Starting phenix.real_space_refine on Sun Apr 5 14:31:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cft_30347/04_2026/7cft_30347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cft_30347/04_2026/7cft_30347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cft_30347/04_2026/7cft_30347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cft_30347/04_2026/7cft_30347.map" model { file = "/net/cci-nas-00/data/ceres_data/7cft_30347/04_2026/7cft_30347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cft_30347/04_2026/7cft_30347.cif" } resolution = 3.9 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= 0.004 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 111 5.16 5 C 7161 2.51 5 N 1878 2.21 5 O 2133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3282 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 399} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 451 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, E, F Time building chain proxies: 2.56, per 1000 atoms: 0.23 Number of scatterers: 11283 At special positions: 0 Unit cell: (107.484, 103.428, 131.82, 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 111 16.00 O 2133 8.00 N 1878 7.00 C 7161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.02 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.04 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" CA CYS B 61 " - pdb=" SG CYS B 61 " distance=2.84 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.04 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.04 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 395 " " NAG A 602 " - " ASN A 368 " " NAG B 601 " - " ASN B 395 " " NAG B 602 " - " ASN B 368 " " NAG C 601 " - " ASN C 395 " " NAG C 602 " - " ASN C 368 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 671.7 milliseconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 31.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.745A pdb=" N ALA A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 4.061A pdb=" N GLN A 102 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.678A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 184 removed outlier: 4.047A pdb=" N ASP A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.590A pdb=" N TYR A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.888A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.838A pdb=" N ARG A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.751A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 removed outlier: 3.658A pdb=" N LEU A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.906A pdb=" N LEU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 430 through 440 removed outlier: 4.281A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 457 removed outlier: 3.519A pdb=" N LEU A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.594A pdb=" N LYS A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 67 removed outlier: 3.745A pdb=" N ALA B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 4.060A pdb=" N GLN B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 103 " --> pdb=" O PHE B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 103' Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.678A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 180 through 184 removed outlier: 4.047A pdb=" N ASP B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.589A pdb=" N TYR B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.888A pdb=" N GLY B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 removed outlier: 3.838A pdb=" N ARG B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 322 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.752A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 352 removed outlier: 3.659A pdb=" N LEU B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 removed outlier: 3.907A pdb=" N LEU B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 430 through 440 removed outlier: 4.280A pdb=" N GLY B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 457 removed outlier: 3.520A pdb=" N LEU B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.594A pdb=" N LYS B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 67 removed outlier: 3.745A pdb=" N ALA C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.060A pdb=" N GLN C 102 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 103 " --> pdb=" O PHE C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.678A pdb=" N ARG C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 180 through 184 removed outlier: 4.047A pdb=" N ASP C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 184' Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.590A pdb=" N TYR C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.889A pdb=" N GLY C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 removed outlier: 3.839A pdb=" N ARG C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 322 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.753A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.659A pdb=" N LEU C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 394 removed outlier: 3.907A pdb=" N LEU C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 430 through 440 removed outlier: 4.281A pdb=" N GLY C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 457 removed outlier: 3.520A pdb=" N LEU C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP C 455 " --> pdb=" O LEU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 462 removed outlier: 3.593A pdb=" N LYS C 462 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 removed outlier: 3.518A pdb=" N GLU A 421 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 274 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 375 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 373 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.516A pdb=" N LEU A 406 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 407 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 409 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 189 removed outlier: 6.734A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 263 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 77 removed outlier: 3.517A pdb=" N GLU B 421 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 274 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 375 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 373 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.516A pdb=" N LEU B 406 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 407 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 409 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.735A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 263 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 77 removed outlier: 3.518A pdb=" N GLU C 421 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU C 418 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU C 277 " --> pdb=" O GLU C 418 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE C 420 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG C 279 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLN C 422 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE C 281 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LYS C 424 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 274 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 375 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 373 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.517A pdb=" N LEU C 406 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL C 407 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 409 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 187 through 189 removed outlier: 6.734A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 263 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB7, first strand: chain 'D' and resid 20 through 22 removed outlier: 3.544A pdb=" N GLY D 36 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 20 through 22 removed outlier: 3.544A pdb=" N GLY E 36 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 20 through 22 removed outlier: 3.544A pdb=" N GLY F 36 " --> pdb=" O TYR F 20 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3536 1.34 - 1.45: 2067 1.45 - 1.57: 5785 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 11532 Sorted by residual: bond pdb=" C VAL C 265 " pdb=" N ALA C 266 " ideal model delta sigma weight residual 1.331 1.235 0.096 2.83e-02 1.25e+03 1.15e+01 bond pdb=" C VAL A 265 " pdb=" N ALA A 266 " ideal model delta sigma weight residual 1.331 1.236 0.095 2.83e-02 1.25e+03 1.13e+01 bond pdb=" C VAL B 265 " pdb=" N ALA B 266 " ideal model delta sigma weight residual 1.331 1.236 0.095 2.83e-02 1.25e+03 1.12e+01 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.23e+00 ... (remaining 11527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 14717 1.92 - 3.84: 750 3.84 - 5.76: 100 5.76 - 7.68: 18 7.68 - 9.60: 9 Bond angle restraints: 15594 Sorted by residual: angle pdb=" C LYS F 17 " pdb=" N PHE F 18 " pdb=" CA PHE F 18 " ideal model delta sigma weight residual 121.31 127.90 -6.59 1.49e+00 4.50e-01 1.96e+01 angle pdb=" C LYS D 17 " pdb=" N PHE D 18 " pdb=" CA PHE D 18 " ideal model delta sigma weight residual 121.31 127.87 -6.56 1.49e+00 4.50e-01 1.94e+01 angle pdb=" C LYS E 17 " pdb=" N PHE E 18 " pdb=" CA PHE E 18 " ideal model delta sigma weight residual 121.31 127.87 -6.56 1.49e+00 4.50e-01 1.94e+01 angle pdb=" C ARG A 201 " pdb=" N ASP A 202 " pdb=" CA ASP A 202 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N PHE E 18 " pdb=" CA PHE E 18 " pdb=" C PHE E 18 " ideal model delta sigma weight residual 110.35 115.63 -5.28 1.40e+00 5.10e-01 1.42e+01 ... (remaining 15589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6197 17.97 - 35.93: 697 35.93 - 53.89: 150 53.89 - 71.86: 9 71.86 - 89.82: 12 Dihedral angle restraints: 7065 sinusoidal: 2898 harmonic: 4167 Sorted by residual: dihedral pdb=" CB CYS B 61 " pdb=" CA CYS B 61 " pdb=" SG CYS B 61 " pdb=" CB CYS B 61 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS C 290 " pdb=" SG CYS C 290 " pdb=" SG CYS C 367 " pdb=" CB CYS C 367 " ideal model delta sinusoidal sigma weight residual 93.00 142.84 -49.84 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 142.84 -49.84 1 1.00e+01 1.00e-02 3.41e+01 ... (remaining 7062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1240 0.060 - 0.121: 393 0.121 - 0.181: 62 0.181 - 0.242: 6 0.242 - 0.302: 6 Chirality restraints: 1707 Sorted by residual: chirality pdb=" CB VAL B 232 " pdb=" CA VAL B 232 " pdb=" CG1 VAL B 232 " pdb=" CG2 VAL B 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL A 232 " pdb=" CA VAL A 232 " pdb=" CG1 VAL A 232 " pdb=" CG2 VAL A 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB VAL C 232 " pdb=" CA VAL C 232 " pdb=" CG1 VAL C 232 " pdb=" CG2 VAL C 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1704 not shown) Planarity restraints: 2034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 381 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO B 382 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 381 " 0.041 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO C 382 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 381 " 0.041 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO A 382 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.035 5.00e-02 4.00e+02 ... (remaining 2031 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 142 2.60 - 3.17: 9071 3.17 - 3.75: 16419 3.75 - 4.32: 22034 4.32 - 4.90: 35729 Nonbonded interactions: 83395 Sorted by model distance: nonbonded pdb=" SG CYS E 50 " pdb=" SG CYS E 55 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS F 50 " pdb=" SG CYS F 55 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS D 50 " pdb=" SG CYS D 55 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS D 12 " pdb=" SG CYS D 37 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS E 41 " pdb=" SG CYS E 49 " model vdw 2.027 3.760 ... (remaining 83390 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.600 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.011 0.805 11560 Z= 0.538 Angle : 1.291 75.160 15656 Z= 0.681 Chirality : 0.059 0.302 1707 Planarity : 0.006 0.061 2028 Dihedral : 15.043 89.823 4323 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.75 % Allowed : 11.75 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -5.25 (0.16), residues: 1413 helix: -4.56 (0.09), residues: 348 sheet: -2.75 (0.32), residues: 213 loop : -3.34 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 311 TYR 0.024 0.002 TYR C 417 PHE 0.021 0.003 PHE A 263 TRP 0.008 0.002 TRP B 233 HIS 0.007 0.002 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00862 (11532) covalent geometry : angle 0.98797 (15594) SS BOND : bond 0.17169 ( 22) SS BOND : angle 15.64334 ( 44) hydrogen bonds : bond 0.30887 ( 273) hydrogen bonds : angle 8.97094 ( 729) link_NAG-ASN : bond 0.00589 ( 6) link_NAG-ASN : angle 2.26263 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.7109 (p) cc_final: 0.6893 (p) REVERT: A 208 LYS cc_start: 0.8899 (mttt) cc_final: 0.8627 (mtpp) REVERT: A 313 ASP cc_start: 0.8385 (t70) cc_final: 0.8056 (t0) REVERT: A 330 MET cc_start: 0.8937 (mtp) cc_final: 0.8693 (mtp) REVERT: B 98 PHE cc_start: 0.8993 (m-80) cc_final: 0.8699 (m-10) REVERT: B 313 ASP cc_start: 0.8346 (t70) cc_final: 0.8095 (t0) REVERT: B 316 THR cc_start: 0.8629 (p) cc_final: 0.8360 (t) REVERT: B 330 MET cc_start: 0.8876 (mtp) cc_final: 0.8481 (mtp) REVERT: C 98 PHE cc_start: 0.9008 (m-80) cc_final: 0.8624 (m-10) REVERT: C 208 LYS cc_start: 0.8807 (mttt) cc_final: 0.8589 (mtpp) REVERT: C 313 ASP cc_start: 0.8267 (t70) cc_final: 0.7961 (t0) REVERT: C 319 LEU cc_start: 0.9393 (tp) cc_final: 0.9150 (tp) REVERT: C 330 MET cc_start: 0.8928 (mtp) cc_final: 0.8582 (mtp) REVERT: D 31 LYS cc_start: 0.7536 (mmtt) cc_final: 0.7325 (mmmt) outliers start: 21 outliers final: 9 residues processed: 267 average time/residue: 0.1323 time to fit residues: 46.8626 Evaluate side-chains 189 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN A 463 HIS B 358 GLN B 463 HIS C 463 HIS D 56 ASN E 56 ASN F 56 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125250 restraints weight = 14980.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124578 restraints weight = 19273.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123555 restraints weight = 16422.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122784 restraints weight = 17915.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123038 restraints weight = 15480.434| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11560 Z= 0.164 Angle : 0.925 55.641 15656 Z= 0.463 Chirality : 0.043 0.142 1707 Planarity : 0.004 0.047 2028 Dihedral : 5.598 26.486 1683 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.75 % Allowed : 16.33 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -4.13 (0.19), residues: 1413 helix: -2.90 (0.20), residues: 351 sheet: -2.38 (0.28), residues: 321 loop : -2.83 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 54 TYR 0.019 0.001 TYR C 417 PHE 0.008 0.001 PHE B 272 TRP 0.009 0.001 TRP A 233 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00361 (11532) covalent geometry : angle 0.72584 (15594) SS BOND : bond 0.01087 ( 22) SS BOND : angle 10.83548 ( 44) hydrogen bonds : bond 0.04546 ( 273) hydrogen bonds : angle 5.61023 ( 729) link_NAG-ASN : bond 0.00381 ( 6) link_NAG-ASN : angle 0.92128 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.8928 (mttt) cc_final: 0.8632 (mtpp) REVERT: A 313 ASP cc_start: 0.8320 (t70) cc_final: 0.8095 (t0) REVERT: A 399 GLN cc_start: 0.7668 (tp40) cc_final: 0.7457 (tp40) REVERT: B 98 PHE cc_start: 0.8881 (m-80) cc_final: 0.8615 (m-10) REVERT: C 98 PHE cc_start: 0.8858 (m-80) cc_final: 0.8448 (m-10) REVERT: C 208 LYS cc_start: 0.8847 (mttt) cc_final: 0.8572 (mtpp) REVERT: C 313 ASP cc_start: 0.8272 (t70) cc_final: 0.8021 (t0) REVERT: E 16 MET cc_start: 0.8196 (ttm) cc_final: 0.7843 (mtp) REVERT: E 20 TYR cc_start: 0.8783 (p90) cc_final: 0.8564 (p90) REVERT: F 38 SER cc_start: 0.8423 (t) cc_final: 0.7970 (m) outliers start: 33 outliers final: 20 residues processed: 253 average time/residue: 0.1044 time to fit residues: 37.2863 Evaluate side-chains 209 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 89 optimal weight: 7.9990 chunk 21 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS F 21 HIS F 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120938 restraints weight = 15268.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120399 restraints weight = 12609.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119832 restraints weight = 11716.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119764 restraints weight = 12805.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119818 restraints weight = 11562.921| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11560 Z= 0.122 Angle : 0.898 55.951 15656 Z= 0.441 Chirality : 0.042 0.286 1707 Planarity : 0.003 0.047 2028 Dihedral : 5.059 23.580 1677 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.17 % Allowed : 19.42 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -3.45 (0.21), residues: 1413 helix: -2.25 (0.22), residues: 378 sheet: -2.15 (0.29), residues: 303 loop : -2.34 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 54 TYR 0.024 0.001 TYR C 67 PHE 0.022 0.001 PHE C 411 TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00264 (11532) covalent geometry : angle 0.68714 (15594) SS BOND : bond 0.01067 ( 22) SS BOND : angle 10.90927 ( 44) hydrogen bonds : bond 0.03496 ( 273) hydrogen bonds : angle 4.98710 ( 729) link_NAG-ASN : bond 0.00311 ( 6) link_NAG-ASN : angle 0.92916 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.400 Fit side-chains REVERT: A 208 LYS cc_start: 0.8946 (mttt) cc_final: 0.8573 (mtpp) REVERT: A 313 ASP cc_start: 0.8511 (t70) cc_final: 0.8178 (t0) REVERT: A 321 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 98 PHE cc_start: 0.8908 (m-80) cc_final: 0.8586 (m-10) REVERT: B 350 LEU cc_start: 0.9247 (mt) cc_final: 0.9014 (mt) REVERT: C 98 PHE cc_start: 0.8838 (m-80) cc_final: 0.8278 (m-10) REVERT: C 208 LYS cc_start: 0.8845 (mttt) cc_final: 0.8588 (mtpp) REVERT: C 313 ASP cc_start: 0.8436 (t70) cc_final: 0.8081 (t0) REVERT: D 28 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7968 (tpp80) REVERT: D 38 SER cc_start: 0.8138 (t) cc_final: 0.7634 (m) REVERT: D 55 CYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7103 (p) outliers start: 38 outliers final: 27 residues processed: 249 average time/residue: 0.0976 time to fit residues: 34.6954 Evaluate side-chains 221 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 0.0070 chunk 130 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.159922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123361 restraints weight = 15344.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122572 restraints weight = 18248.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120261 restraints weight = 15380.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119864 restraints weight = 14829.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120454 restraints weight = 13280.263| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11560 Z= 0.170 Angle : 0.900 55.966 15656 Z= 0.444 Chirality : 0.044 0.308 1707 Planarity : 0.003 0.038 2028 Dihedral : 4.993 22.641 1677 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.33 % Allowed : 20.25 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.95 (0.22), residues: 1413 helix: -1.72 (0.24), residues: 360 sheet: -1.46 (0.32), residues: 282 loop : -2.29 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 54 TYR 0.019 0.001 TYR C 67 PHE 0.017 0.001 PHE C 411 TRP 0.008 0.002 TRP A 233 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00391 (11532) covalent geometry : angle 0.69252 (15594) SS BOND : bond 0.01083 ( 22) SS BOND : angle 10.83422 ( 44) hydrogen bonds : bond 0.03562 ( 273) hydrogen bonds : angle 4.92052 ( 729) link_NAG-ASN : bond 0.00098 ( 6) link_NAG-ASN : angle 1.31263 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.9018 (mttt) cc_final: 0.8743 (mtpp) REVERT: A 313 ASP cc_start: 0.8577 (t70) cc_final: 0.8228 (t0) REVERT: B 98 PHE cc_start: 0.8907 (m-80) cc_final: 0.8640 (m-10) REVERT: C 98 PHE cc_start: 0.8918 (m-80) cc_final: 0.8282 (m-10) REVERT: C 208 LYS cc_start: 0.8899 (mttt) cc_final: 0.8577 (mtpp) REVERT: C 313 ASP cc_start: 0.8462 (t70) cc_final: 0.8065 (t0) REVERT: D 9 VAL cc_start: 0.8979 (p) cc_final: 0.8725 (m) REVERT: E 20 TYR cc_start: 0.8908 (p90) cc_final: 0.8593 (p90) outliers start: 52 outliers final: 37 residues processed: 237 average time/residue: 0.0994 time to fit residues: 33.4772 Evaluate side-chains 217 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113513 restraints weight = 15137.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114893 restraints weight = 11918.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115635 restraints weight = 10391.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116261 restraints weight = 9514.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116261 restraints weight = 9090.030| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11560 Z= 0.167 Angle : 0.908 55.971 15656 Z= 0.446 Chirality : 0.043 0.294 1707 Planarity : 0.003 0.038 2028 Dihedral : 5.027 22.262 1677 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.50 % Allowed : 21.00 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.74 (0.22), residues: 1413 helix: -1.48 (0.25), residues: 363 sheet: -1.42 (0.31), residues: 282 loop : -2.17 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 28 TYR 0.018 0.001 TYR C 67 PHE 0.014 0.001 PHE C 411 TRP 0.009 0.002 TRP B 233 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00386 (11532) covalent geometry : angle 0.70368 (15594) SS BOND : bond 0.01080 ( 22) SS BOND : angle 10.84401 ( 44) hydrogen bonds : bond 0.03417 ( 273) hydrogen bonds : angle 4.87982 ( 729) link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 1.14838 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 0.422 Fit side-chains REVERT: A 208 LYS cc_start: 0.9021 (mttt) cc_final: 0.8736 (mtpp) REVERT: A 313 ASP cc_start: 0.8679 (t70) cc_final: 0.8306 (t0) REVERT: A 341 GLN cc_start: 0.8258 (pt0) cc_final: 0.7812 (pt0) REVERT: A 399 GLN cc_start: 0.8121 (tp40) cc_final: 0.7919 (tp40) REVERT: A 421 GLU cc_start: 0.7490 (pm20) cc_final: 0.7283 (pm20) REVERT: B 98 PHE cc_start: 0.8956 (m-80) cc_final: 0.8635 (m-10) REVERT: B 344 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: C 98 PHE cc_start: 0.8898 (m-80) cc_final: 0.8248 (m-10) REVERT: C 208 LYS cc_start: 0.8957 (mttt) cc_final: 0.8715 (mtpp) REVERT: C 224 ILE cc_start: 0.9126 (pt) cc_final: 0.8892 (mt) REVERT: C 313 ASP cc_start: 0.8623 (t70) cc_final: 0.8207 (t0) REVERT: E 20 TYR cc_start: 0.9107 (p90) cc_final: 0.8702 (p90) outliers start: 54 outliers final: 36 residues processed: 224 average time/residue: 0.1034 time to fit residues: 32.9557 Evaluate side-chains 214 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS D 21 HIS D 35 GLN E 35 GLN F 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108618 restraints weight = 15706.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109855 restraints weight = 12819.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110443 restraints weight = 11356.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110619 restraints weight = 10552.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110920 restraints weight = 10225.389| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11560 Z= 0.174 Angle : 0.912 55.977 15656 Z= 0.448 Chirality : 0.044 0.303 1707 Planarity : 0.003 0.042 2028 Dihedral : 5.173 27.458 1677 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.67 % Allowed : 21.25 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.59 (0.22), residues: 1413 helix: -1.47 (0.24), residues: 381 sheet: -1.43 (0.31), residues: 282 loop : -1.95 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.018 0.001 TYR B 417 PHE 0.013 0.001 PHE C 411 TRP 0.008 0.002 TRP A 233 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00402 (11532) covalent geometry : angle 0.70786 (15594) SS BOND : bond 0.01099 ( 22) SS BOND : angle 10.84055 ( 44) hydrogen bonds : bond 0.03380 ( 273) hydrogen bonds : angle 4.87128 ( 729) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 1.30010 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 0.458 Fit side-chains REVERT: A 208 LYS cc_start: 0.9059 (mttt) cc_final: 0.8837 (mtpm) REVERT: A 313 ASP cc_start: 0.8725 (t70) cc_final: 0.8330 (t0) REVERT: A 341 GLN cc_start: 0.8549 (pt0) cc_final: 0.8092 (pt0) REVERT: B 98 PHE cc_start: 0.8978 (m-80) cc_final: 0.8710 (m-10) REVERT: B 344 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: C 98 PHE cc_start: 0.8929 (m-80) cc_final: 0.8272 (m-10) REVERT: C 208 LYS cc_start: 0.8979 (mttt) cc_final: 0.8730 (mtpp) REVERT: C 313 ASP cc_start: 0.8623 (t70) cc_final: 0.8174 (t0) REVERT: C 382 PRO cc_start: 0.8260 (Cg_exo) cc_final: 0.8024 (Cg_endo) REVERT: D 55 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7167 (p) REVERT: E 20 TYR cc_start: 0.9143 (p90) cc_final: 0.8702 (p90) outliers start: 56 outliers final: 41 residues processed: 221 average time/residue: 0.0963 time to fit residues: 30.3684 Evaluate side-chains 220 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 127 optimal weight: 0.0000 chunk 51 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN F 35 GLN F 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109982 restraints weight = 15580.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111324 restraints weight = 12241.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111589 restraints weight = 10077.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111711 restraints weight = 10026.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111789 restraints weight = 9705.455| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11560 Z= 0.147 Angle : 0.900 55.981 15656 Z= 0.439 Chirality : 0.043 0.302 1707 Planarity : 0.003 0.045 2028 Dihedral : 5.090 31.188 1677 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.33 % Allowed : 22.17 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.30 (0.22), residues: 1413 helix: -1.21 (0.25), residues: 381 sheet: -1.20 (0.31), residues: 279 loop : -1.81 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.016 0.001 TYR A 417 PHE 0.012 0.001 PHE E 27 TRP 0.008 0.002 TRP A 233 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00340 (11532) covalent geometry : angle 0.69355 (15594) SS BOND : bond 0.01058 ( 22) SS BOND : angle 10.81814 ( 44) hydrogen bonds : bond 0.03108 ( 273) hydrogen bonds : angle 4.74732 ( 729) link_NAG-ASN : bond 0.00421 ( 6) link_NAG-ASN : angle 1.46679 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 0.434 Fit side-chains REVERT: A 313 ASP cc_start: 0.8698 (t70) cc_final: 0.8333 (t0) REVERT: A 341 GLN cc_start: 0.8553 (pt0) cc_final: 0.8111 (pt0) REVERT: B 98 PHE cc_start: 0.8932 (m-80) cc_final: 0.8634 (m-10) REVERT: B 134 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6890 (tm-30) REVERT: B 224 ILE cc_start: 0.9111 (pt) cc_final: 0.8888 (mm) REVERT: B 321 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 344 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: C 98 PHE cc_start: 0.8838 (m-80) cc_final: 0.8208 (m-10) REVERT: C 208 LYS cc_start: 0.8930 (mttt) cc_final: 0.8704 (mtpp) REVERT: C 313 ASP cc_start: 0.8580 (t70) cc_final: 0.8136 (t0) REVERT: D 31 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7195 (mmmt) REVERT: D 55 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7262 (p) REVERT: E 20 TYR cc_start: 0.9124 (p90) cc_final: 0.8799 (p90) REVERT: E 35 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7911 (pp30) outliers start: 52 outliers final: 36 residues processed: 229 average time/residue: 0.1024 time to fit residues: 33.3529 Evaluate side-chains 224 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 20 optimal weight: 0.2980 chunk 126 optimal weight: 9.9990 chunk 88 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN E 35 GLN F 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116360 restraints weight = 15390.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115001 restraints weight = 11534.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114474 restraints weight = 11032.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114533 restraints weight = 11139.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114593 restraints weight = 10751.667| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11560 Z= 0.116 Angle : 0.886 55.986 15656 Z= 0.430 Chirality : 0.042 0.299 1707 Planarity : 0.003 0.050 2028 Dihedral : 4.802 27.265 1677 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.75 % Allowed : 23.42 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.17 (0.22), residues: 1413 helix: -1.07 (0.25), residues: 399 sheet: -0.90 (0.33), residues: 255 loop : -1.85 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 54 TYR 0.017 0.001 TYR B 417 PHE 0.014 0.001 PHE E 27 TRP 0.008 0.001 TRP A 233 HIS 0.004 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00265 (11532) covalent geometry : angle 0.67596 (15594) SS BOND : bond 0.01045 ( 22) SS BOND : angle 10.78164 ( 44) hydrogen bonds : bond 0.02860 ( 273) hydrogen bonds : angle 4.63992 ( 729) link_NAG-ASN : bond 0.00426 ( 6) link_NAG-ASN : angle 1.41531 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8664 (t70) cc_final: 0.8285 (t0) REVERT: A 341 GLN cc_start: 0.8526 (pt0) cc_final: 0.8067 (pt0) REVERT: B 98 PHE cc_start: 0.8863 (m-80) cc_final: 0.8521 (m-10) REVERT: B 134 GLN cc_start: 0.7170 (tm-30) cc_final: 0.6890 (tm-30) REVERT: B 344 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: C 98 PHE cc_start: 0.8798 (m-80) cc_final: 0.8157 (m-10) REVERT: C 141 LYS cc_start: 0.7541 (mtmt) cc_final: 0.7290 (mtmt) REVERT: C 208 LYS cc_start: 0.8943 (mttt) cc_final: 0.8674 (mtpp) REVERT: C 313 ASP cc_start: 0.8610 (t70) cc_final: 0.8125 (t0) REVERT: D 22 ASN cc_start: 0.8748 (t0) cc_final: 0.8360 (t0) REVERT: D 31 LYS cc_start: 0.7494 (mmtt) cc_final: 0.7202 (mmmt) REVERT: D 35 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7616 (pp30) REVERT: D 55 CYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7243 (p) REVERT: E 31 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7276 (mmmt) REVERT: E 35 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7945 (pp30) REVERT: F 35 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7792 (pp30) outliers start: 45 outliers final: 34 residues processed: 237 average time/residue: 0.1054 time to fit residues: 35.6467 Evaluate side-chains 229 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN E 35 GLN F 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121260 restraints weight = 15236.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120689 restraints weight = 19952.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121627 restraints weight = 17900.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120935 restraints weight = 14039.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121144 restraints weight = 14545.896| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11560 Z= 0.116 Angle : 0.887 55.986 15656 Z= 0.433 Chirality : 0.042 0.295 1707 Planarity : 0.003 0.055 2028 Dihedral : 4.689 26.806 1677 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.42 % Allowed : 24.00 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.23), residues: 1413 helix: -0.87 (0.26), residues: 399 sheet: -0.64 (0.33), residues: 255 loop : -1.79 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 54 TYR 0.024 0.001 TYR C 67 PHE 0.020 0.001 PHE C 411 TRP 0.007 0.001 TRP A 233 HIS 0.004 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00267 (11532) covalent geometry : angle 0.67844 (15594) SS BOND : bond 0.01042 ( 22) SS BOND : angle 10.77770 ( 44) hydrogen bonds : bond 0.02794 ( 273) hydrogen bonds : angle 4.59812 ( 729) link_NAG-ASN : bond 0.00421 ( 6) link_NAG-ASN : angle 1.38000 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7350 (tm-30) cc_final: 0.7112 (tm-30) REVERT: A 313 ASP cc_start: 0.8580 (t70) cc_final: 0.8207 (t0) REVERT: A 341 GLN cc_start: 0.8254 (pt0) cc_final: 0.7812 (pt0) REVERT: B 98 PHE cc_start: 0.8702 (m-80) cc_final: 0.8430 (m-10) REVERT: B 134 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6803 (tm-30) REVERT: B 344 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: C 98 PHE cc_start: 0.8726 (m-80) cc_final: 0.8109 (m-10) REVERT: C 208 LYS cc_start: 0.8911 (mttt) cc_final: 0.8691 (mtpp) REVERT: C 313 ASP cc_start: 0.8523 (t70) cc_final: 0.8081 (t0) REVERT: D 22 ASN cc_start: 0.8791 (t0) cc_final: 0.8385 (t0) REVERT: D 31 LYS cc_start: 0.7217 (mmtt) cc_final: 0.6888 (mmmt) REVERT: D 35 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8133 (pp30) REVERT: D 55 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.6884 (p) REVERT: E 31 LYS cc_start: 0.7559 (mmtm) cc_final: 0.7242 (mmmt) outliers start: 41 outliers final: 34 residues processed: 224 average time/residue: 0.0979 time to fit residues: 31.4581 Evaluate side-chains 223 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 55 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 134 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 59 optimal weight: 0.0030 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 56 ASN E 35 GLN F 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113735 restraints weight = 15461.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114174 restraints weight = 13690.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114376 restraints weight = 11588.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114487 restraints weight = 10988.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114576 restraints weight = 10728.059| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11560 Z= 0.123 Angle : 0.894 55.986 15656 Z= 0.437 Chirality : 0.042 0.298 1707 Planarity : 0.003 0.056 2028 Dihedral : 4.618 26.777 1677 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.50 % Allowed : 24.17 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.23), residues: 1413 helix: -0.71 (0.26), residues: 399 sheet: -0.99 (0.31), residues: 297 loop : -1.63 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 54 TYR 0.024 0.001 TYR C 67 PHE 0.020 0.001 PHE C 411 TRP 0.008 0.001 TRP A 233 HIS 0.004 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00285 (11532) covalent geometry : angle 0.68757 (15594) SS BOND : bond 0.01045 ( 22) SS BOND : angle 10.78207 ( 44) hydrogen bonds : bond 0.02724 ( 273) hydrogen bonds : angle 4.52366 ( 729) link_NAG-ASN : bond 0.00385 ( 6) link_NAG-ASN : angle 1.39762 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8678 (t70) cc_final: 0.8297 (t0) REVERT: A 341 GLN cc_start: 0.8453 (pt0) cc_final: 0.8004 (pt0) REVERT: B 98 PHE cc_start: 0.8764 (m-80) cc_final: 0.8411 (m-10) REVERT: B 134 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 344 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: B 382 PRO cc_start: 0.8262 (Cg_exo) cc_final: 0.8037 (Cg_endo) REVERT: C 98 PHE cc_start: 0.8779 (m-80) cc_final: 0.8101 (m-10) REVERT: C 313 ASP cc_start: 0.8590 (t70) cc_final: 0.8115 (t0) REVERT: D 22 ASN cc_start: 0.8763 (t0) cc_final: 0.8392 (t0) REVERT: D 31 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7148 (mmmt) REVERT: D 35 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7934 (pp30) REVERT: D 55 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7151 (p) REVERT: E 22 ASN cc_start: 0.8861 (t0) cc_final: 0.8535 (t0) REVERT: E 31 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7429 (mmmt) REVERT: F 35 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7825 (pp30) outliers start: 42 outliers final: 35 residues processed: 220 average time/residue: 0.1036 time to fit residues: 32.5801 Evaluate side-chains 229 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 55 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 126 optimal weight: 0.8980 chunk 32 optimal weight: 0.0370 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112701 restraints weight = 15532.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113783 restraints weight = 12585.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114482 restraints weight = 11168.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114783 restraints weight = 10375.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114783 restraints weight = 9957.386| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.384 11560 Z= 0.439 Angle : 1.330 59.199 15656 Z= 0.750 Chirality : 0.050 0.926 1707 Planarity : 0.004 0.152 2028 Dihedral : 4.612 26.773 1677 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.25 % Allowed : 24.50 % Favored : 72.25 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.23), residues: 1413 helix: -0.71 (0.26), residues: 399 sheet: -0.98 (0.31), residues: 297 loop : -1.63 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 54 TYR 0.023 0.001 TYR C 67 PHE 0.019 0.001 PHE C 411 TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00888 (11532) covalent geometry : angle 1.20214 (15594) SS BOND : bond 0.01043 ( 22) SS BOND : angle 10.77929 ( 44) hydrogen bonds : bond 0.02714 ( 273) hydrogen bonds : angle 4.52259 ( 729) link_NAG-ASN : bond 0.00383 ( 6) link_NAG-ASN : angle 1.39771 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1758.98 seconds wall clock time: 31 minutes 7.64 seconds (1867.64 seconds total)