Starting phenix.real_space_refine on Wed Mar 4 03:15:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vtl_21381/03_2026/6vtl_21381.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vtl_21381/03_2026/6vtl_21381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vtl_21381/03_2026/6vtl_21381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vtl_21381/03_2026/6vtl_21381.map" model { file = "/net/cci-nas-00/data/ceres_data/6vtl_21381/03_2026/6vtl_21381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vtl_21381/03_2026/6vtl_21381.cif" } resolution = 3.65 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= 0.001 sd= 0.024 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 81 5.16 5 C 6591 2.51 5 N 1674 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10242 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3386 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 12, 'ASP:plan': 6, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 134 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, B Time building chain proxies: 2.18, per 1000 atoms: 0.21 Number of scatterers: 10242 At special positions: 0 Unit cell: (94.608, 97.2, 129.6, 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 81 16.00 O 1896 8.00 N 1674 7.00 C 6591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 195 " distance=2.04 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 366 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 366 " distance=2.04 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.04 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 336 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 394 " " NAG A 602 " - " ASN A 367 " " NAG B 601 " - " ASN B 394 " " NAG B 602 " - " ASN B 367 " " NAG C 601 " - " ASN C 394 " " NAG C 602 " - " ASN C 367 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 354.2 milliseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 41.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.653A pdb=" N SER A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 41 through 53 removed outlier: 4.149A pdb=" N VAL A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.671A pdb=" N VAL A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.628A pdb=" N ALA A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 removed outlier: 3.731A pdb=" N ILE A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.778A pdb=" N TYR A 230 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.622A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.698A pdb=" N ARG A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.716A pdb=" N GLU A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 removed outlier: 3.933A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.718A pdb=" N CYS A 360 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 392 removed outlier: 3.744A pdb=" N LYS A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.866A pdb=" N GLY A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 434 through 442 removed outlier: 3.962A pdb=" N LEU A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 removed outlier: 3.548A pdb=" N VAL A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.653A pdb=" N SER C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 41 through 53 removed outlier: 4.149A pdb=" N VAL C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 removed outlier: 3.671A pdb=" N VAL C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.627A pdb=" N ALA C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.731A pdb=" N ILE C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 181 through 185 Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.776A pdb=" N TYR C 230 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.622A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.697A pdb=" N ARG C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR C 317 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.717A pdb=" N GLU C 343 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.933A pdb=" N ASP C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.720A pdb=" N CYS C 360 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 392 removed outlier: 3.745A pdb=" N LYS C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.866A pdb=" N GLY C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 434 through 442 removed outlier: 3.962A pdb=" N LEU C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 460 removed outlier: 3.549A pdb=" N VAL C 449 " --> pdb=" O SER C 445 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.652A pdb=" N SER B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 41 through 53 removed outlier: 4.149A pdb=" N VAL B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 removed outlier: 3.671A pdb=" N VAL B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.627A pdb=" N ALA B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 removed outlier: 3.732A pdb=" N ILE B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.777A pdb=" N TYR B 230 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.622A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.698A pdb=" N ARG B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.716A pdb=" N GLU B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 3.933A pdb=" N ASP B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 351 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.719A pdb=" N CYS B 360 " --> pdb=" O ASN B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 392 removed outlier: 3.745A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.867A pdb=" N GLY B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.961A pdb=" N LEU B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 460 removed outlier: 3.548A pdb=" N VAL B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 82 removed outlier: 8.526A pdb=" N ASN A 415 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 278 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A 270 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A 406 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 410 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 405 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82 removed outlier: 8.526A pdb=" N ASN A 415 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 278 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 277 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.842A pdb=" N LYS A 194 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN A 95 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A 251 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 246 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA6, first strand: chain 'C' and resid 74 through 82 removed outlier: 8.527A pdb=" N ASN C 415 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU C 278 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE C 270 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 406 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 410 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 405 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 82 removed outlier: 8.527A pdb=" N ASN C 415 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU C 278 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 277 " --> pdb=" O GLY C 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.843A pdb=" N LYS C 194 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN C 95 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS C 251 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 246 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 74 through 82 removed outlier: 8.526A pdb=" N ASN B 415 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 278 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE B 270 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 406 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 410 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 405 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 74 through 82 removed outlier: 8.526A pdb=" N ASN B 415 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 278 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 277 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB5, first strand: chain 'B' and resid 186 through 190 removed outlier: 6.843A pdb=" N LYS B 194 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN B 95 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS B 251 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 246 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 175 426 hydrogen bonds defined for protein. 1179 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: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3300 1.35 - 1.47: 2614 1.47 - 1.59: 4457 1.59 - 1.72: 0 1.72 - 1.84: 111 Bond restraints: 10482 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" CB GLU A 137 " pdb=" CG GLU A 137 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CB GLU C 137 " pdb=" CG GLU C 137 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.22e+00 ... (remaining 10477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 13845 2.07 - 4.14: 348 4.14 - 6.21: 47 6.21 - 8.28: 13 8.28 - 10.35: 3 Bond angle restraints: 14256 Sorted by residual: angle pdb=" CA GLY C 245 " pdb=" C GLY C 245 " pdb=" N ILE C 246 " ideal model delta sigma weight residual 114.23 117.83 -3.60 8.80e-01 1.29e+00 1.67e+01 angle pdb=" CA GLY A 245 " pdb=" C GLY A 245 " pdb=" N ILE A 246 " ideal model delta sigma weight residual 114.23 117.80 -3.57 8.80e-01 1.29e+00 1.65e+01 angle pdb=" CA GLY B 245 " pdb=" C GLY B 245 " pdb=" N ILE B 246 " ideal model delta sigma weight residual 114.23 117.75 -3.52 8.80e-01 1.29e+00 1.60e+01 angle pdb=" CA CYS B 180 " pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " ideal model delta sigma weight residual 114.40 122.23 -7.83 2.30e+00 1.89e-01 1.16e+01 angle pdb=" CA CYS C 180 " pdb=" CB CYS C 180 " pdb=" SG CYS C 180 " ideal model delta sigma weight residual 114.40 122.17 -7.77 2.30e+00 1.89e-01 1.14e+01 ... (remaining 14251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5735 17.86 - 35.71: 517 35.71 - 53.57: 72 53.57 - 71.43: 3 71.43 - 89.28: 18 Dihedral angle restraints: 6345 sinusoidal: 2436 harmonic: 3909 Sorted by residual: dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 360 " pdb=" CB CYS B 360 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " pdb=" SG CYS C 360 " pdb=" CB CYS C 360 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual 93.00 178.28 -85.28 1 1.00e+01 1.00e-02 8.81e+01 ... (remaining 6342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 870 0.030 - 0.061: 431 0.061 - 0.091: 185 0.091 - 0.121: 92 0.121 - 0.152: 39 Chirality restraints: 1617 Sorted by residual: chirality pdb=" CA CYS B 366 " pdb=" N CYS B 366 " pdb=" C CYS B 366 " pdb=" CB CYS B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA CYS A 366 " pdb=" N CYS A 366 " pdb=" C CYS A 366 " pdb=" CB CYS A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CB ILE B 125 " pdb=" CA ILE B 125 " pdb=" CG1 ILE B 125 " pdb=" CG2 ILE B 125 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1614 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 125 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO B 126 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 125 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO C 126 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 125 " 0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 126 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " 0.037 5.00e-02 4.00e+02 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3312 2.82 - 3.34: 8710 3.34 - 3.86: 16794 3.86 - 4.38: 19292 4.38 - 4.90: 32481 Nonbonded interactions: 80589 Sorted by model distance: nonbonded pdb=" OD1 ASN B 95 " pdb=" OH TYR B 230 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASN C 95 " pdb=" OH TYR C 230 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASN A 95 " pdb=" OH TYR A 230 " model vdw 2.307 3.040 nonbonded pdb=" NE1 TRP A 47 " pdb=" OD2 ASP C 454 " model vdw 2.332 3.120 nonbonded pdb=" O SER A 36 " pdb=" NH2 ARG A 44 " model vdw 2.349 3.120 ... (remaining 80584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.470 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10509 Z= 0.193 Angle : 0.803 10.354 14316 Z= 0.426 Chirality : 0.048 0.152 1617 Planarity : 0.006 0.068 1839 Dihedral : 13.731 89.283 3774 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.96 (0.18), residues: 1332 helix: -4.73 (0.10), residues: 447 sheet: -3.46 (0.29), residues: 237 loop : -1.95 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.011 0.001 TYR B 416 PHE 0.013 0.001 PHE A 264 TRP 0.005 0.001 TRP B 47 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00412 (10482) covalent geometry : angle 0.79560 (14256) SS BOND : bond 0.00682 ( 21) SS BOND : angle 2.08597 ( 42) hydrogen bonds : bond 0.29192 ( 387) hydrogen bonds : angle 10.83466 ( 1179) link_NAG-ASN : bond 0.00079 ( 6) link_NAG-ASN : angle 1.29645 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.398 Fit side-chains REVERT: A 57 LEU cc_start: 0.8200 (tp) cc_final: 0.7795 (tp) REVERT: A 139 LEU cc_start: 0.6892 (tt) cc_final: 0.6520 (mp) REVERT: A 277 GLN cc_start: 0.8650 (tp40) cc_final: 0.8074 (tp40) REVERT: A 329 MET cc_start: 0.8639 (mtt) cc_final: 0.8309 (mtp) REVERT: C 57 LEU cc_start: 0.8258 (tp) cc_final: 0.7811 (tp) REVERT: C 277 GLN cc_start: 0.8609 (tp40) cc_final: 0.8074 (tp40) REVERT: C 329 MET cc_start: 0.8584 (mtt) cc_final: 0.8110 (mtp) REVERT: B 57 LEU cc_start: 0.8149 (tp) cc_final: 0.7818 (tp) REVERT: B 101 PHE cc_start: 0.7788 (t80) cc_final: 0.7349 (t80) REVERT: B 139 LEU cc_start: 0.6814 (tt) cc_final: 0.6426 (mp) REVERT: B 277 GLN cc_start: 0.8632 (tp40) cc_final: 0.8070 (tp40) REVERT: B 329 MET cc_start: 0.8598 (mtt) cc_final: 0.8180 (mtp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0834 time to fit residues: 19.5867 Evaluate side-chains 103 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN C 217 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.162111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.125928 restraints weight = 19624.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.128125 restraints weight = 11712.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.129712 restraints weight = 8895.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.129934 restraints weight = 6745.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.130578 restraints weight = 6635.617| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10509 Z= 0.199 Angle : 0.640 7.322 14316 Z= 0.333 Chirality : 0.043 0.156 1617 Planarity : 0.005 0.053 1839 Dihedral : 5.148 17.544 1572 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.97 % Allowed : 11.31 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.21), residues: 1332 helix: -3.47 (0.16), residues: 432 sheet: -2.66 (0.29), residues: 285 loop : -1.28 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.017 0.002 TYR C 416 PHE 0.009 0.001 PHE C 158 TRP 0.009 0.002 TRP C 47 HIS 0.005 0.002 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00438 (10482) covalent geometry : angle 0.63544 (14256) SS BOND : bond 0.00214 ( 21) SS BOND : angle 1.27295 ( 42) hydrogen bonds : bond 0.04610 ( 387) hydrogen bonds : angle 6.56258 ( 1179) link_NAG-ASN : bond 0.00300 ( 6) link_NAG-ASN : angle 1.38362 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.398 Fit side-chains REVERT: A 57 LEU cc_start: 0.8257 (tp) cc_final: 0.7948 (tp) REVERT: A 139 LEU cc_start: 0.7224 (tt) cc_final: 0.6697 (mp) REVERT: A 277 GLN cc_start: 0.8626 (tp40) cc_final: 0.8121 (tp40) REVERT: A 329 MET cc_start: 0.8686 (mtt) cc_final: 0.8425 (mtp) REVERT: C 57 LEU cc_start: 0.8274 (tp) cc_final: 0.7937 (tp) REVERT: C 277 GLN cc_start: 0.8617 (tp40) cc_final: 0.8158 (tp-100) REVERT: C 329 MET cc_start: 0.8561 (mtt) cc_final: 0.8219 (mtp) REVERT: B 57 LEU cc_start: 0.8273 (tp) cc_final: 0.7925 (tp) REVERT: B 101 PHE cc_start: 0.7896 (t80) cc_final: 0.7613 (t80) REVERT: B 277 GLN cc_start: 0.8639 (tp40) cc_final: 0.8248 (tp40) REVERT: B 283 TYR cc_start: 0.8230 (m-80) cc_final: 0.7942 (m-80) REVERT: B 329 MET cc_start: 0.8625 (mtt) cc_final: 0.8343 (mtp) outliers start: 20 outliers final: 11 residues processed: 126 average time/residue: 0.0715 time to fit residues: 14.5420 Evaluate side-chains 111 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN C 398 GLN B 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.158368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.115080 restraints weight = 20649.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.118991 restraints weight = 11237.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.121662 restraints weight = 8000.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.122801 restraints weight = 6653.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.123721 restraints weight = 6068.382| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10509 Z= 0.242 Angle : 0.646 6.754 14316 Z= 0.326 Chirality : 0.044 0.169 1617 Planarity : 0.004 0.046 1839 Dihedral : 5.078 16.801 1572 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.03 % Allowed : 12.68 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.22), residues: 1332 helix: -2.50 (0.20), residues: 441 sheet: -2.79 (0.28), residues: 285 loop : -1.21 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 100 TYR 0.020 0.002 TYR C 416 PHE 0.010 0.002 PHE A 70 TRP 0.012 0.002 TRP A 47 HIS 0.007 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00547 (10482) covalent geometry : angle 0.64170 (14256) SS BOND : bond 0.00235 ( 21) SS BOND : angle 1.08426 ( 42) hydrogen bonds : bond 0.03995 ( 387) hydrogen bonds : angle 5.97255 ( 1179) link_NAG-ASN : bond 0.00233 ( 6) link_NAG-ASN : angle 1.64557 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.381 Fit side-chains REVERT: A 57 LEU cc_start: 0.8286 (tp) cc_final: 0.7962 (tp) REVERT: A 329 MET cc_start: 0.8594 (mtt) cc_final: 0.8217 (mtp) REVERT: C 57 LEU cc_start: 0.8343 (tp) cc_final: 0.7996 (tp) REVERT: C 329 MET cc_start: 0.8502 (mtt) cc_final: 0.8144 (mtp) REVERT: B 57 LEU cc_start: 0.8328 (tp) cc_final: 0.7972 (tp) REVERT: B 101 PHE cc_start: 0.8002 (t80) cc_final: 0.7737 (t80) REVERT: B 277 GLN cc_start: 0.8707 (tp40) cc_final: 0.8394 (tp40) REVERT: B 329 MET cc_start: 0.8569 (mtt) cc_final: 0.8195 (mtp) outliers start: 41 outliers final: 30 residues processed: 143 average time/residue: 0.0648 time to fit residues: 15.2196 Evaluate side-chains 129 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.170534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.131444 restraints weight = 21019.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.133861 restraints weight = 13168.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.134213 restraints weight = 8776.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.134798 restraints weight = 8909.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.135260 restraints weight = 7868.237| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10509 Z= 0.130 Angle : 0.566 7.504 14316 Z= 0.283 Chirality : 0.042 0.183 1617 Planarity : 0.004 0.044 1839 Dihedral : 4.717 16.323 1572 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.16 % Allowed : 15.73 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.22), residues: 1332 helix: -1.89 (0.21), residues: 444 sheet: -2.64 (0.28), residues: 285 loop : -0.97 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 100 TYR 0.017 0.001 TYR B 416 PHE 0.010 0.001 PHE B 264 TRP 0.012 0.001 TRP A 47 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00290 (10482) covalent geometry : angle 0.56197 (14256) SS BOND : bond 0.00171 ( 21) SS BOND : angle 0.90111 ( 42) hydrogen bonds : bond 0.03289 ( 387) hydrogen bonds : angle 5.63050 ( 1179) link_NAG-ASN : bond 0.00160 ( 6) link_NAG-ASN : angle 1.64745 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.412 Fit side-chains REVERT: C 57 LEU cc_start: 0.8207 (tp) cc_final: 0.7986 (tp) REVERT: B 57 LEU cc_start: 0.8219 (tp) cc_final: 0.7975 (tp) REVERT: B 101 PHE cc_start: 0.7910 (t80) cc_final: 0.7677 (t80) REVERT: B 277 GLN cc_start: 0.8655 (tp40) cc_final: 0.8424 (tp40) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.0702 time to fit residues: 14.6827 Evaluate side-chains 122 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 405 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 chunk 76 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.167129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.122429 restraints weight = 21074.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.126090 restraints weight = 11999.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.128771 restraints weight = 8799.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.129899 restraints weight = 7363.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.129899 restraints weight = 6728.154| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10509 Z= 0.228 Angle : 0.639 10.608 14316 Z= 0.315 Chirality : 0.044 0.164 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.835 17.614 1572 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.24 % Allowed : 16.13 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.22), residues: 1332 helix: -1.39 (0.23), residues: 450 sheet: -2.74 (0.28), residues: 285 loop : -0.93 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 44 TYR 0.029 0.002 TYR B 416 PHE 0.010 0.001 PHE C 264 TRP 0.013 0.002 TRP C 47 HIS 0.004 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00515 (10482) covalent geometry : angle 0.63512 (14256) SS BOND : bond 0.00295 ( 21) SS BOND : angle 0.99417 ( 42) hydrogen bonds : bond 0.03453 ( 387) hydrogen bonds : angle 5.64584 ( 1179) link_NAG-ASN : bond 0.00176 ( 6) link_NAG-ASN : angle 1.68750 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.400 Fit side-chains REVERT: A 78 LEU cc_start: 0.9100 (mm) cc_final: 0.8892 (mm) REVERT: C 57 LEU cc_start: 0.8303 (tp) cc_final: 0.8017 (tp) REVERT: B 57 LEU cc_start: 0.8307 (tp) cc_final: 0.7970 (tp) REVERT: B 78 LEU cc_start: 0.9078 (mm) cc_final: 0.8869 (mm) REVERT: B 101 PHE cc_start: 0.8030 (t80) cc_final: 0.7779 (t80) REVERT: B 277 GLN cc_start: 0.8682 (tp40) cc_final: 0.8345 (tp40) outliers start: 33 outliers final: 25 residues processed: 128 average time/residue: 0.0730 time to fit residues: 15.0021 Evaluate side-chains 124 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.170099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.126307 restraints weight = 21008.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.130163 restraints weight = 11919.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.132706 restraints weight = 8707.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.133633 restraints weight = 7322.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.133633 restraints weight = 6739.194| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10509 Z= 0.134 Angle : 0.577 7.528 14316 Z= 0.284 Chirality : 0.042 0.188 1617 Planarity : 0.004 0.043 1839 Dihedral : 4.617 21.639 1572 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.34 % Allowed : 16.03 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.23), residues: 1332 helix: -1.02 (0.23), residues: 453 sheet: -2.66 (0.27), residues: 291 loop : -0.85 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.030 0.001 TYR C 416 PHE 0.012 0.001 PHE B 264 TRP 0.014 0.002 TRP A 47 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00303 (10482) covalent geometry : angle 0.57065 (14256) SS BOND : bond 0.00244 ( 21) SS BOND : angle 1.31769 ( 42) hydrogen bonds : bond 0.03050 ( 387) hydrogen bonds : angle 5.44969 ( 1179) link_NAG-ASN : bond 0.00155 ( 6) link_NAG-ASN : angle 1.66725 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.508 Fit side-chains REVERT: A 78 LEU cc_start: 0.9044 (mm) cc_final: 0.8792 (mm) REVERT: C 57 LEU cc_start: 0.8198 (tp) cc_final: 0.7947 (tp) REVERT: B 57 LEU cc_start: 0.8239 (tp) cc_final: 0.8020 (tp) REVERT: B 78 LEU cc_start: 0.9055 (mm) cc_final: 0.8781 (mm) REVERT: B 101 PHE cc_start: 0.7986 (t80) cc_final: 0.7736 (t80) REVERT: B 277 GLN cc_start: 0.8574 (tp40) cc_final: 0.8176 (tp40) outliers start: 34 outliers final: 29 residues processed: 131 average time/residue: 0.0706 time to fit residues: 15.8487 Evaluate side-chains 133 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.170564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.127201 restraints weight = 20820.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.131094 restraints weight = 11616.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.133749 restraints weight = 8382.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.134733 restraints weight = 7008.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.134744 restraints weight = 6436.002| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10509 Z= 0.125 Angle : 0.555 7.212 14316 Z= 0.273 Chirality : 0.041 0.168 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.440 19.408 1572 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.64 % Allowed : 16.13 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.23), residues: 1332 helix: -0.73 (0.24), residues: 459 sheet: -2.44 (0.28), residues: 285 loop : -0.75 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.024 0.001 TYR C 416 PHE 0.011 0.001 PHE B 264 TRP 0.014 0.002 TRP A 47 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00284 (10482) covalent geometry : angle 0.55091 (14256) SS BOND : bond 0.00212 ( 21) SS BOND : angle 1.01655 ( 42) hydrogen bonds : bond 0.02943 ( 387) hydrogen bonds : angle 5.31510 ( 1179) link_NAG-ASN : bond 0.00124 ( 6) link_NAG-ASN : angle 1.57780 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.411 Fit side-chains REVERT: A 78 LEU cc_start: 0.9050 (mm) cc_final: 0.8774 (mm) REVERT: B 78 LEU cc_start: 0.9071 (mm) cc_final: 0.8777 (mm) REVERT: B 101 PHE cc_start: 0.7986 (t80) cc_final: 0.7754 (t80) REVERT: B 277 GLN cc_start: 0.8592 (tp40) cc_final: 0.8257 (tp40) outliers start: 37 outliers final: 34 residues processed: 135 average time/residue: 0.0686 time to fit residues: 15.1490 Evaluate side-chains 134 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.164776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.122505 restraints weight = 21220.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.124449 restraints weight = 12567.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.125335 restraints weight = 9019.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.125995 restraints weight = 8364.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.126188 restraints weight = 8036.578| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10509 Z= 0.297 Angle : 0.684 8.349 14316 Z= 0.343 Chirality : 0.046 0.201 1617 Planarity : 0.004 0.040 1839 Dihedral : 4.914 18.704 1572 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.13 % Allowed : 16.42 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.23), residues: 1332 helix: -0.75 (0.24), residues: 462 sheet: -2.57 (0.29), residues: 258 loop : -1.04 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 44 TYR 0.021 0.002 TYR C 416 PHE 0.011 0.002 PHE B 273 TRP 0.016 0.002 TRP A 47 HIS 0.006 0.002 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00673 (10482) covalent geometry : angle 0.67948 (14256) SS BOND : bond 0.00425 ( 21) SS BOND : angle 1.27617 ( 42) hydrogen bonds : bond 0.03628 ( 387) hydrogen bonds : angle 5.67896 ( 1179) link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 1.70015 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 0.392 Fit side-chains REVERT: A 78 LEU cc_start: 0.9159 (mm) cc_final: 0.8918 (mm) REVERT: A 192 TYR cc_start: 0.7480 (m-80) cc_final: 0.7210 (m-80) REVERT: B 78 LEU cc_start: 0.9147 (mm) cc_final: 0.8879 (mm) REVERT: B 101 PHE cc_start: 0.8077 (t80) cc_final: 0.7828 (t80) outliers start: 42 outliers final: 36 residues processed: 136 average time/residue: 0.0694 time to fit residues: 15.5042 Evaluate side-chains 137 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.169541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.126888 restraints weight = 20859.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.130361 restraints weight = 12376.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.130982 restraints weight = 9086.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.131124 restraints weight = 7995.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.132673 restraints weight = 7882.808| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10509 Z= 0.138 Angle : 0.585 7.488 14316 Z= 0.288 Chirality : 0.043 0.200 1617 Planarity : 0.004 0.040 1839 Dihedral : 4.616 18.014 1572 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.24 % Allowed : 17.21 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.24), residues: 1332 helix: -0.55 (0.24), residues: 465 sheet: -2.65 (0.28), residues: 285 loop : -0.67 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.022 0.001 TYR C 416 PHE 0.010 0.001 PHE B 264 TRP 0.016 0.002 TRP C 47 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00311 (10482) covalent geometry : angle 0.58018 (14256) SS BOND : bond 0.00294 ( 21) SS BOND : angle 1.03028 ( 42) hydrogen bonds : bond 0.03029 ( 387) hydrogen bonds : angle 5.43872 ( 1179) link_NAG-ASN : bond 0.00114 ( 6) link_NAG-ASN : angle 1.63059 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.395 Fit side-chains REVERT: A 78 LEU cc_start: 0.9096 (mm) cc_final: 0.8833 (mm) REVERT: B 78 LEU cc_start: 0.9085 (mm) cc_final: 0.8798 (mm) REVERT: B 101 PHE cc_start: 0.7971 (t80) cc_final: 0.7749 (t80) outliers start: 33 outliers final: 29 residues processed: 127 average time/residue: 0.0710 time to fit residues: 14.8047 Evaluate side-chains 131 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 0.0770 chunk 115 optimal weight: 9.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS B 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.171764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.136335 restraints weight = 20566.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.140074 restraints weight = 13507.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.141023 restraints weight = 10149.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.141419 restraints weight = 7652.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.142072 restraints weight = 7303.001| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10509 Z= 0.107 Angle : 0.578 8.413 14316 Z= 0.278 Chirality : 0.042 0.180 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.323 16.619 1572 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.15 % Allowed : 17.01 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.24), residues: 1332 helix: -0.26 (0.25), residues: 450 sheet: -2.44 (0.28), residues: 285 loop : -0.44 (0.28), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.022 0.001 TYR C 416 PHE 0.009 0.001 PHE B 264 TRP 0.017 0.002 TRP A 47 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00240 (10482) covalent geometry : angle 0.57423 (14256) SS BOND : bond 0.00238 ( 21) SS BOND : angle 0.89441 ( 42) hydrogen bonds : bond 0.02869 ( 387) hydrogen bonds : angle 5.26298 ( 1179) link_NAG-ASN : bond 0.00099 ( 6) link_NAG-ASN : angle 1.57257 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.381 Fit side-chains REVERT: A 78 LEU cc_start: 0.9070 (mm) cc_final: 0.8783 (mm) REVERT: B 78 LEU cc_start: 0.9076 (mm) cc_final: 0.8773 (mm) REVERT: B 101 PHE cc_start: 0.7923 (t80) cc_final: 0.7715 (t80) outliers start: 32 outliers final: 26 residues processed: 135 average time/residue: 0.0715 time to fit residues: 15.8725 Evaluate side-chains 131 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS B 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.171501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.135633 restraints weight = 20007.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.136592 restraints weight = 11326.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.138269 restraints weight = 9936.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.138739 restraints weight = 7226.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.139304 restraints weight = 6830.335| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10509 Z= 0.112 Angle : 0.590 9.776 14316 Z= 0.280 Chirality : 0.042 0.174 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.246 16.338 1572 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.65 % Allowed : 18.09 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.24), residues: 1332 helix: -0.15 (0.25), residues: 447 sheet: -2.35 (0.28), residues: 285 loop : -0.42 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.021 0.001 TYR C 416 PHE 0.017 0.001 PHE C 441 TRP 0.015 0.002 TRP A 47 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00257 (10482) covalent geometry : angle 0.58585 (14256) SS BOND : bond 0.00209 ( 21) SS BOND : angle 0.99526 ( 42) hydrogen bonds : bond 0.02830 ( 387) hydrogen bonds : angle 5.20946 ( 1179) link_NAG-ASN : bond 0.00089 ( 6) link_NAG-ASN : angle 1.55355 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.03 seconds wall clock time: 30 minutes 35.13 seconds (1835.13 seconds total)