Starting phenix.real_space_refine on Sun Sep 13 22:01:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9usu_64471/09_2026/9usu_64471.cif Found real_map, /net/cci-nas-00/data/ceres_data/9usu_64471/09_2026/9usu_64471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9usu_64471/09_2026/9usu_64471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9usu_64471/09_2026/9usu_64471.map" model { file = "/net/cci-nas-00/data/ceres_data/9usu_64471/09_2026/9usu_64471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9usu_64471/09_2026/9usu_64471.cif" } resolution = 2.9 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= 0.015 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 72 5.16 5 C 16176 2.51 5 N 4110 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25296 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "C" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "D" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "E" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "F" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Time building chain proxies: 5.10, per 1000 atoms: 0.20 Number of scatterers: 25296 At special positions: 0 Unit cell: (158.27, 144.97, 111.72, 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 72 16.00 O 4938 8.00 N 4110 7.00 C 16176 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: 2.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 68 sheets defined 18.2% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.828A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.588A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.946A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.509A pdb=" N VAL A 521 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.892A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.674A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.557A pdb=" N THR B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.051A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.807A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 395 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.828A pdb=" N ASP D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 363 Processing helix chain 'D' and resid 389 through 395 removed outlier: 3.588A pdb=" N THR D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 removed outlier: 3.946A pdb=" N TRP D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 401' Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.509A pdb=" N VAL D 521 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.893A pdb=" N VAL E 164 " --> pdb=" O PRO E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 189 Processing helix chain 'E' and resid 198 through 206 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.674A pdb=" N ASP E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 395 removed outlier: 3.558A pdb=" N THR E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 removed outlier: 4.051A pdb=" N TRP E 400 " --> pdb=" O PRO E 396 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR E 401 " --> pdb=" O VAL E 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 396 through 401' Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'E' and resid 458 through 469 Processing helix chain 'E' and resid 516 through 521 Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 186 through 189 Processing helix chain 'F' and resid 198 through 206 Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.809A pdb=" N ASP F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP F 294 " --> pdb=" O ARG F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 395 Processing helix chain 'F' and resid 413 through 418 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'F' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.133A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.133A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.674A pdb=" N ASN A 96 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU A 111 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 98 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU A 109 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 100 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.565A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 236 removed outlier: 3.955A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 252 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.657A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.578A pdb=" N ARG A 442 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 443 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 454 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 445 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 299 removed outlier: 3.521A pdb=" N SER A 299 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.522A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR A 371 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE A 381 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER A 373 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N THR A 379 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 40 removed outlier: 4.149A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 40 removed outlier: 4.149A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.515A pdb=" N ILE B 178 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR B 179 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 100 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR B 181 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 98 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 183 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER B 102 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.518A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AB8, first strand: chain 'B' and resid 227 through 236 removed outlier: 3.611A pdb=" N ASP B 531 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN B 522 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN B 524 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 259 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 526 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 257 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 528 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 255 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN B 530 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA B 251 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 475 through 478 removed outlier: 5.823A pdb=" N ALA B 251 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN B 530 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 255 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 528 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 257 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 526 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 259 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN B 524 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN B 522 " --> pdb=" O PRO B 261 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 243 through 246 removed outlier: 3.560A pdb=" N ARG B 442 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 443 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B 454 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 445 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 450 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AC3, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AC4, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.772A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR B 369 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AC6, first strand: chain 'C' and resid 34 through 39 removed outlier: 4.303A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 34 through 39 removed outlier: 4.303A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.782A pdb=" N THR C 179 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE C 100 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C 181 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL C 98 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 183 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN C 96 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU C 111 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 98 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 109 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 100 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.598A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.749A pdb=" N GLY C 82 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG C 83 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 227 through 236 removed outlier: 3.854A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 227 through 236 Processing sheet with id=AD4, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.560A pdb=" N ARG C 442 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE C 447 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AD6, first strand: chain 'C' and resid 320 through 323 removed outlier: 6.397A pdb=" N ASP C 327 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE C 368 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR C 329 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLY C 370 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS C 331 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR C 372 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP C 333 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER C 385 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE C 368 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N HIS C 383 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY C 370 " --> pdb=" O PHE C 381 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE C 381 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 372 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C 379 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AD8, first strand: chain 'D' and resid 34 through 39 removed outlier: 4.134A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU D 69 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 34 through 39 removed outlier: 4.134A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.673A pdb=" N ASN D 96 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU D 111 " --> pdb=" O ASN D 96 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL D 98 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 100 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 78 through 79 removed outlier: 6.565A pdb=" N VAL D 78 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AE4, first strand: chain 'D' and resid 227 through 236 removed outlier: 3.955A pdb=" N GLN D 522 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA D 252 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.657A pdb=" N ARG D 475 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN D 522 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 243 through 246 removed outlier: 3.578A pdb=" N ARG D 442 " --> pdb=" O VAL D 508 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU D 443 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER D 454 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL D 445 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AE8, first strand: chain 'D' and resid 296 through 299 removed outlier: 3.521A pdb=" N SER D 299 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 320 through 323 removed outlier: 6.522A pdb=" N ASP D 327 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE D 368 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR D 329 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLY D 370 " --> pdb=" O TYR D 329 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS D 331 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR D 372 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP D 333 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR D 371 " --> pdb=" O PHE D 381 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE D 381 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER D 373 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N THR D 379 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 32 through 40 removed outlier: 4.149A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU E 69 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 32 through 40 removed outlier: 4.149A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.515A pdb=" N ILE E 178 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR E 179 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE E 100 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR E 181 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL E 98 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR E 183 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER E 102 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 78 through 79 removed outlier: 6.518A pdb=" N VAL E 78 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 139 through 141 Processing sheet with id=AF6, first strand: chain 'E' and resid 227 through 236 removed outlier: 3.611A pdb=" N ASP E 531 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN E 522 " --> pdb=" O PRO E 261 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN E 524 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR E 259 " --> pdb=" O GLN E 524 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 526 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL E 257 " --> pdb=" O VAL E 526 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 528 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU E 255 " --> pdb=" O VAL E 528 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN E 530 " --> pdb=" O THR E 253 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA E 251 " --> pdb=" O LEU E 532 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 475 through 478 removed outlier: 5.822A pdb=" N ALA E 251 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN E 530 " --> pdb=" O THR E 253 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU E 255 " --> pdb=" O VAL E 528 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 528 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL E 257 " --> pdb=" O VAL E 526 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 526 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR E 259 " --> pdb=" O GLN E 524 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN E 524 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN E 522 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 243 through 246 removed outlier: 3.560A pdb=" N ARG E 442 " --> pdb=" O VAL E 508 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU E 443 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER E 454 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL E 445 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP E 450 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AG1, first strand: chain 'E' and resid 296 through 299 Processing sheet with id=AG2, first strand: chain 'E' and resid 320 through 323 removed outlier: 6.772A pdb=" N ASP E 327 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE E 368 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR E 329 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLY E 370 " --> pdb=" O TYR E 329 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS E 331 " --> pdb=" O GLY E 370 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TYR E 372 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP E 333 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE E 365 " --> pdb=" O HIS E 386 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N HIS E 386 " --> pdb=" O PHE E 365 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA E 367 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE E 384 " --> pdb=" O ALA E 367 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR E 369 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 349 through 350 Processing sheet with id=AG4, first strand: chain 'F' and resid 34 through 39 removed outlier: 4.303A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 69 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 34 through 39 removed outlier: 4.303A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 42 through 44 removed outlier: 6.782A pdb=" N THR F 179 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE F 100 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR F 181 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL F 98 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR F 183 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN F 96 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU F 111 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 98 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU F 109 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE F 100 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.598A pdb=" N VAL F 78 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.749A pdb=" N GLY F 82 " --> pdb=" O GLY F 141 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG F 83 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 227 through 236 removed outlier: 3.854A pdb=" N GLN F 522 " --> pdb=" O TYR F 262 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 227 through 236 Processing sheet with id=AH2, first strand: chain 'F' and resid 243 through 246 removed outlier: 3.560A pdb=" N ARG F 442 " --> pdb=" O VAL F 508 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE F 447 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL F 451 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 296 through 299 Processing sheet with id=AH4, first strand: chain 'F' and resid 320 through 323 removed outlier: 6.398A pdb=" N ASP F 327 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE F 368 " --> pdb=" O ASP F 327 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR F 329 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY F 370 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS F 331 " --> pdb=" O GLY F 370 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR F 372 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP F 333 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER F 385 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE F 368 " --> pdb=" O HIS F 383 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N HIS F 383 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY F 370 " --> pdb=" O PHE F 381 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE F 381 " --> pdb=" O GLY F 370 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR F 372 " --> pdb=" O THR F 379 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR F 379 " --> pdb=" O TYR F 372 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 349 through 350 944 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7377 1.33 - 1.45: 4034 1.45 - 1.57: 14317 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 25848 Sorted by residual: bond pdb=" C ASP B 501 " pdb=" N LYS B 502 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.25e-02 6.40e+03 1.54e+01 bond pdb=" C ASP E 501 " pdb=" N LYS E 502 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" C GLY E 540 " pdb=" N VAL E 541 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.26e-02 6.30e+03 1.32e+01 bond pdb=" C GLY B 540 " pdb=" N VAL B 541 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.26e-02 6.30e+03 1.32e+01 bond pdb=" C LYS B 377 " pdb=" N ARG B 378 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.23e-02 6.61e+03 1.23e+01 ... (remaining 25843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 33582 1.29 - 2.58: 1225 2.58 - 3.87: 297 3.87 - 5.17: 46 5.17 - 6.46: 10 Bond angle restraints: 35160 Sorted by residual: angle pdb=" O THR B 143 " pdb=" C THR B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 121.57 117.65 3.92 9.70e-01 1.06e+00 1.63e+01 angle pdb=" O THR E 143 " pdb=" C THR E 143 " pdb=" N PRO E 144 " ideal model delta sigma weight residual 121.57 117.66 3.91 9.70e-01 1.06e+00 1.63e+01 angle pdb=" CA MET F 218 " pdb=" C MET F 218 " pdb=" O MET F 218 " ideal model delta sigma weight residual 122.13 118.12 4.01 1.13e+00 7.83e-01 1.26e+01 angle pdb=" CA MET C 218 " pdb=" C MET C 218 " pdb=" O MET C 218 " ideal model delta sigma weight residual 122.13 118.13 4.00 1.13e+00 7.83e-01 1.25e+01 angle pdb=" CA LYS E 377 " pdb=" C LYS E 377 " pdb=" N ARG E 378 " ideal model delta sigma weight residual 115.51 119.99 -4.48 1.30e+00 5.92e-01 1.19e+01 ... (remaining 35155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 13523 17.15 - 34.30: 1548 34.30 - 51.45: 367 51.45 - 68.60: 72 68.60 - 85.75: 24 Dihedral angle restraints: 15534 sinusoidal: 6114 harmonic: 9420 Sorted by residual: dihedral pdb=" CD ARG E 378 " pdb=" NE ARG E 378 " pdb=" CZ ARG E 378 " pdb=" NH1 ARG E 378 " ideal model delta sinusoidal sigma weight residual 0.00 -32.83 32.83 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CD ARG B 378 " pdb=" NE ARG B 378 " pdb=" CZ ARG B 378 " pdb=" NH1 ARG B 378 " ideal model delta sinusoidal sigma weight residual 0.00 -32.82 32.82 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CD ARG F 404 " pdb=" NE ARG F 404 " pdb=" CZ ARG F 404 " pdb=" NH1 ARG F 404 " ideal model delta sinusoidal sigma weight residual 0.00 -28.83 28.83 1 1.00e+01 1.00e-02 1.19e+01 ... (remaining 15531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2999 0.050 - 0.099: 636 0.099 - 0.149: 382 0.149 - 0.198: 28 0.198 - 0.248: 11 Chirality restraints: 4056 Sorted by residual: chirality pdb=" CA ARG C 193 " pdb=" N ARG C 193 " pdb=" C ARG C 193 " pdb=" CB ARG C 193 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ARG F 193 " pdb=" N ARG F 193 " pdb=" C ARG F 193 " pdb=" CB ARG F 193 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE E 192 " pdb=" N ILE E 192 " pdb=" C ILE E 192 " pdb=" CB ILE E 192 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 4053 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 378 " -0.578 9.50e-02 1.11e+02 2.59e-01 4.10e+01 pdb=" NE ARG B 378 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG B 378 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 378 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 378 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 378 " -0.578 9.50e-02 1.11e+02 2.59e-01 4.10e+01 pdb=" NE ARG E 378 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG E 378 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 378 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 378 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 404 " -0.511 9.50e-02 1.11e+02 2.29e-01 3.21e+01 pdb=" NE ARG F 404 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG F 404 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 404 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 404 " -0.016 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 541 2.68 - 3.24: 23433 3.24 - 3.79: 38430 3.79 - 4.35: 54905 4.35 - 4.90: 92054 Nonbonded interactions: 209363 Sorted by model distance: nonbonded pdb=" OH TYR B 359 " pdb=" OD1 ASP B 392 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR E 359 " pdb=" OD1 ASP E 392 " model vdw 2.127 3.040 nonbonded pdb=" OG SER D 373 " pdb=" OG1 THR D 376 " model vdw 2.147 3.040 nonbonded pdb=" OG SER A 373 " pdb=" OG1 THR A 376 " model vdw 2.147 3.040 nonbonded pdb=" OE1 GLU C 230 " pdb=" OG1 THR C 253 " model vdw 2.165 3.040 ... (remaining 209358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.54 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: 4.750 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: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.510 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.004 0.049 25848 Z= 0.269 Angle : 0.588 6.457 35160 Z= 0.378 Chirality : 0.052 0.248 4056 Planarity : 0.009 0.259 4488 Dihedral : 15.563 85.752 9474 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 22.34 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3156 helix: -0.01 (0.25), residues: 480 sheet: 0.68 (0.18), residues: 906 loop : -0.19 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 59 TYR 0.023 0.001 TYR E 519 PHE 0.017 0.001 PHE E 206 TRP 0.004 0.001 TRP A 108 HIS 0.002 0.000 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.27 (25848) covalent geometry : angle 0.58822 / 0.38 (35160) hydrogen bonds : bond 0.18684 / 12.32 ( 840) hydrogen bonds : angle 8.27206 / 5.87 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.946 Fit side-chains REVERT: A 220 LYS cc_start: 0.8256 (tttt) cc_final: 0.7869 (mppt) REVERT: B 218 MET cc_start: 0.8724 (ttt) cc_final: 0.8091 (mmt) REVERT: B 407 TYR cc_start: 0.7937 (m-10) cc_final: 0.7708 (m-10) REVERT: B 415 GLU cc_start: 0.8064 (mp0) cc_final: 0.7558 (mp0) REVERT: D 220 LYS cc_start: 0.8230 (tttt) cc_final: 0.7901 (mppt) REVERT: E 218 MET cc_start: 0.8706 (ttt) cc_final: 0.8085 (mmt) REVERT: E 253 THR cc_start: 0.9242 (m) cc_final: 0.8987 (m) REVERT: E 407 TYR cc_start: 0.7823 (m-10) cc_final: 0.7615 (m-10) REVERT: E 415 GLU cc_start: 0.8052 (mp0) cc_final: 0.7525 (mp0) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.6353 time to fit residues: 220.3279 Evaluate side-chains 267 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 344 HIS A 456 ASN A 472 ASN D 50 ASN D 344 HIS D 456 ASN D 472 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.093185 restraints weight = 33787.039| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.00 r_work: 0.2929 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25848 Z= 0.220 Angle : 0.521 5.296 35160 Z= 0.280 Chirality : 0.050 0.157 4056 Planarity : 0.004 0.042 4488 Dihedral : 3.971 18.837 3468 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.76 % Allowed : 20.08 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3156 helix: -0.09 (0.25), residues: 474 sheet: 0.52 (0.18), residues: 876 loop : -0.11 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 59 TYR 0.014 0.001 TYR E 520 PHE 0.011 0.002 PHE C 199 TRP 0.007 0.001 TRP D 108 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (25848) covalent geometry : angle 0.52072 / 0.28 (35160) hydrogen bonds : bond 0.04480 / 2.91 ( 840) hydrogen bonds : angle 5.76894 / 4.06 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 281 time to evaluate : 1.048 Fit side-chains REVERT: A 134 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: A 220 LYS cc_start: 0.8548 (tttt) cc_final: 0.7957 (mppt) REVERT: A 436 LYS cc_start: 0.8193 (mtpm) cc_final: 0.7824 (tttm) REVERT: A 444 GLU cc_start: 0.8643 (tt0) cc_final: 0.8430 (tt0) REVERT: A 520 TYR cc_start: 0.8954 (m-80) cc_final: 0.8751 (m-80) REVERT: B 138 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8415 (mm) REVERT: B 218 MET cc_start: 0.8777 (ttt) cc_final: 0.7776 (mmt) REVERT: B 223 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: B 339 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7266 (mmm) REVERT: B 407 TYR cc_start: 0.8072 (m-10) cc_final: 0.7798 (m-10) REVERT: B 415 GLU cc_start: 0.8331 (mp0) cc_final: 0.7981 (pm20) REVERT: B 472 ASN cc_start: 0.8486 (m110) cc_final: 0.8285 (m-40) REVERT: C 205 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: C 495 ASN cc_start: 0.7747 (t0) cc_final: 0.7538 (t0) REVERT: D 134 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: D 220 LYS cc_start: 0.8568 (tttt) cc_final: 0.7978 (mppt) REVERT: D 520 TYR cc_start: 0.8956 (m-80) cc_final: 0.8751 (m-80) REVERT: E 138 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8398 (mm) REVERT: E 204 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7950 (ttmm) REVERT: E 218 MET cc_start: 0.8764 (ttt) cc_final: 0.7786 (mmt) REVERT: E 223 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8297 (mp10) REVERT: E 339 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7281 (mmm) REVERT: E 415 GLU cc_start: 0.8300 (mp0) cc_final: 0.7966 (pm20) REVERT: E 472 ASN cc_start: 0.8328 (m110) cc_final: 0.8119 (m-40) REVERT: F 205 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: F 339 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.6746 (ptp) REVERT: F 495 ASN cc_start: 0.7811 (t0) cc_final: 0.7585 (t0) outliers start: 110 outliers final: 34 residues processed: 365 average time/residue: 0.6506 time to fit residues: 275.4952 Evaluate side-chains 295 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 105 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 135 optimal weight: 0.0030 chunk 88 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 246 optimal weight: 0.3980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN D 50 ASN D 456 ASN D 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095711 restraints weight = 33462.501| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.08 r_work: 0.2959 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 25848 Z= 0.103 Angle : 0.437 6.945 35160 Z= 0.236 Chirality : 0.047 0.150 4056 Planarity : 0.003 0.038 4488 Dihedral : 3.692 17.315 3468 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.07 % Allowed : 20.87 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3156 helix: 0.05 (0.25), residues: 474 sheet: 0.50 (0.18), residues: 876 loop : -0.06 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 59 TYR 0.011 0.001 TYR E 520 PHE 0.008 0.001 PHE D 199 TRP 0.004 0.001 TRP D 108 HIS 0.002 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (25848) covalent geometry : angle 0.43685 / 0.24 (35160) hydrogen bonds : bond 0.03347 / 2.17 ( 840) hydrogen bonds : angle 5.22040 / 3.68 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 283 time to evaluate : 1.276 Fit side-chains REVERT: A 134 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: A 177 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8462 (ttmt) REVERT: A 189 ASP cc_start: 0.8477 (m-30) cc_final: 0.8175 (m-30) REVERT: A 218 MET cc_start: 0.9034 (ttm) cc_final: 0.8721 (ttp) REVERT: A 220 LYS cc_start: 0.8443 (tttt) cc_final: 0.7848 (mppt) REVERT: A 241 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7831 (tt0) REVERT: A 329 TYR cc_start: 0.8126 (t80) cc_final: 0.7752 (t80) REVERT: A 436 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7728 (tttm) REVERT: A 444 GLU cc_start: 0.8604 (tt0) cc_final: 0.8284 (tt0) REVERT: A 520 TYR cc_start: 0.8884 (m-80) cc_final: 0.8598 (m-80) REVERT: B 218 MET cc_start: 0.8778 (ttt) cc_final: 0.7688 (mmt) REVERT: B 220 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6270 (mmtp) REVERT: B 407 TYR cc_start: 0.7873 (m-10) cc_final: 0.7549 (m-10) REVERT: B 415 GLU cc_start: 0.8190 (mp0) cc_final: 0.7941 (pm20) REVERT: B 472 ASN cc_start: 0.8064 (m110) cc_final: 0.7863 (m-40) REVERT: C 205 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: C 339 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.6639 (ptp) REVERT: C 495 ASN cc_start: 0.7567 (t0) cc_final: 0.7338 (t0) REVERT: D 134 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: D 177 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8473 (ttmt) REVERT: D 189 ASP cc_start: 0.8454 (m-30) cc_final: 0.8125 (m-30) REVERT: D 220 LYS cc_start: 0.8451 (tttt) cc_final: 0.7866 (mppt) REVERT: D 241 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7861 (tt0) REVERT: D 329 TYR cc_start: 0.8061 (t80) cc_final: 0.7682 (t80) REVERT: D 436 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7654 (ttpp) REVERT: D 520 TYR cc_start: 0.8866 (m-80) cc_final: 0.8566 (m-80) REVERT: E 218 MET cc_start: 0.8795 (ttt) cc_final: 0.7695 (mmt) REVERT: E 220 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6194 (mmtp) REVERT: E 415 GLU cc_start: 0.8188 (mp0) cc_final: 0.7930 (pm20) REVERT: E 472 ASN cc_start: 0.8027 (m110) cc_final: 0.7826 (m-40) REVERT: F 205 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: F 339 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.6509 (ptp) REVERT: F 516 HIS cc_start: 0.8285 (t-90) cc_final: 0.7939 (t70) outliers start: 90 outliers final: 38 residues processed: 354 average time/residue: 0.6910 time to fit residues: 281.8821 Evaluate side-chains 311 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 209 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 265 optimal weight: 0.0970 chunk 204 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 GLN D 456 ASN D 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094558 restraints weight = 33537.488| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.00 r_work: 0.2948 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25848 Z= 0.157 Angle : 0.466 5.587 35160 Z= 0.248 Chirality : 0.048 0.145 4056 Planarity : 0.004 0.056 4488 Dihedral : 3.780 17.620 3468 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.55 % Allowed : 20.80 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3156 helix: -0.04 (0.25), residues: 474 sheet: 0.35 (0.17), residues: 876 loop : -0.10 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 59 TYR 0.013 0.001 TYR D 258 PHE 0.011 0.001 PHE D 199 TRP 0.006 0.001 TRP D 108 HIS 0.004 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (25848) covalent geometry : angle 0.46624 / 0.25 (35160) hydrogen bonds : bond 0.03494 / 2.28 ( 840) hydrogen bonds : angle 5.07280 / 3.56 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 270 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: A 177 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8296 (ttpt) REVERT: A 220 LYS cc_start: 0.8526 (tttt) cc_final: 0.7915 (mppt) REVERT: A 329 TYR cc_start: 0.8182 (t80) cc_final: 0.7821 (t80) REVERT: A 436 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7790 (tttm) REVERT: A 520 TYR cc_start: 0.8916 (m-80) cc_final: 0.8683 (m-80) REVERT: A 547 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8059 (mmt) REVERT: B 138 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8349 (mm) REVERT: B 218 MET cc_start: 0.8809 (ttt) cc_final: 0.7829 (mpt) REVERT: B 407 TYR cc_start: 0.7992 (m-10) cc_final: 0.7698 (m-10) REVERT: B 415 GLU cc_start: 0.8184 (mp0) cc_final: 0.7956 (pm20) REVERT: C 205 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: C 339 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.6680 (ptp) REVERT: D 134 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: D 177 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8311 (ttpt) REVERT: D 220 LYS cc_start: 0.8520 (tttt) cc_final: 0.7919 (mppt) REVERT: D 241 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7912 (tt0) REVERT: D 329 TYR cc_start: 0.8147 (t80) cc_final: 0.7802 (t80) REVERT: D 436 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7693 (ttpp) REVERT: D 520 TYR cc_start: 0.8919 (m-80) cc_final: 0.8678 (m-80) REVERT: D 547 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8047 (mmt) REVERT: E 138 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8331 (mm) REVERT: E 218 MET cc_start: 0.8815 (ttt) cc_final: 0.7823 (mpt) REVERT: E 415 GLU cc_start: 0.8163 (mp0) cc_final: 0.7927 (pm20) REVERT: F 205 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: F 320 ILE cc_start: 0.8302 (mt) cc_final: 0.8042 (mp) REVERT: F 339 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.6695 (ptp) REVERT: F 495 ASN cc_start: 0.7771 (t0) cc_final: 0.7571 (t0) outliers start: 104 outliers final: 54 residues processed: 351 average time/residue: 0.6499 time to fit residues: 264.1251 Evaluate side-chains 322 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 254 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 10 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 275 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN D 50 ASN D 456 ASN D 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.091064 restraints weight = 33859.190| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.09 r_work: 0.2887 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 25848 Z= 0.294 Angle : 0.563 6.261 35160 Z= 0.297 Chirality : 0.052 0.152 4056 Planarity : 0.004 0.062 4488 Dihedral : 4.239 20.727 3468 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.05 % Allowed : 19.71 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 3156 helix: -0.38 (0.24), residues: 474 sheet: 0.07 (0.17), residues: 900 loop : -0.27 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 59 TYR 0.014 0.002 TYR B 463 PHE 0.016 0.002 PHE F 199 TRP 0.009 0.002 TRP A 108 HIS 0.007 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.29 (25848) covalent geometry : angle 0.56340 / 0.30 (35160) hydrogen bonds : bond 0.04288 / 2.80 ( 840) hydrogen bonds : angle 5.40230 / 3.78 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 262 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: A 241 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7782 (tt0) REVERT: A 436 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8100 (tttm) REVERT: A 493 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8627 (m) REVERT: A 547 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8043 (mmt) REVERT: B 138 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8484 (mm) REVERT: B 142 LEU cc_start: 0.8027 (mp) cc_final: 0.7784 (mp) REVERT: B 218 MET cc_start: 0.8857 (ttt) cc_final: 0.7793 (mpt) REVERT: B 220 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6423 (mmtp) REVERT: B 223 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: B 380 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8740 (mm) REVERT: B 404 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7435 (mtm180) REVERT: B 415 GLU cc_start: 0.8260 (mp0) cc_final: 0.7942 (pm20) REVERT: B 446 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8541 (mtt90) REVERT: C 43 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8382 (tpp) REVERT: C 205 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: D 81 MET cc_start: 0.8572 (mmm) cc_final: 0.8329 (mmm) REVERT: D 134 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: D 138 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8408 (mm) REVERT: D 241 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7784 (tt0) REVERT: D 436 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8061 (ttpp) REVERT: E 114 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8505 (mm-30) REVERT: E 138 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8463 (mm) REVERT: E 218 MET cc_start: 0.8846 (ttt) cc_final: 0.7824 (mpt) REVERT: E 220 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6408 (mmtp) REVERT: E 223 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: E 234 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8071 (ttt180) REVERT: E 380 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8750 (mm) REVERT: E 404 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7496 (mtm180) REVERT: E 415 GLU cc_start: 0.8267 (mp0) cc_final: 0.7949 (pm20) REVERT: F 43 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8355 (tpp) REVERT: F 205 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7163 (pm20) outliers start: 148 outliers final: 71 residues processed: 378 average time/residue: 0.6466 time to fit residues: 283.1710 Evaluate side-chains 340 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 247 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 223 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 309 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN A 515 ASN A 539 GLN D 50 ASN D 456 ASN D 472 ASN D 515 ASN D 539 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.093844 restraints weight = 33680.602| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.11 r_work: 0.2931 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25848 Z= 0.128 Angle : 0.458 4.966 35160 Z= 0.245 Chirality : 0.047 0.144 4056 Planarity : 0.004 0.046 4488 Dihedral : 3.884 19.019 3468 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.79 % Allowed : 21.45 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3156 helix: -0.17 (0.24), residues: 474 sheet: 0.06 (0.17), residues: 876 loop : -0.17 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 59 TYR 0.011 0.001 TYR E 520 PHE 0.009 0.001 PHE D 422 TRP 0.006 0.001 TRP D 108 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (25848) covalent geometry : angle 0.45836 / 0.25 (35160) hydrogen bonds : bond 0.03265 / 2.13 ( 840) hydrogen bonds : angle 5.00243 / 3.51 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 284 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8283 (m-40) cc_final: 0.7982 (m-40) REVERT: A 134 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7127 (pm20) REVERT: A 189 ASP cc_start: 0.8485 (m-30) cc_final: 0.8143 (m-30) REVERT: A 241 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7732 (tt0) REVERT: A 436 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7936 (tttm) REVERT: A 442 ARG cc_start: 0.7983 (ttt90) cc_final: 0.7221 (ttp-110) REVERT: A 520 TYR cc_start: 0.8780 (m-80) cc_final: 0.8466 (m-80) REVERT: A 547 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8028 (mmt) REVERT: B 81 MET cc_start: 0.8208 (mtp) cc_final: 0.7813 (mtt) REVERT: B 218 MET cc_start: 0.8822 (ttt) cc_final: 0.7680 (mpt) REVERT: B 380 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8665 (mm) REVERT: B 404 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7569 (mtm180) REVERT: B 407 TYR cc_start: 0.7932 (m-10) cc_final: 0.7464 (m-10) REVERT: B 415 GLU cc_start: 0.8177 (mp0) cc_final: 0.7911 (pm20) REVERT: B 446 ARG cc_start: 0.8799 (mtt-85) cc_final: 0.8556 (mtt90) REVERT: C 43 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8373 (tpp) REVERT: C 205 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: C 339 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.6689 (ptp) REVERT: C 384 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7907 (mt) REVERT: D 121 ASN cc_start: 0.8273 (m-40) cc_final: 0.7955 (m-40) REVERT: D 134 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: D 138 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8268 (mm) REVERT: D 177 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8202 (ttpt) REVERT: D 189 ASP cc_start: 0.8465 (m-30) cc_final: 0.8118 (m-30) REVERT: D 241 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7750 (tt0) REVERT: D 436 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7859 (ttpp) REVERT: D 520 TYR cc_start: 0.8774 (m-80) cc_final: 0.8449 (m-80) REVERT: E 81 MET cc_start: 0.8148 (mtp) cc_final: 0.7889 (mtm) REVERT: E 218 MET cc_start: 0.8820 (ttt) cc_final: 0.7697 (mpt) REVERT: E 380 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8700 (mm) REVERT: E 404 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7581 (mtm180) REVERT: E 415 GLU cc_start: 0.8197 (mp0) cc_final: 0.7932 (pm20) REVERT: F 43 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8338 (tpp) REVERT: F 205 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7265 (pm20) REVERT: F 384 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7879 (mt) REVERT: F 404 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7125 (mtm-85) REVERT: F 498 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7466 (mtp-110) outliers start: 111 outliers final: 55 residues processed: 365 average time/residue: 0.6650 time to fit residues: 279.9017 Evaluate side-chains 329 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 45 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 106 optimal weight: 0.0770 chunk 296 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.112086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091252 restraints weight = 33664.011| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.08 r_work: 0.2889 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25848 Z= 0.264 Angle : 0.550 5.901 35160 Z= 0.291 Chirality : 0.051 0.169 4056 Planarity : 0.004 0.051 4488 Dihedral : 4.190 20.551 3468 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.10 % Allowed : 21.35 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3156 helix: -0.41 (0.24), residues: 474 sheet: -0.10 (0.17), residues: 900 loop : -0.27 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 59 TYR 0.014 0.002 TYR C 520 PHE 0.021 0.002 BPHE F 357 TRP 0.008 0.002 TRP A 108 HIS 0.006 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.26 (25848) covalent geometry : angle 0.54957 / 0.29 (35160) hydrogen bonds : bond 0.04063 / 2.66 ( 840) hydrogen bonds : angle 5.29362 / 3.71 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 247 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8375 (m-40) cc_final: 0.8102 (m-40) REVERT: A 134 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: A 241 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7798 (tt0) REVERT: A 436 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (tttm) REVERT: A 472 ASN cc_start: 0.9018 (m110) cc_final: 0.8797 (m110) REVERT: A 493 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8621 (m) REVERT: A 520 TYR cc_start: 0.8899 (m-80) cc_final: 0.8663 (m-80) REVERT: A 547 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8079 (mmt) REVERT: B 81 MET cc_start: 0.8166 (mtp) cc_final: 0.7750 (mtt) REVERT: B 138 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8480 (mm) REVERT: B 218 MET cc_start: 0.8823 (ttt) cc_final: 0.7682 (mpt) REVERT: B 380 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (mm) REVERT: B 404 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7507 (mtm180) REVERT: B 415 GLU cc_start: 0.8250 (mp0) cc_final: 0.7948 (pm20) REVERT: B 446 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.8590 (mtt90) REVERT: C 17 LYS cc_start: 0.7720 (tmtt) cc_final: 0.7237 (mttt) REVERT: C 43 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8386 (tpp) REVERT: C 205 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: C 339 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7305 (ptp) REVERT: D 121 ASN cc_start: 0.8362 (m-40) cc_final: 0.8093 (m-40) REVERT: D 134 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: D 138 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8346 (mm) REVERT: D 241 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7827 (tt0) REVERT: D 472 ASN cc_start: 0.9013 (m110) cc_final: 0.8792 (m110) REVERT: D 520 TYR cc_start: 0.8912 (m-80) cc_final: 0.8678 (m-80) REVERT: E 81 MET cc_start: 0.8202 (mtp) cc_final: 0.7987 (mtm) REVERT: E 138 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8479 (mm) REVERT: E 218 MET cc_start: 0.8862 (ttt) cc_final: 0.7809 (mpt) REVERT: E 380 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8742 (mm) REVERT: E 404 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7508 (mtm180) REVERT: E 415 GLU cc_start: 0.8262 (mp0) cc_final: 0.7957 (pm20) REVERT: F 17 LYS cc_start: 0.7710 (tmtt) cc_final: 0.7229 (mttt) REVERT: F 43 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8345 (tpp) REVERT: F 205 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: F 339 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7136 (ptp) outliers start: 120 outliers final: 70 residues processed: 336 average time/residue: 0.6720 time to fit residues: 263.4806 Evaluate side-chains 331 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 243 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 495 ASN Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 253 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 chunk 84 optimal weight: 0.0870 chunk 114 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 GLN B 136 ASN D 50 ASN D 539 GLN E 136 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.095094 restraints weight = 33464.185| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.08 r_work: 0.2950 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25848 Z= 0.104 Angle : 0.453 5.328 35160 Z= 0.243 Chirality : 0.047 0.146 4056 Planarity : 0.004 0.056 4488 Dihedral : 3.810 17.964 3468 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.90 % Allowed : 22.47 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3156 helix: -0.22 (0.24), residues: 474 sheet: -0.01 (0.17), residues: 876 loop : -0.13 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 59 TYR 0.031 0.001 TYR E 519 PHE 0.009 0.001 PHE A 422 TRP 0.005 0.001 TRP D 108 HIS 0.002 0.000 HIS E 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (25848) covalent geometry : angle 0.45269 / 0.24 (35160) hydrogen bonds : bond 0.03044 / 1.98 ( 840) hydrogen bonds : angle 4.89772 / 3.44 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 280 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8276 (m-40) cc_final: 0.8013 (m-40) REVERT: A 177 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8151 (ttpt) REVERT: A 189 ASP cc_start: 0.8477 (m-30) cc_final: 0.8172 (m-30) REVERT: A 241 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7765 (tt0) REVERT: A 378 ARG cc_start: 0.7362 (mtm110) cc_final: 0.6980 (ttp80) REVERT: A 472 ASN cc_start: 0.8993 (m110) cc_final: 0.8779 (m110) REVERT: A 520 TYR cc_start: 0.8834 (m-80) cc_final: 0.8532 (m-80) REVERT: B 81 MET cc_start: 0.8223 (mtp) cc_final: 0.7829 (mtt) REVERT: B 218 MET cc_start: 0.8843 (ttt) cc_final: 0.7747 (mpt) REVERT: B 281 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7738 (mtpm) REVERT: B 380 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8707 (mm) REVERT: B 404 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7537 (mtm180) REVERT: B 407 TYR cc_start: 0.7956 (m-10) cc_final: 0.7563 (m-10) REVERT: B 415 GLU cc_start: 0.8161 (mp0) cc_final: 0.7908 (pm20) REVERT: B 446 ARG cc_start: 0.8807 (mtt-85) cc_final: 0.8571 (mtt90) REVERT: C 17 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7184 (mttt) REVERT: C 43 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8351 (tpp) REVERT: C 204 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7824 (mptm) REVERT: C 205 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: C 320 ILE cc_start: 0.8259 (mt) cc_final: 0.7999 (mp) REVERT: D 121 ASN cc_start: 0.8282 (m-40) cc_final: 0.8013 (m-40) REVERT: D 138 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8223 (mm) REVERT: D 189 ASP cc_start: 0.8453 (m-30) cc_final: 0.8139 (m-30) REVERT: D 241 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7783 (tt0) REVERT: D 432 ASP cc_start: 0.8569 (p0) cc_final: 0.8333 (p0) REVERT: D 472 ASN cc_start: 0.9004 (m110) cc_final: 0.8786 (m110) REVERT: D 520 TYR cc_start: 0.8824 (m-80) cc_final: 0.8507 (m-80) REVERT: E 81 MET cc_start: 0.8214 (mtp) cc_final: 0.7972 (mtm) REVERT: E 218 MET cc_start: 0.8849 (ttt) cc_final: 0.7747 (mpt) REVERT: E 380 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8710 (mm) REVERT: E 404 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7586 (mtm180) REVERT: E 415 GLU cc_start: 0.8191 (mp0) cc_final: 0.7887 (pm20) REVERT: E 533 TYR cc_start: 0.8970 (m-80) cc_final: 0.8641 (m-80) REVERT: F 43 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8369 (tpp) REVERT: F 205 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: F 320 ILE cc_start: 0.8258 (mt) cc_final: 0.8007 (mp) REVERT: F 339 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.6700 (ptp) outliers start: 85 outliers final: 48 residues processed: 342 average time/residue: 0.6149 time to fit residues: 243.1135 Evaluate side-chains 314 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 155 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 302 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 224 optimal weight: 0.0040 chunk 138 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 480 ASN D 50 ASN E 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095052 restraints weight = 33553.174| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.98 r_work: 0.2955 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25848 Z= 0.123 Angle : 0.467 6.084 35160 Z= 0.249 Chirality : 0.047 0.155 4056 Planarity : 0.004 0.062 4488 Dihedral : 3.797 16.929 3468 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.66 % Allowed : 22.98 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3156 helix: -0.21 (0.24), residues: 474 sheet: 0.01 (0.17), residues: 888 loop : -0.10 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 378 TYR 0.029 0.001 TYR B 519 PHE 0.023 0.001 BPHE F 357 TRP 0.005 0.001 TRP A 108 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (25848) covalent geometry : angle 0.46666 / 0.25 (35160) hydrogen bonds : bond 0.03148 / 2.06 ( 840) hydrogen bonds : angle 4.88061 / 3.43 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 275 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8250 (m-40) cc_final: 0.8010 (m-40) REVERT: A 189 ASP cc_start: 0.8467 (m-30) cc_final: 0.8139 (m-30) REVERT: A 241 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7906 (tt0) REVERT: A 432 ASP cc_start: 0.8562 (p0) cc_final: 0.8315 (p0) REVERT: A 520 TYR cc_start: 0.8911 (m-80) cc_final: 0.8662 (m-80) REVERT: B 218 MET cc_start: 0.8859 (ttt) cc_final: 0.7878 (mpt) REVERT: B 281 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7854 (mtpm) REVERT: B 339 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7346 (mmm) REVERT: B 380 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8788 (mm) REVERT: B 404 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7520 (mtm180) REVERT: B 407 TYR cc_start: 0.8046 (m-10) cc_final: 0.7585 (m-10) REVERT: B 415 GLU cc_start: 0.8194 (mp0) cc_final: 0.7965 (pm20) REVERT: B 436 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8170 (mtpt) REVERT: B 446 ARG cc_start: 0.8834 (mtt-85) cc_final: 0.8613 (mtt90) REVERT: C 17 LYS cc_start: 0.7622 (tmtt) cc_final: 0.7272 (mttt) REVERT: C 43 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8357 (tpp) REVERT: C 81 MET cc_start: 0.7795 (tpp) cc_final: 0.7508 (mmm) REVERT: C 204 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7864 (mptm) REVERT: C 205 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: C 320 ILE cc_start: 0.8364 (mt) cc_final: 0.8123 (mp) REVERT: C 339 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.6833 (ptp) REVERT: C 384 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7547 (mm) REVERT: C 498 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7540 (mtt-85) REVERT: D 121 ASN cc_start: 0.8267 (m-40) cc_final: 0.8018 (m-40) REVERT: D 134 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: D 138 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8319 (mm) REVERT: D 177 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8298 (ttpt) REVERT: D 189 ASP cc_start: 0.8441 (m-30) cc_final: 0.8110 (m-30) REVERT: D 241 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7893 (tt0) REVERT: D 378 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7536 (mtm110) REVERT: D 432 ASP cc_start: 0.8580 (p0) cc_final: 0.8351 (p0) REVERT: D 520 TYR cc_start: 0.8914 (m-80) cc_final: 0.8669 (m-80) REVERT: E 138 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8540 (mm) REVERT: E 218 MET cc_start: 0.8852 (ttt) cc_final: 0.7884 (mpt) REVERT: E 281 LYS cc_start: 0.8398 (tptp) cc_final: 0.7985 (mtpm) REVERT: E 380 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8790 (mm) REVERT: E 404 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7584 (mtm180) REVERT: E 415 GLU cc_start: 0.8210 (mp0) cc_final: 0.7972 (pm20) REVERT: F 43 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8391 (tpp) REVERT: F 81 MET cc_start: 0.7768 (tpp) cc_final: 0.7474 (mmm) REVERT: F 205 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: F 320 ILE cc_start: 0.8365 (mt) cc_final: 0.8127 (mp) REVERT: F 339 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.6831 (ptp) REVERT: F 384 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7527 (mm) outliers start: 78 outliers final: 48 residues processed: 335 average time/residue: 0.6119 time to fit residues: 237.8971 Evaluate side-chains 323 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 155 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 292 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 262 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN B 104 ASN D 472 ASN E 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094501 restraints weight = 33349.288| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.09 r_work: 0.2939 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25848 Z= 0.132 Angle : 0.479 6.222 35160 Z= 0.256 Chirality : 0.048 0.150 4056 Planarity : 0.004 0.064 4488 Dihedral : 3.823 17.783 3468 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.63 % Allowed : 23.36 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3156 helix: -0.25 (0.24), residues: 474 sheet: -0.01 (0.17), residues: 888 loop : -0.12 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 378 TYR 0.030 0.001 TYR E 519 PHE 0.009 0.001 PHE C 199 TRP 0.005 0.001 TRP A 108 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (25848) covalent geometry : angle 0.47916 / 0.26 (35160) hydrogen bonds : bond 0.03232 / 2.12 ( 840) hydrogen bonds : angle 4.89080 / 3.43 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 264 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8272 (m-40) cc_final: 0.8020 (m-40) REVERT: A 134 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: A 189 ASP cc_start: 0.8460 (m-30) cc_final: 0.8123 (m-30) REVERT: A 241 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7760 (tt0) REVERT: A 378 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7548 (mtm110) REVERT: A 432 ASP cc_start: 0.8571 (p0) cc_final: 0.8296 (p0) REVERT: A 520 TYR cc_start: 0.8875 (m-80) cc_final: 0.8601 (m-80) REVERT: B 81 MET cc_start: 0.8448 (mtm) cc_final: 0.8167 (mtt) REVERT: B 138 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8471 (mm) REVERT: B 218 MET cc_start: 0.8847 (ttt) cc_final: 0.7710 (mpt) REVERT: B 281 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7678 (mtpm) REVERT: B 339 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7097 (mmm) REVERT: B 380 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 404 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7551 (mtm180) REVERT: B 407 TYR cc_start: 0.7978 (m-10) cc_final: 0.7566 (m-10) REVERT: B 415 GLU cc_start: 0.8198 (mp0) cc_final: 0.7929 (pm20) REVERT: B 436 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8106 (mtpt) REVERT: B 446 ARG cc_start: 0.8789 (mtt-85) cc_final: 0.8544 (mtt90) REVERT: C 17 LYS cc_start: 0.7726 (tmtt) cc_final: 0.7229 (mttt) REVERT: C 43 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8344 (tpp) REVERT: C 204 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7806 (mptm) REVERT: C 205 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: C 320 ILE cc_start: 0.8223 (mt) cc_final: 0.7970 (mp) REVERT: C 339 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.6850 (ptp) REVERT: C 384 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7556 (mm) REVERT: C 404 ARG cc_start: 0.7411 (mtm180) cc_final: 0.7138 (mtp85) REVERT: C 436 LYS cc_start: 0.7950 (mttp) cc_final: 0.7330 (mmtt) REVERT: D 121 ASN cc_start: 0.8290 (m-40) cc_final: 0.8045 (m-40) REVERT: D 134 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: D 138 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8188 (mm) REVERT: D 177 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8186 (ttpt) REVERT: D 189 ASP cc_start: 0.8443 (m-30) cc_final: 0.8127 (m-30) REVERT: D 241 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7767 (tt0) REVERT: D 378 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7542 (mtm110) REVERT: D 432 ASP cc_start: 0.8574 (p0) cc_final: 0.8309 (p0) REVERT: D 520 TYR cc_start: 0.8836 (m-80) cc_final: 0.8561 (m-80) REVERT: E 138 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8466 (mm) REVERT: E 218 MET cc_start: 0.8844 (ttt) cc_final: 0.7720 (mpt) REVERT: E 281 LYS cc_start: 0.7906 (tptp) cc_final: 0.7365 (mtpm) REVERT: E 380 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8730 (mm) REVERT: E 404 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7581 (mtm180) REVERT: E 415 GLU cc_start: 0.8206 (mp0) cc_final: 0.7934 (pm20) REVERT: F 43 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8398 (tpp) REVERT: F 205 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: F 320 ILE cc_start: 0.8218 (mt) cc_final: 0.7968 (mp) REVERT: F 339 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.6650 (ptp) REVERT: F 384 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7481 (mm) outliers start: 77 outliers final: 47 residues processed: 322 average time/residue: 0.6467 time to fit residues: 240.0605 Evaluate side-chains 326 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 258 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 296 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.114063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.093204 restraints weight = 33554.076| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.08 r_work: 0.2910 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25848 Z= 0.174 Angle : 0.501 6.671 35160 Z= 0.266 Chirality : 0.049 0.160 4056 Planarity : 0.004 0.063 4488 Dihedral : 3.962 17.791 3468 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.70 % Allowed : 23.29 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3156 helix: -0.29 (0.24), residues: 474 sheet: -0.06 (0.17), residues: 888 loop : -0.15 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 59 TYR 0.031 0.001 TYR B 519 PHE 0.026 0.001 BPHE C 357 TRP 0.006 0.001 TRP A 108 HIS 0.004 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (25848) covalent geometry : angle 0.50131 / 0.27 (35160) hydrogen bonds : bond 0.03532 / 2.31 ( 840) hydrogen bonds : angle 5.03844 / 3.53 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8261.82 seconds wall clock time: 141 minutes 43.71 seconds (8503.71 seconds total)