Starting phenix.real_space_refine on Fri Oct 23 20:35:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cft_30347/10_2026/7cft_30347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cft_30347/10_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7cft_30347/10_2026/7cft_30347.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cft_30347/10_2026/7cft_30347.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cft_30347/10_2026/7cft_30347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cft_30347/10_2026/7cft_30347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cft_30347/10_2026/7cft_30347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cft_30347/10_2026/7cft_30347.map" } 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-2.3rc1-6221/lib/python3.11/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 chiralities: 2 Restraints were copied for chains: B, C, E, F Time building chain proxies: 2.84, per 1000 atoms: 0.25 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=33, 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=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.04 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 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 93 " - pdb=" SG CYS C 194 " distance=2.02 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.04 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 19 " distance=2.03 Simple disulfide: pdb=" SG CYS D 12 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 50 " - pdb=" SG CYS D 55 " distance=2.02 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 19 " distance=2.03 Simple disulfide: pdb=" SG CYS E 12 " - pdb=" SG CYS E 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 49 " distance=2.03 Simple disulfide: pdb=" SG CYS E 50 " - pdb=" SG CYS E 55 " distance=2.02 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 19 " distance=2.03 Simple disulfide: pdb=" SG CYS F 12 " - pdb=" SG CYS F 37 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 49 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 55 " distance=2.02 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: 0.89 Conformation dependent library (CDL) restraints added in 541.0 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: 0.24 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: 1.60 Time building geometry restraints manager: 1.20 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: 6083 17.97 - 35.93: 703 35.93 - 53.89: 165 53.89 - 71.86: 12 71.86 - 89.82: 9 Dihedral angle restraints: 6972 sinusoidal: 2805 harmonic: 4167 Sorted by residual: dihedral pdb=" CB CYS F 3 " pdb=" SG CYS F 3 " pdb=" SG CYS F 19 " pdb=" CB CYS F 19 " ideal model delta sinusoidal sigma weight residual 93.00 147.05 -54.05 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS D 3 " pdb=" SG CYS D 3 " pdb=" SG CYS D 19 " pdb=" CB CYS D 19 " ideal model delta sinusoidal sigma weight residual 93.00 147.05 -54.05 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS E 3 " pdb=" SG CYS E 3 " pdb=" SG CYS E 19 " pdb=" CB CYS E 19 " ideal model delta sinusoidal sigma weight residual 93.00 147.04 -54.04 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 6969 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: 2.28 - 2.80: 3285 2.80 - 3.33: 9695 3.33 - 3.85: 17433 3.85 - 4.38: 19720 4.38 - 4.90: 33228 Nonbonded interactions: 83361 Sorted by model distance: nonbonded pdb=" O LEU A 441 " pdb=" OG SER C 446 " model vdw 2.276 3.040 nonbonded pdb=" OG SER B 383 " pdb=" O PHE C 241 " model vdw 2.278 3.040 nonbonded pdb=" OG SER A 383 " pdb=" O PHE B 241 " model vdw 2.282 3.040 nonbonded pdb=" OG SER B 446 " pdb=" O LEU C 441 " model vdw 2.293 3.040 nonbonded pdb=" O HIS C 163 " pdb=" OH TYR C 195 " model vdw 2.309 3.040 ... (remaining 83356 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.070 Set scattering table: 0.020 Process input model: 10.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.009 0.096 11571 Z= 0.387 Angle : 1.001 9.596 15678 Z= 0.560 Chirality : 0.059 0.302 1707 Planarity : 0.006 0.061 2028 Dihedral : 15.222 89.823 4197 Min Nonbonded Distance : 2.276 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/Z covalent geometry : bond 0.00862 / 0.39 (11532) covalent geometry : angle 0.98797 / 0.56 (15594) SS BOND : bond 0.00686 / 0.42 ( 33) SS BOND : angle 2.44513 / 1.51 ( 66) hydrogen bonds : bond 0.30887 / 20.48 ( 273) hydrogen bonds : angle 8.97094 / 6.04 ( 729) link_NAG-ASN : bond 0.00589 / 0.30 ( 6) link_NAG-ASN : angle 2.26263 / 1.65 ( 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 : 0.523 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: 0.1288 time to fit residues: 46.4455 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 : 0.379 ------------------------------------------------------------------------------- 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: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] 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: 8.9990 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... ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN A 463 HIS B 358 GLN B 463 HIS C 463 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.160414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121503 restraints weight = 15105.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120789 restraints weight = 19488.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121512 restraints weight = 18505.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121247 restraints weight = 15335.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121483 restraints weight = 13758.043| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11571 Z= 0.160 Angle : 0.638 6.708 15678 Z= 0.340 Chirality : 0.043 0.153 1707 Planarity : 0.004 0.047 2028 Dihedral : 5.776 26.479 1557 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.83 % Allowed : 16.42 % Favored : 80.75 % 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: -4.08 (0.19), residues: 1413 helix: -2.94 (0.20), residues: 351 sheet: -2.02 (0.30), residues: 279 loop : -2.93 (0.19), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 279 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/Z covalent geometry : bond 0.00362 / 0.16 (11532) covalent geometry : angle 0.63260 / 0.34 (15594) SS BOND : bond 0.00483 / 0.32 ( 33) SS BOND : angle 1.35202 / 0.85 ( 66) hydrogen bonds : bond 0.04571 / 2.90 ( 273) hydrogen bonds : angle 5.61271 / 3.89 ( 729) link_NAG-ASN : bond 0.00267 / 0.15 ( 6) link_NAG-ASN : angle 0.89762 / 0.61 ( 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 250 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.433 Fit side-chains REVERT: A 92 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8911 (pp) REVERT: A 208 LYS cc_start: 0.8949 (mttt) cc_final: 0.8629 (mtpp) REVERT: A 313 ASP cc_start: 0.8323 (t70) cc_final: 0.8111 (t0) REVERT: A 399 GLN cc_start: 0.7704 (tp40) cc_final: 0.7483 (tp40) REVERT: B 98 PHE cc_start: 0.8894 (m-80) cc_final: 0.8620 (m-10) REVERT: C 98 PHE cc_start: 0.8870 (m-80) cc_final: 0.8453 (m-10) REVERT: C 208 LYS cc_start: 0.8861 (mttt) cc_final: 0.8578 (mtpp) REVERT: C 313 ASP cc_start: 0.8290 (t70) cc_final: 0.8033 (t0) outliers start: 34 outliers final: 21 residues processed: 239 average time/residue: 0.1028 time to fit residues: 35.0400 Evaluate side-chains 207 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE 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 11 THR Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 27 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [89, 21, 63, 93, 92, 51, 9, 83, 131, 24, 95] chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 92 optimal weight: 0.0050 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 21 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124071 restraints weight = 15267.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123339 restraints weight = 19027.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124406 restraints weight = 17370.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123796 restraints weight = 14074.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123994 restraints weight = 14232.480| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11571 Z= 0.114 Angle : 0.597 7.948 15678 Z= 0.311 Chirality : 0.042 0.284 1707 Planarity : 0.003 0.041 2028 Dihedral : 5.101 23.480 1554 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.58 % Allowed : 18.17 % Favored : 78.25 % 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: -3.39 (0.20), residues: 1413 helix: -2.28 (0.22), residues: 378 sheet: -1.71 (0.33), residues: 261 loop : -2.46 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 54 TYR 0.024 0.001 TYR C 67 PHE 0.023 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/Z covalent geometry : bond 0.00255 / 0.11 (11532) covalent geometry : angle 0.58839 / 0.31 (15594) SS BOND : bond 0.00443 / 0.28 ( 33) SS BOND : angle 1.60152 / 0.99 ( 66) hydrogen bonds : bond 0.03479 / 2.24 ( 273) hydrogen bonds : angle 4.94299 / 3.45 ( 729) link_NAG-ASN : bond 0.00354 / 0.20 ( 6) link_NAG-ASN : angle 0.87142 / 0.58 ( 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 251 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.8985 (mttt) cc_final: 0.8583 (mtpp) REVERT: A 313 ASP cc_start: 0.8463 (t70) cc_final: 0.8155 (t0) REVERT: A 321 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7683 (tm-30) REVERT: B 98 PHE cc_start: 0.8870 (m-80) cc_final: 0.8580 (m-10) REVERT: B 350 LEU cc_start: 0.9265 (mt) cc_final: 0.9063 (mt) REVERT: C 98 PHE cc_start: 0.8803 (m-80) cc_final: 0.8254 (m-10) REVERT: C 208 LYS cc_start: 0.8885 (mttt) cc_final: 0.8620 (mtpp) REVERT: C 216 ASN cc_start: 0.8149 (m-40) cc_final: 0.7640 (m-40) REVERT: C 313 ASP cc_start: 0.8416 (t70) cc_final: 0.8065 (t0) REVERT: C 421 GLU cc_start: 0.7556 (pm20) cc_final: 0.7304 (pm20) REVERT: D 28 ARG cc_start: 0.8081 (tpp80) cc_final: 0.7870 (tpp80) REVERT: E 20 TYR cc_start: 0.8736 (p90) cc_final: 0.8408 (p90) outliers start: 43 outliers final: 30 residues processed: 237 average time/residue: 0.0996 time to fit residues: 34.0048 Evaluate side-chains 216 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 210 MET 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 C residue 441 LEU 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 37 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 37 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 20 TYR Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 37 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [71, 130, 21, 22, 41, 30, 27, 11, 103, 26, 31] chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS ** E 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 = 0.3859 r_free = 0.3859 target = 0.160803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115212 restraints weight = 15410.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115958 restraints weight = 12227.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115898 restraints weight = 10219.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115903 restraints weight = 10354.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115973 restraints weight = 10113.528| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11571 Z= 0.164 Angle : 0.599 7.267 15678 Z= 0.314 Chirality : 0.044 0.321 1707 Planarity : 0.003 0.040 2028 Dihedral : 5.009 21.235 1551 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.08 % Allowed : 19.58 % Favored : 76.33 % 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: -2.94 (0.22), residues: 1413 helix: -1.73 (0.25), residues: 360 sheet: -1.43 (0.32), residues: 282 loop : -2.29 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 B 233 HIS 0.004 0.001 HIS D 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (11532) covalent geometry : angle 0.59345 / 0.31 (15594) SS BOND : bond 0.00470 / 0.29 ( 33) SS BOND : angle 1.31361 / 0.85 ( 66) hydrogen bonds : bond 0.03540 / 2.28 ( 273) hydrogen bonds : angle 4.88521 / 3.43 ( 729) link_NAG-ASN : bond 0.00194 / 0.11 ( 6) link_NAG-ASN : angle 1.08988 / 0.77 ( 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 234 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.9038 (mttt) cc_final: 0.8752 (mtpp) REVERT: A 313 ASP cc_start: 0.8660 (t70) cc_final: 0.8298 (t0) REVERT: A 403 GLU cc_start: 0.7780 (tp30) cc_final: 0.7383 (tp30) REVERT: B 98 PHE cc_start: 0.8982 (m-80) cc_final: 0.8697 (m-10) REVERT: C 98 PHE cc_start: 0.8990 (m-80) cc_final: 0.8291 (m-10) REVERT: C 208 LYS cc_start: 0.8965 (mttt) cc_final: 0.8617 (mtpp) REVERT: C 313 ASP cc_start: 0.8516 (t70) cc_final: 0.8084 (t0) REVERT: E 38 SER cc_start: 0.8810 (t) cc_final: 0.8572 (m) outliers start: 49 outliers final: 36 residues processed: 224 average time/residue: 0.0979 time to fit residues: 31.9221 Evaluate side-chains 208 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 311 ARG 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 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 37 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 37 CYS Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 37 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [66, 114, 60, 43, 110, 12, 21, 53, 50, 31, 132] chunk 66 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 13 HIS ** E 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 = 0.3881 r_free = 0.3881 target = 0.162803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116659 restraints weight = 15087.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118056 restraints weight = 11987.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118125 restraints weight = 9567.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118216 restraints weight = 9561.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118292 restraints weight = 9310.605| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11571 Z= 0.118 Angle : 0.574 8.151 15678 Z= 0.298 Chirality : 0.042 0.280 1707 Planarity : 0.003 0.038 2028 Dihedral : 4.655 19.456 1551 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.75 % Allowed : 20.08 % Favored : 75.17 % 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: -2.75 (0.22), residues: 1413 helix: -1.65 (0.24), residues: 396 sheet: -1.29 (0.33), residues: 258 loop : -2.12 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 28 TYR 0.017 0.001 TYR C 67 PHE 0.013 0.001 PHE C 411 TRP 0.008 0.001 TRP B 233 HIS 0.003 0.001 HIS D 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11532) covalent geometry : angle 0.57050 / 0.30 (15594) SS BOND : bond 0.00381 / 0.24 ( 33) SS BOND : angle 1.08067 / 0.71 ( 66) hydrogen bonds : bond 0.03042 / 1.94 ( 273) hydrogen bonds : angle 4.69786 / 3.31 ( 729) link_NAG-ASN : bond 0.00330 / 0.19 ( 6) link_NAG-ASN : angle 0.99654 / 0.68 ( 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 253 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.8975 (mttt) cc_final: 0.8712 (mtpp) REVERT: A 313 ASP cc_start: 0.8609 (t70) cc_final: 0.8238 (t0) REVERT: A 341 GLN cc_start: 0.8481 (pt0) cc_final: 0.8039 (pt0) REVERT: B 98 PHE cc_start: 0.8884 (m-80) cc_final: 0.8623 (m-10) REVERT: B 321 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7652 (mm-30) REVERT: B 344 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: C 98 PHE cc_start: 0.8816 (m-80) cc_final: 0.8142 (m-10) REVERT: C 208 LYS cc_start: 0.8915 (mttt) cc_final: 0.8679 (mtpp) REVERT: C 313 ASP cc_start: 0.8575 (t70) cc_final: 0.8196 (t0) outliers start: 57 outliers final: 40 residues processed: 236 average time/residue: 0.0935 time to fit residues: 32.1130 Evaluate side-chains 218 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 75 THR Chi-restraints excluded: chain B residue 90 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 344 GLU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 441 LEU 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 290 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 32 LEU Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 37 CYS Chi-restraints excluded: chain E residue 50 CYS 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 37 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [45, 98, 75, 85, 10, 34, 79, 6, 124, 133, 38] chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN D 13 HIS E 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112309 restraints weight = 15591.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113275 restraints weight = 12566.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113276 restraints weight = 10458.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113281 restraints weight = 10435.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113304 restraints weight = 10221.548| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11571 Z= 0.152 Angle : 0.596 8.581 15678 Z= 0.308 Chirality : 0.043 0.290 1707 Planarity : 0.003 0.043 2028 Dihedral : 4.697 17.917 1551 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.25 % Allowed : 21.25 % 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: -2.37 (0.22), residues: 1413 helix: -1.11 (0.26), residues: 360 sheet: -1.17 (0.31), residues: 282 loop : -1.98 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 279 TYR 0.018 0.001 TYR C 417 PHE 0.022 0.001 PHE C 411 TRP 0.008 0.001 TRP A 233 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (11532) covalent geometry : angle 0.59143 / 0.31 (15594) SS BOND : bond 0.00397 / 0.25 ( 33) SS BOND : angle 1.16819 / 0.75 ( 66) hydrogen bonds : bond 0.03205 / 2.06 ( 273) hydrogen bonds : angle 4.73449 / 3.33 ( 729) link_NAG-ASN : bond 0.00418 / 0.26 ( 6) link_NAG-ASN : angle 1.25947 / 0.80 ( 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 232 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.9043 (mttt) cc_final: 0.8739 (mtpp) REVERT: A 313 ASP cc_start: 0.8679 (t70) cc_final: 0.8311 (t0) REVERT: A 341 GLN cc_start: 0.8502 (pt0) cc_final: 0.8092 (pt0) REVERT: A 403 GLU cc_start: 0.7849 (tp30) cc_final: 0.7368 (tp30) REVERT: B 98 PHE cc_start: 0.8924 (m-80) cc_final: 0.8660 (m-10) REVERT: B 134 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6883 (tm-30) REVERT: B 224 ILE cc_start: 0.9094 (pt) cc_final: 0.8873 (mm) REVERT: B 321 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 344 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: C 98 PHE cc_start: 0.8857 (m-80) cc_final: 0.8167 (m-10) REVERT: C 208 LYS cc_start: 0.8962 (mttt) cc_final: 0.8695 (mtpp) REVERT: C 313 ASP cc_start: 0.8675 (t70) cc_final: 0.8255 (t0) outliers start: 51 outliers final: 41 residues processed: 217 average time/residue: 0.0966 time to fit residues: 30.3872 Evaluate side-chains 219 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 290 CYS 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 441 LEU 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 290 CYS Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 9 VAL 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 37 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 37 CYS Chi-restraints excluded: chain E residue 50 CYS 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 37 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [115, 72, 44, 85, 11, 127, 51, 109, 95, 49, 78] chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 127 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125545 restraints weight = 15335.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124170 restraints weight = 19044.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125363 restraints weight = 17296.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125180 restraints weight = 13269.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125210 restraints weight = 13528.642| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11571 Z= 0.106 Angle : 0.581 8.662 15678 Z= 0.296 Chirality : 0.042 0.284 1707 Planarity : 0.002 0.044 2028 Dihedral : 4.416 23.243 1551 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.75 % Allowed : 22.25 % Favored : 74.00 % 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: -2.19 (0.22), residues: 1413 helix: -1.14 (0.25), residues: 396 sheet: -0.85 (0.33), residues: 258 loop : -1.84 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 28 TYR 0.015 0.001 TYR C 67 PHE 0.018 0.001 PHE C 411 TRP 0.007 0.001 TRP A 233 HIS 0.002 0.000 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (11532) covalent geometry : angle 0.57614 / 0.29 (15594) SS BOND : bond 0.00337 / 0.20 ( 33) SS BOND : angle 1.01507 / 0.59 ( 66) hydrogen bonds : bond 0.02758 / 1.76 ( 273) hydrogen bonds : angle 4.55543 / 3.22 ( 729) link_NAG-ASN : bond 0.00428 / 0.26 ( 6) link_NAG-ASN : angle 1.49108 / 1.03 ( 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 246 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8540 (t70) cc_final: 0.8194 (t0) REVERT: B 134 GLN cc_start: 0.6937 (tm-30) cc_final: 0.6714 (tm-30) REVERT: B 344 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 365 MET cc_start: 0.8666 (pmm) cc_final: 0.8429 (pmm) REVERT: C 98 PHE cc_start: 0.8635 (m-80) cc_final: 0.8018 (m-10) REVERT: C 208 LYS cc_start: 0.8880 (mttt) cc_final: 0.8655 (mtpp) REVERT: C 313 ASP cc_start: 0.8537 (t70) cc_final: 0.8136 (t0) outliers start: 45 outliers final: 37 residues processed: 234 average time/residue: 0.0981 time to fit residues: 33.1224 Evaluate side-chains 230 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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 75 THR Chi-restraints excluded: chain B residue 90 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 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 290 CYS Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 37 CYS Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [20, 126, 88, 13, 53, 51, 104, 85, 110, 55, 37] chunk 20 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 0.0470 chunk 110 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117846 restraints weight = 15321.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118248 restraints weight = 13479.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118715 restraints weight = 12458.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118734 restraints weight = 11119.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118775 restraints weight = 11195.254| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11571 Z= 0.103 Angle : 0.581 9.256 15678 Z= 0.297 Chirality : 0.042 0.278 1707 Planarity : 0.003 0.051 2028 Dihedral : 4.189 18.276 1548 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.58 % Allowed : 22.83 % Favored : 73.58 % 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: -1.95 (0.23), residues: 1413 helix: -0.90 (0.25), residues: 396 sheet: -1.06 (0.31), residues: 300 loop : -1.58 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 54 TYR 0.024 0.001 TYR C 67 PHE 0.019 0.001 PHE A 98 TRP 0.007 0.001 TRP A 233 HIS 0.003 0.000 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (11532) covalent geometry : angle 0.57720 / 0.30 (15594) SS BOND : bond 0.00311 / 0.19 ( 33) SS BOND : angle 0.85637 / 0.52 ( 66) hydrogen bonds : bond 0.02703 / 1.75 ( 273) hydrogen bonds : angle 4.42755 / 3.14 ( 729) link_NAG-ASN : bond 0.00488 / 0.29 ( 6) link_NAG-ASN : angle 1.55617 / 1.07 ( 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 245 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8601 (t70) cc_final: 0.8229 (t0) REVERT: B 75 THR cc_start: 0.7275 (OUTLIER) cc_final: 0.6980 (p) REVERT: B 134 GLN cc_start: 0.7125 (tm-30) cc_final: 0.6872 (tm-30) REVERT: B 344 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: B 365 MET cc_start: 0.8677 (pmm) cc_final: 0.8388 (pmm) REVERT: C 98 PHE cc_start: 0.8613 (m-80) cc_final: 0.7963 (m-10) REVERT: C 141 LYS cc_start: 0.7482 (mtmt) cc_final: 0.7235 (mtmt) REVERT: C 208 LYS cc_start: 0.8854 (mttt) cc_final: 0.8653 (mtpp) REVERT: C 313 ASP cc_start: 0.8559 (t70) cc_final: 0.8136 (t0) REVERT: C 330 MET cc_start: 0.8339 (ptm) cc_final: 0.8070 (ptm) REVERT: C 350 LEU cc_start: 0.9183 (mt) cc_final: 0.8916 (mt) REVERT: E 20 TYR cc_start: 0.8490 (p90) cc_final: 0.8157 (p90) REVERT: E 35 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7738 (pp30) outliers start: 43 outliers final: 33 residues processed: 230 average time/residue: 0.0988 time to fit residues: 32.8080 Evaluate side-chains 220 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 75 THR Chi-restraints excluded: chain B residue 90 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 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 290 CYS Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 11 THR 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 E residue 37 CYS Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 37 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [71, 80, 13, 120, 43, 20, 62, 91, 103, 15, 116] chunk 71 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN A 341 GLN B 270 GLN E 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112490 restraints weight = 15472.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113029 restraints weight = 12615.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112911 restraints weight = 10780.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112954 restraints weight = 10839.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112987 restraints weight = 10555.152| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11571 Z= 0.164 Angle : 0.628 8.948 15678 Z= 0.323 Chirality : 0.044 0.288 1707 Planarity : 0.003 0.048 2028 Dihedral : 4.460 18.815 1548 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.83 % Allowed : 22.83 % Favored : 73.33 % 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: -1.68 (0.23), residues: 1413 helix: -0.40 (0.27), residues: 363 sheet: -1.03 (0.30), residues: 321 loop : -1.49 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 279 TYR 0.024 0.001 TYR C 67 PHE 0.023 0.001 PHE C 411 TRP 0.008 0.001 TRP C 233 HIS 0.005 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (11532) covalent geometry : angle 0.62123 / 0.32 (15594) SS BOND : bond 0.00440 / 0.28 ( 33) SS BOND : angle 1.31929 / 0.80 ( 66) hydrogen bonds : bond 0.03100 / 2.02 ( 273) hydrogen bonds : angle 4.58994 / 3.25 ( 729) link_NAG-ASN : bond 0.00379 / 0.22 ( 6) link_NAG-ASN : angle 1.65016 / 1.15 ( 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 235 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8656 (t70) cc_final: 0.8258 (t0) REVERT: A 403 GLU cc_start: 0.7780 (tp30) cc_final: 0.7343 (tp30) REVERT: B 134 GLN cc_start: 0.7159 (tm-30) cc_final: 0.6828 (tm-30) REVERT: B 254 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7588 (tt0) REVERT: B 344 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: B 421 GLU cc_start: 0.7583 (pm20) cc_final: 0.7377 (pm20) REVERT: C 98 PHE cc_start: 0.8807 (m-80) cc_final: 0.8120 (m-10) REVERT: C 208 LYS cc_start: 0.8921 (mttt) cc_final: 0.8679 (mtpp) REVERT: C 313 ASP cc_start: 0.8591 (t70) cc_final: 0.8157 (t0) REVERT: C 350 LEU cc_start: 0.9160 (mt) cc_final: 0.8950 (mt) REVERT: D 31 LYS cc_start: 0.7351 (mmtt) cc_final: 0.7116 (mmmt) REVERT: E 35 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7519 (pp30) outliers start: 46 outliers final: 34 residues processed: 222 average time/residue: 0.0977 time to fit residues: 31.3481 Evaluate side-chains 218 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 279 ARG Chi-restraints excluded: chain B residue 290 CYS 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 441 LEU 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 290 CYS Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 CYS Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [134, 6, 21, 75, 118, 23, 112, 59, 7, 18, 77] chunk 134 optimal weight: 9.9990 chunk 6 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 7 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111934 restraints weight = 15496.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113177 restraints weight = 12973.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113782 restraints weight = 11498.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114099 restraints weight = 10676.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114099 restraints weight = 10248.998| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11571 Z= 0.134 Angle : 0.623 9.536 15678 Z= 0.320 Chirality : 0.043 0.303 1707 Planarity : 0.003 0.056 2028 Dihedral : 4.349 15.010 1548 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.67 % Allowed : 24.67 % Favored : 72.67 % 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: -1.62 (0.23), residues: 1413 helix: -0.45 (0.27), residues: 381 sheet: -1.01 (0.31), residues: 303 loop : -1.41 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 28 TYR 0.023 0.001 TYR C 67 PHE 0.022 0.001 PHE C 411 TRP 0.008 0.001 TRP B 233 HIS 0.005 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (11532) covalent geometry : angle 0.61688 / 0.32 (15594) SS BOND : bond 0.00404 / 0.25 ( 33) SS BOND : angle 1.14376 / 0.73 ( 66) hydrogen bonds : bond 0.02890 / 1.86 ( 273) hydrogen bonds : angle 4.53055 / 3.21 ( 729) link_NAG-ASN : bond 0.00471 / 0.27 ( 6) link_NAG-ASN : angle 1.83319 / 1.26 ( 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 219 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8692 (t70) cc_final: 0.8310 (t0) REVERT: B 134 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6854 (tm-30) REVERT: B 254 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7491 (tt0) REVERT: B 344 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: C 98 PHE cc_start: 0.8728 (m-80) cc_final: 0.8057 (m-10) REVERT: C 208 LYS cc_start: 0.8927 (mttt) cc_final: 0.8720 (mtpp) REVERT: C 313 ASP cc_start: 0.8637 (t70) cc_final: 0.8183 (t0) REVERT: C 330 MET cc_start: 0.8661 (ptm) cc_final: 0.8455 (ptm) REVERT: C 350 LEU cc_start: 0.9176 (mt) cc_final: 0.8971 (mt) REVERT: E 35 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7838 (pp30) outliers start: 32 outliers final: 27 residues processed: 211 average time/residue: 0.0995 time to fit residues: 30.1270 Evaluate side-chains 214 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 441 LEU 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 D residue 27 PHE Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 CYS Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [126, 32, 6, 27, 114, 95, 8, 60, 31, 78, 39] chunk 126 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 341 GLN ** E 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 = 0.3812 r_free = 0.3812 target = 0.156342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110881 restraints weight = 15570.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112092 restraints weight = 13223.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112057 restraints weight = 11346.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112230 restraints weight = 11084.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112288 restraints weight = 11026.448| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11571 Z= 0.171 Angle : 0.651 9.446 15678 Z= 0.336 Chirality : 0.044 0.309 1707 Planarity : 0.003 0.057 2028 Dihedral : 4.558 17.850 1548 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.00 % Allowed : 23.92 % Favored : 73.08 % 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: -1.60 (0.23), residues: 1413 helix: -0.50 (0.27), residues: 381 sheet: -1.04 (0.30), residues: 321 loop : -1.31 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 166 TYR 0.023 0.001 TYR C 67 PHE 0.023 0.001 PHE C 411 TRP 0.008 0.001 TRP B 233 HIS 0.004 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (11532) covalent geometry : angle 0.64278 / 0.33 (15594) SS BOND : bond 0.00431 / 0.27 ( 33) SS BOND : angle 1.41439 / 0.88 ( 66) hydrogen bonds : bond 0.03121 / 2.02 ( 273) hydrogen bonds : angle 4.59871 / 3.24 ( 729) link_NAG-ASN : bond 0.00474 / 0.27 ( 6) link_NAG-ASN : angle 1.85664 / 1.26 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1837.69 seconds wall clock time: 32 minutes 41.56 seconds (1961.56 seconds total)