc_final: 0.9056 (ptt-90) REVERT: D 129 LYS cc_start: 0.9277 (mttt) cc_final: 0.9030 (tptm) REVERT: D 499 MET cc_start: 0.9094 (mmm) cc_final: 0.8731 (mmm) outliers start: 61 outliers final: 24 residues processed: 196 average time/residue: 0.1195 time to fit residues: 37.8743 Evaluate side-chains 155 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 146 TYR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [45, 43, 200, 36, 227, 220, 2, 57, 53, 140, 234] chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 489 HIS B 489 HIS D 489 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.049007 restraints weight = 61125.819| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 4.50 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 19696 Z= 0.283 Angle : 0.561 5.923 26612 Z= 0.307 Chirality : 0.041 0.130 2848 Planarity : 0.004 0.045 3440 Dihedral : 4.492 39.110 2700 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.44 % Allowed : 18.90 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.48 (0.17), residues: 2372 helix: 2.54 (0.15), residues: 1132 sheet: -0.85 (0.40), residues: 148 loop : -0.43 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 59 TYR 0.018 0.001 TYR A 467 PHE 0.013 0.001 PHE B 510 TRP 0.010 0.001 TRP C 246 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.28 (19696) covalent geometry : angle 0.56133 / 0.31 (26612) hydrogen bonds : bond 0.06425 / 4.30 ( 908) hydrogen bonds : angle 4.48929 / 3.19 ( 2676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9662 (mtm) cc_final: 0.9292 (mpp) REVERT: A 394 MET cc_start: 0.8302 (mmm) cc_final: 0.7961 (mmt) REVERT: A 573 MET cc_start: 0.9049 (mmm) cc_final: 0.8693 (mmm) REVERT: B 52 MET cc_start: 0.9679 (mtm) cc_final: 0.9306 (mpp) REVERT: B 394 MET cc_start: 0.8282 (mmm) cc_final: 0.7947 (mmt) REVERT: C 52 MET cc_start: 0.9664 (mtm) cc_final: 0.9190 (mpp) REVERT: C 104 MET cc_start: 0.9178 (mtp) cc_final: 0.8770 (mtp) REVERT: C 129 LYS cc_start: 0.9338 (mttt) cc_final: 0.9114 (tmtt) REVERT: C 196 ASN cc_start: 0.8706 (t0) cc_final: 0.8499 (t0) REVERT: C 394 MET cc_start: 0.8279 (mmm) cc_final: 0.7950 (mmt) REVERT: D 52 MET cc_start: 0.9683 (mtm) cc_final: 0.9308 (mpp) REVERT: D 104 MET cc_start: 0.9178 (mtp) cc_final: 0.8676 (mtp) REVERT: D 129 LYS cc_start: 0.9336 (mttt) cc_final: 0.9114 (tmtt) REVERT: D 394 MET cc_start: 0.8280 (mmm) cc_final: 0.7949 (mmt) outliers start: 50 outliers final: 22 residues processed: 166 average time/residue: 0.1223 time to fit residues: 31.9862 Evaluate side-chains 137 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [145, 141, 232, 60, 184, 36, 57, 102, 199, 120, 146] chunk 145 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 184 optimal weight: 0.1980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.073614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.052408 restraints weight = 59250.347| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.53 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19696 Z= 0.112 Angle : 0.424 4.738 26612 Z= 0.234 Chirality : 0.038 0.129 2848 Planarity : 0.003 0.044 3440 Dihedral : 3.688 27.664 2684 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.71 % Allowed : 20.17 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.72 (0.17), residues: 2372 helix: 2.84 (0.15), residues: 1132 sheet: -0.95 (0.39), residues: 148 loop : -0.41 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 59 TYR 0.017 0.001 TYR B 467 PHE 0.019 0.001 PHE A 130 TRP 0.008 0.001 TRP D 246 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (19696) covalent geometry : angle 0.42381 / 0.23 (26612) hydrogen bonds : bond 0.04556 / 3.06 ( 908) hydrogen bonds : angle 4.03839 / 2.88 ( 2676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9641 (mtm) cc_final: 0.9409 (mmm) REVERT: A 68 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7794 (m-30) REVERT: A 196 ASN cc_start: 0.8706 (t0) cc_final: 0.8503 (t0) REVERT: A 361 THR cc_start: 0.8878 (m) cc_final: 0.8579 (p) REVERT: A 394 MET cc_start: 0.8389 (mmt) cc_final: 0.8119 (mmt) REVERT: A 467 TYR cc_start: 0.8910 (t80) cc_final: 0.8242 (t80) REVERT: B 52 MET cc_start: 0.9643 (mtm) cc_final: 0.9428 (mmm) REVERT: B 68 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: B 196 ASN cc_start: 0.8692 (t0) cc_final: 0.8473 (t0) REVERT: B 299 MET cc_start: 0.9501 (OUTLIER) cc_final: 0.9276 (ttm) REVERT: B 361 THR cc_start: 0.8867 (m) cc_final: 0.8567 (p) REVERT: B 394 MET cc_start: 0.8335 (mmt) cc_final: 0.8056 (mmt) REVERT: B 467 TYR cc_start: 0.8910 (t80) cc_final: 0.8221 (t80) REVERT: B 553 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9027 (mptt) REVERT: C 68 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: C 196 ASN cc_start: 0.8709 (t0) cc_final: 0.8506 (t0) REVERT: C 361 THR cc_start: 0.8877 (m) cc_final: 0.8578 (p) REVERT: C 394 MET cc_start: 0.8376 (mmt) cc_final: 0.8118 (mmt) REVERT: D 52 MET cc_start: 0.9649 (mtm) cc_final: 0.9430 (mmm) REVERT: D 68 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: D 196 ASN cc_start: 0.8693 (t0) cc_final: 0.8484 (t0) REVERT: D 299 MET cc_start: 0.9488 (OUTLIER) cc_final: 0.9278 (ttm) REVERT: D 361 THR cc_start: 0.8867 (m) cc_final: 0.8567 (p) REVERT: D 394 MET cc_start: 0.8385 (mmt) cc_final: 0.8126 (mmt) outliers start: 35 outliers final: 19 residues processed: 160 average time/residue: 0.1367 time to fit residues: 33.9779 Evaluate side-chains 155 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 146 TYR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [141, 75, 103, 46, 157, 9, 34, 130, 112, 95, 134] chunk 141 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.050214 restraints weight = 59889.739| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.52 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19696 Z= 0.199 Angle : 0.484 6.830 26612 Z= 0.262 Chirality : 0.039 0.126 2848 Planarity : 0.003 0.073 3440 Dihedral : 3.767 27.495 2684 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.90 % Allowed : 18.75 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.75 (0.17), residues: 2372 helix: 2.93 (0.15), residues: 1120 sheet: -0.99 (0.40), residues: 148 loop : -0.42 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 59 TYR 0.015 0.001 TYR A 467 PHE 0.019 0.001 PHE A 130 TRP 0.011 0.001 TRP C 48 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (19696) covalent geometry : angle 0.48361 / 0.26 (26612) hydrogen bonds : bond 0.05319 / 3.57 ( 908) hydrogen bonds : angle 4.18019 / 2.98 ( 2676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9643 (mtm) cc_final: 0.9369 (mmm) REVERT: A 59 ARG cc_start: 0.9282 (ptp-170) cc_final: 0.9058 (ptt-90) REVERT: A 68 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: A 225 MET cc_start: 0.9464 (tmm) cc_final: 0.9254 (tmm) REVERT: A 263 MET cc_start: 0.8097 (mmt) cc_final: 0.7832 (mmt) REVERT: A 394 MET cc_start: 0.8380 (mmt) cc_final: 0.8108 (mmt) REVERT: B 52 MET cc_start: 0.9647 (mtm) cc_final: 0.9347 (mmm) REVERT: B 59 ARG cc_start: 0.9286 (ptp-170) cc_final: 0.9075 (ptt-90) REVERT: B 68 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: B 225 MET cc_start: 0.9453 (tmm) cc_final: 0.9246 (tmm) REVERT: B 263 MET cc_start: 0.8112 (mmt) cc_final: 0.7844 (mmt) REVERT: B 394 MET cc_start: 0.8357 (mmt) cc_final: 0.8072 (mmt) REVERT: C 52 MET cc_start: 0.9137 (mmm) cc_final: 0.8921 (mpp) REVERT: C 68 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: C 225 MET cc_start: 0.9455 (tmm) cc_final: 0.9244 (tmm) REVERT: C 394 MET cc_start: 0.8357 (mmt) cc_final: 0.8096 (mmt) REVERT: D 52 MET cc_start: 0.9651 (mtm) cc_final: 0.9349 (mmm) REVERT: D 59 ARG cc_start: 0.9280 (ptp-170) cc_final: 0.9067 (ptt-90) REVERT: D 68 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: D 225 MET cc_start: 0.9454 (tmm) cc_final: 0.9247 (tmm) REVERT: D 394 MET cc_start: 0.8365 (mmt) cc_final: 0.8104 (mmt) outliers start: 39 outliers final: 17 residues processed: 159 average time/residue: 0.1349 time to fit residues: 33.8892 Evaluate side-chains 140 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [233, 88, 201, 166, 196, 72, 6, 136, 50, 87, 97] chunk 233 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.050993 restraints weight = 60788.374| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.61 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19696 Z= 0.158 Angle : 0.450 5.720 26612 Z= 0.248 Chirality : 0.039 0.127 2848 Planarity : 0.003 0.043 3440 Dihedral : 3.721 27.239 2684 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.37 % Allowed : 19.82 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.87 (0.18), residues: 2372 helix: 3.05 (0.15), residues: 1112 sheet: -0.71 (0.39), residues: 168 loop : -0.38 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 611 TYR 0.012 0.001 TYR A 467 PHE 0.015 0.001 PHE A 130 TRP 0.010 0.001 TRP C 48 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (19696) covalent geometry : angle 0.44969 / 0.25 (26612) hydrogen bonds : bond 0.04858 / 3.26 ( 908) hydrogen bonds : angle 4.00669 / 2.85 ( 2676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9667 (mtm) cc_final: 0.9353 (mmm) REVERT: A 59 ARG cc_start: 0.9331 (ptp-170) cc_final: 0.9094 (ptt-90) REVERT: A 68 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: A 263 MET cc_start: 0.8164 (mmt) cc_final: 0.7961 (mmt) REVERT: B 52 MET cc_start: 0.9670 (mtm) cc_final: 0.9422 (mmm) REVERT: B 59 ARG cc_start: 0.9319 (ptp-170) cc_final: 0.9087 (ptt-90) REVERT: B 68 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: B 263 MET cc_start: 0.8175 (mmt) cc_final: 0.7971 (mmt) REVERT: B 394 MET cc_start: 0.8144 (mmt) cc_final: 0.7899 (mmt) REVERT: B 553 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8851 (mptt) REVERT: C 68 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: C 129 LYS cc_start: 0.9304 (mttt) cc_final: 0.8946 (tmtt) REVERT: D 52 MET cc_start: 0.9682 (mtm) cc_final: 0.9429 (mmm) REVERT: D 59 ARG cc_start: 0.9323 (ptp-170) cc_final: 0.9091 (ptt-90) REVERT: D 68 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: D 129 LYS cc_start: 0.9296 (mttt) cc_final: 0.8940 (tmtt) outliers start: 28 outliers final: 15 residues processed: 143 average time/residue: 0.1363 time to fit residues: 30.6360 Evaluate side-chains 135 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [49, 166, 81, 136, 51, 173, 77, 162, 83, 177, 45] chunk 49 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.050652 restraints weight = 61533.741| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.66 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19696 Z= 0.168 Angle : 0.466 6.521 26612 Z= 0.255 Chirality : 0.039 0.185 2848 Planarity : 0.003 0.075 3440 Dihedral : 3.744 27.491 2684 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.42 % Allowed : 19.38 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.83 (0.17), residues: 2372 helix: 3.05 (0.15), residues: 1096 sheet: -0.56 (0.39), residues: 164 loop : -0.42 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 59 TYR 0.015 0.001 TYR B 375 PHE 0.014 0.001 PHE A 130 TRP 0.010 0.001 TRP D 246 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (19696) covalent geometry : angle 0.46643 / 0.26 (26612) hydrogen bonds : bond 0.04973 / 3.34 ( 908) hydrogen bonds : angle 4.01983 / 2.86 ( 2676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.9344 (ptp-170) cc_final: 0.9119 (ptt-90) REVERT: A 68 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: A 225 MET cc_start: 0.9294 (tmm) cc_final: 0.9073 (tmm) REVERT: A 263 MET cc_start: 0.8297 (mmt) cc_final: 0.7993 (mmp) REVERT: A 352 MET cc_start: 0.8155 (mmp) cc_final: 0.7897 (tpp) REVERT: A 394 MET cc_start: 0.8051 (mmt) cc_final: 0.7847 (mmt) REVERT: B 52 MET cc_start: 0.9680 (mtm) cc_final: 0.9396 (mmm) REVERT: B 59 ARG cc_start: 0.9332 (ptp-170) cc_final: 0.9107 (ptt-90) REVERT: B 68 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: B 225 MET cc_start: 0.9302 (tmm) cc_final: 0.9080 (tmm) REVERT: B 263 MET cc_start: 0.8203 (mmt) cc_final: 0.7912 (mmp) REVERT: B 553 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8858 (mptt) REVERT: C 59 ARG cc_start: 0.9449 (mtm-85) cc_final: 0.9192 (ptp90) REVERT: C 68 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: C 129 LYS cc_start: 0.9317 (mttt) cc_final: 0.8964 (tmtt) REVERT: C 394 MET cc_start: 0.8052 (mmt) cc_final: 0.7850 (mmt) REVERT: D 52 MET cc_start: 0.9672 (mtm) cc_final: 0.9429 (mmm) REVERT: D 59 ARG cc_start: 0.9338 (ptp-170) cc_final: 0.9122 (ptt-90) REVERT: D 68 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: D 129 LYS cc_start: 0.9308 (mttt) cc_final: 0.8957 (tmtt) REVERT: D 225 MET cc_start: 0.9296 (tmm) cc_final: 0.9076 (tmm) REVERT: D 394 MET cc_start: 0.8056 (mmt) cc_final: 0.7855 (mmt) outliers start: 29 outliers final: 19 residues processed: 142 average time/residue: 0.1360 time to fit residues: 30.3324 Evaluate side-chains 140 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [129, 112, 46, 70, 110, 8, 217, 174, 219, 91, 150] chunk 129 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 217 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.073557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.052593 restraints weight = 61000.476| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.68 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19696 Z= 0.104 Angle : 0.420 5.667 26612 Z= 0.231 Chirality : 0.038 0.145 2848 Planarity : 0.003 0.063 3440 Dihedral : 3.590 27.564 2684 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.27 % Allowed : 19.78 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.95 (0.18), residues: 2372 helix: 3.08 (0.15), residues: 1108 sheet: -0.58 (0.39), residues: 164 loop : -0.29 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 59 TYR 0.009 0.001 TYR A 467 PHE 0.012 0.001 PHE A 130 TRP 0.012 0.001 TRP A 48 HIS 0.003 0.000 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (19696) covalent geometry : angle 0.41982 / 0.23 (26612) hydrogen bonds : bond 0.04118 / 2.77 ( 908) hydrogen bonds : angle 3.81922 / 2.73 ( 2676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9415 (mmm) cc_final: 0.9066 (mpp) REVERT: A 59 ARG cc_start: 0.9343 (ptp-170) cc_final: 0.9107 (ptt-90) REVERT: A 68 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: A 361 THR cc_start: 0.8627 (m) cc_final: 0.8372 (p) REVERT: B 59 ARG cc_start: 0.9336 (ptp-170) cc_final: 0.9110 (ptt-90) REVERT: B 68 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: B 361 THR cc_start: 0.8644 (m) cc_final: 0.8389 (p) REVERT: B 394 MET cc_start: 0.8046 (mmt) cc_final: 0.7841 (mmt) REVERT: C 52 MET cc_start: 0.9351 (mmm) cc_final: 0.9010 (mpp) REVERT: C 68 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: C 129 LYS cc_start: 0.9337 (mttt) cc_final: 0.9057 (tmtt) REVERT: C 361 THR cc_start: 0.8619 (m) cc_final: 0.8366 (p) REVERT: D 52 MET cc_start: 0.9646 (mtm) cc_final: 0.9425 (mmm) REVERT: D 59 ARG cc_start: 0.9326 (ptp-170) cc_final: 0.9098 (ptt-90) REVERT: D 68 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: D 129 LYS cc_start: 0.9331 (mttt) cc_final: 0.9049 (tmtt) REVERT: D 361 THR cc_start: 0.8645 (m) cc_final: 0.8391 (p) outliers start: 26 outliers final: 21 residues processed: 148 average time/residue: 0.1272 time to fit residues: 29.6174 Evaluate side-chains 147 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 146 TYR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [89, 103, 154, 222, 49, 208, 85, 214, 140, 221, 27] chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.050826 restraints weight = 61151.978| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 4.64 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19696 Z= 0.178 Angle : 0.475 6.374 26612 Z= 0.258 Chirality : 0.039 0.170 2848 Planarity : 0.003 0.048 3440 Dihedral : 3.716 27.881 2684 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.07 % Allowed : 20.02 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.92 (0.18), residues: 2372 helix: 3.14 (0.15), residues: 1084 sheet: -0.53 (0.40), residues: 164 loop : -0.34 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 59 TYR 0.011 0.001 TYR D 131 PHE 0.021 0.001 PHE D 130 TRP 0.011 0.001 TRP D 246 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (19696) covalent geometry : angle 0.47472 / 0.26 (26612) hydrogen bonds : bond 0.04983 / 3.34 ( 908) hydrogen bonds : angle 3.98686 / 2.84 ( 2676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9432 (mmm) cc_final: 0.9163 (mpp) REVERT: A 68 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: B 52 MET cc_start: 0.9424 (mmm) cc_final: 0.9156 (mpp) REVERT: B 68 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: B 553 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8851 (mptt) REVERT: C 59 ARG cc_start: 0.9368 (mtm-85) cc_final: 0.9096 (ptp90) REVERT: C 68 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: C 129 LYS cc_start: 0.9355 (mttt) cc_final: 0.8996 (tptt) REVERT: D 68 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7844 (m-30) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 0.1347 time to fit residues: 28.6538 Evaluate side-chains 134 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [172, 130, 124, 155, 126, 167, 22, 120, 75, 144, 96] chunk 172 optimal weight: 0.0270 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 75 optimal weight: 0.0670 chunk 144 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.074873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.054094 restraints weight = 60512.072| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 4.67 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19696 Z= 0.090 Angle : 0.425 7.347 26612 Z= 0.232 Chirality : 0.038 0.153 2848 Planarity : 0.003 0.049 3440 Dihedral : 3.596 27.425 2684 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.27 % Allowed : 20.02 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.96 (0.18), residues: 2372 helix: 3.09 (0.15), residues: 1092 sheet: -0.50 (0.39), residues: 164 loop : -0.27 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 59 TYR 0.009 0.001 TYR B 131 PHE 0.017 0.001 PHE B 130 TRP 0.010 0.001 TRP D 48 HIS 0.003 0.000 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (19696) covalent geometry : angle 0.42481 / 0.23 (26612) hydrogen bonds : bond 0.03790 / 2.55 ( 908) hydrogen bonds : angle 3.76592 / 2.70 ( 2676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9411 (mmm) cc_final: 0.9148 (mpp) REVERT: A 68 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: A 361 THR cc_start: 0.8614 (m) cc_final: 0.8367 (p) REVERT: A 488 MET cc_start: 0.8833 (mmm) cc_final: 0.8552 (mmm) REVERT: B 52 MET cc_start: 0.9414 (mmm) cc_final: 0.9126 (mpp) REVERT: B 68 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: B 361 THR cc_start: 0.8605 (m) cc_final: 0.8361 (p) REVERT: B 488 MET cc_start: 0.8823 (mmm) cc_final: 0.8558 (mmm) REVERT: C 52 MET cc_start: 0.9391 (mmm) cc_final: 0.9053 (mpp) REVERT: C 59 ARG cc_start: 0.9296 (mtm-85) cc_final: 0.9026 (ptp90) REVERT: C 68 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: C 134 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.7682 (mtm-85) REVERT: C 263 MET cc_start: 0.8072 (mmt) cc_final: 0.7856 (mmt) REVERT: C 361 THR cc_start: 0.8620 (m) cc_final: 0.8379 (p) REVERT: C 488 MET cc_start: 0.8832 (mmm) cc_final: 0.8557 (mmm) REVERT: D 52 MET cc_start: 0.9394 (mmm) cc_final: 0.9125 (mpp) REVERT: D 68 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: D 134 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: D 263 MET cc_start: 0.8142 (mmt) cc_final: 0.7897 (mmt) REVERT: D 361 THR cc_start: 0.8576 (m) cc_final: 0.8341 (p) REVERT: D 488 MET cc_start: 0.8840 (mmm) cc_final: 0.8567 (mmm) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.1517 time to fit residues: 35.4887 Evaluate side-chains 149 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 146 TYR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 553 LYS Chi-restraints excluded: chain D residue 591 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [64, 107, 88, 132, 57, 52, 136, 180, 117, 76, 11] chunk 64 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 117 optimal weight: 0.0040 chunk 76 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.072630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.051482 restraints weight = 61385.049| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 4.70 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19696 Z= 0.164 Angle : 0.464 5.808 26612 Z= 0.253 Chirality : 0.039 0.141 2848 Planarity : 0.003 0.045 3440 Dihedral : 3.708 28.133 2684 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.98 % Allowed : 20.46 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.95 (0.18), residues: 2372 helix: 3.10 (0.15), residues: 1092 sheet: -0.38 (0.39), residues: 172 loop : -0.31 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 59 TYR 0.010 0.001 TYR B 131 PHE 0.068 0.001 PHE B 130 TRP 0.010 0.001 TRP D 246 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (19696) covalent geometry : angle 0.46433 / 0.25 (26612) hydrogen bonds : bond 0.04733 / 3.17 ( 908) hydrogen bonds : angle 3.93125 / 2.81 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2862.42 seconds wall clock time: 50 minutes 25.98 seconds (3025.98 seconds total)