Starting phenix.real_space_refine on Fri Sep 11 16:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vtl_21381/09_2026/6vtl_21381.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vtl_21381/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vtl_21381/09_2026/6vtl_21381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vtl_21381/09_2026/6vtl_21381.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vtl_21381/09_2026/6vtl_21381.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vtl_21381/09_2026/6vtl_21381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vtl_21381/09_2026/6vtl_21381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vtl_21381/09_2026/6vtl_21381.map" } 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-2.2.1-6174/lib/python3.11/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 chiralities: 2 Restraints were copied for chains: C, B Time building chain proxies: 2.47, per 1000 atoms: 0.24 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: 0.67 Conformation dependent library (CDL) restraints added in 458.4 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: 0.30 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: 1.74 Time building geometry restraints manager: 0.93 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: 5609 17.86 - 35.71: 517 35.71 - 53.57: 72 53.57 - 71.43: 3 71.43 - 89.28: 18 Dihedral angle restraints: 6219 sinusoidal: 2310 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 6216 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: 0.03 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: 6.450 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 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 : 13.919 89.283 3648 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/Z covalent geometry : bond 0.00412 / 0.19 (10482) covalent geometry : angle 0.79560 / 0.42 (14256) SS BOND : bond 0.00682 / 0.41 ( 21) SS BOND : angle 2.08597 / 1.39 ( 42) hydrogen bonds : bond 0.29192 / 19.44 ( 387) hydrogen bonds : angle 10.83466 / 7.36 ( 1179) link_NAG-ASN : bond 0.00079 / 0.05 ( 6) link_NAG-ASN : angle 1.29645 / 0.75 ( 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 : 0.306 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: 0.0810 time to fit residues: 19.0732 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 : 0.435 ------------------------------------------------------------------------------- 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... 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 = 0.162061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.125959 restraints weight = 19625.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.127863 restraints weight = 11678.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.129417 restraints weight = 9004.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.130380 restraints weight = 6882.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.130730 restraints weight = 6568.197| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10509 Z= 0.195 Angle : 0.636 7.376 14316 Z= 0.330 Chirality : 0.043 0.155 1617 Planarity : 0.005 0.053 1839 Dihedral : 5.174 17.287 1446 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.16 % Allowed : 11.90 % Favored : 85.94 % 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: -2.68 (0.29), residues: 285 loop : -1.27 (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 0.010 0.001 PHE C 158 TRP 0.010 0.003 TRP B 234 HIS 0.007 0.002 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (10482) covalent geometry : angle 0.63167 / 0.33 (14256) SS BOND : bond 0.00189 / 0.12 ( 21) SS BOND : angle 1.29227 / 0.82 ( 42) hydrogen bonds : bond 0.04607 / 3.06 ( 387) hydrogen bonds : angle 6.54460 / 4.46 ( 1179) link_NAG-ASN : bond 0.00275 / 0.16 ( 6) link_NAG-ASN : angle 1.27254 / 0.70 ( 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 140 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.432 Fit side-chains REVERT: A 57 LEU cc_start: 0.8250 (tp) cc_final: 0.7941 (tp) REVERT: A 139 LEU cc_start: 0.7229 (tt) cc_final: 0.6709 (mp) REVERT: A 277 GLN cc_start: 0.8640 (tp40) cc_final: 0.8138 (tp40) REVERT: A 329 MET cc_start: 0.8674 (mtt) cc_final: 0.8408 (mtp) REVERT: C 57 LEU cc_start: 0.8280 (tp) cc_final: 0.7936 (tp) REVERT: C 277 GLN cc_start: 0.8632 (tp40) cc_final: 0.8175 (tp-100) REVERT: C 329 MET cc_start: 0.8560 (mtt) cc_final: 0.8174 (mtp) REVERT: B 57 LEU cc_start: 0.8269 (tp) cc_final: 0.7921 (tp) REVERT: B 101 PHE cc_start: 0.7897 (t80) cc_final: 0.7620 (t80) REVERT: B 277 GLN cc_start: 0.8655 (tp40) cc_final: 0.8296 (tp40) REVERT: B 283 TYR cc_start: 0.8226 (m-80) cc_final: 0.7944 (m-80) REVERT: B 329 MET cc_start: 0.8621 (mtt) cc_final: 0.8336 (mtp) outliers start: 22 outliers final: 12 residues processed: 131 average time/residue: 0.0768 time to fit residues: 15.8211 Evaluate side-chains 115 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 42 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: 3.9990 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: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4466 r_free = 0.4466 target = 0.155877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.112169 restraints weight = 20778.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.116229 restraints weight = 11040.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.118814 restraints weight = 7763.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.119877 restraints weight = 6447.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.120834 restraints weight = 5907.698| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10509 Z= 0.316 Angle : 0.716 7.572 14316 Z= 0.364 Chirality : 0.046 0.167 1617 Planarity : 0.004 0.045 1839 Dihedral : 5.417 17.150 1446 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.03 % Allowed : 14.16 % Favored : 81.81 % 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: -3.30 (0.21), residues: 1332 helix: -2.51 (0.20), residues: 423 sheet: -3.05 (0.27), residues: 285 loop : -1.30 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.019 0.002 TYR A 393 PHE 0.013 0.002 PHE C 441 TRP 0.009 0.002 TRP A 47 HIS 0.007 0.002 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.32 (10482) covalent geometry : angle 0.71147 / 0.36 (14256) SS BOND : bond 0.00336 / 0.22 ( 21) SS BOND : angle 1.40240 / 0.87 ( 42) hydrogen bonds : bond 0.04359 / 2.89 ( 387) hydrogen bonds : angle 6.20154 / 4.18 ( 1179) link_NAG-ASN : bond 0.00296 / 0.17 ( 6) link_NAG-ASN : angle 1.65883 / 0.94 ( 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 156 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.325 Fit side-chains REVERT: A 57 LEU cc_start: 0.8368 (tp) cc_final: 0.8032 (tp) REVERT: A 329 MET cc_start: 0.8586 (mtt) cc_final: 0.8207 (mtp) REVERT: C 57 LEU cc_start: 0.8378 (tp) cc_final: 0.8012 (tp) REVERT: C 329 MET cc_start: 0.8509 (mtt) cc_final: 0.8157 (mtp) REVERT: B 57 LEU cc_start: 0.8365 (tp) cc_final: 0.8074 (tp) REVERT: B 101 PHE cc_start: 0.8057 (t80) cc_final: 0.7782 (t80) REVERT: B 277 GLN cc_start: 0.8771 (tp40) cc_final: 0.8443 (tp40) REVERT: B 329 MET cc_start: 0.8571 (mtt) cc_final: 0.8160 (mtp) outliers start: 41 outliers final: 33 residues processed: 146 average time/residue: 0.0689 time to fit residues: 16.2878 Evaluate side-chains 136 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 380 ILE 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 60 LEU Chi-restraints excluded: chain C residue 78 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 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 60 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 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: 10.0000 chunk 61 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 127 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.166520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.123444 restraints weight = 20766.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.127518 restraints weight = 11051.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.130440 restraints weight = 7809.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.131709 restraints weight = 6439.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.132888 restraints weight = 5833.125| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10509 Z= 0.116 Angle : 0.580 8.706 14316 Z= 0.288 Chirality : 0.042 0.181 1617 Planarity : 0.004 0.045 1839 Dihedral : 4.833 20.529 1446 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.36 % Allowed : 15.93 % Favored : 81.71 % 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: -2.75 (0.22), residues: 1332 helix: -1.93 (0.21), residues: 444 sheet: -2.72 (0.27), residues: 291 loop : -0.99 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 100 TYR 0.033 0.001 TYR C 416 PHE 0.013 0.001 PHE B 264 TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10482) covalent geometry : angle 0.57333 / 0.29 (14256) SS BOND : bond 0.00382 / 0.20 ( 21) SS BOND : angle 1.33719 / 0.80 ( 42) hydrogen bonds : bond 0.03318 / 2.23 ( 387) hydrogen bonds : angle 5.68552 / 3.85 ( 1179) link_NAG-ASN : bond 0.00185 / 0.11 ( 6) link_NAG-ASN : angle 1.60813 / 0.88 ( 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 139 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.274 Fit side-chains REVERT: A 57 LEU cc_start: 0.8170 (tp) cc_final: 0.7960 (tp) REVERT: A 329 MET cc_start: 0.8576 (mtt) cc_final: 0.8273 (mtp) REVERT: C 57 LEU cc_start: 0.8197 (tp) cc_final: 0.7947 (tp) REVERT: C 329 MET cc_start: 0.8557 (mtt) cc_final: 0.8233 (mtp) REVERT: B 57 LEU cc_start: 0.8187 (tp) cc_final: 0.7979 (tp) REVERT: B 101 PHE cc_start: 0.7951 (t80) cc_final: 0.7708 (t80) REVERT: B 277 GLN cc_start: 0.8625 (tp40) cc_final: 0.8187 (tp40) REVERT: B 329 MET cc_start: 0.8533 (mtt) cc_final: 0.8250 (mtp) outliers start: 24 outliers final: 16 residues processed: 129 average time/residue: 0.0698 time to fit residues: 14.4926 Evaluate side-chains 123 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 364 MET 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 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: 4.9990 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.165760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.121266 restraints weight = 21116.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.125050 restraints weight = 11969.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.126997 restraints weight = 8701.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.128903 restraints weight = 7426.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.129487 restraints weight = 6707.308| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10509 Z= 0.259 Angle : 0.664 9.515 14316 Z= 0.330 Chirality : 0.045 0.165 1617 Planarity : 0.004 0.042 1839 Dihedral : 5.040 17.583 1446 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.83 % Allowed : 16.03 % Favored : 80.14 % 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: -2.51 (0.23), residues: 1332 helix: -1.43 (0.23), residues: 435 sheet: -2.86 (0.28), residues: 285 loop : -1.00 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.030 0.002 TYR B 416 PHE 0.010 0.002 PHE C 264 TRP 0.009 0.002 TRP C 47 HIS 0.005 0.002 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 (10482) covalent geometry : angle 0.66038 / 0.33 (14256) SS BOND : bond 0.00386 / 0.23 ( 21) SS BOND : angle 1.15225 / 0.70 ( 42) hydrogen bonds : bond 0.03640 / 2.41 ( 387) hydrogen bonds : angle 5.76952 / 3.91 ( 1179) link_NAG-ASN : bond 0.00238 / 0.14 ( 6) link_NAG-ASN : angle 1.62877 / 0.93 ( 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 141 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.335 Fit side-chains REVERT: A 57 LEU cc_start: 0.8319 (tp) cc_final: 0.8021 (tp) REVERT: A 78 LEU cc_start: 0.9144 (mm) cc_final: 0.8924 (mm) REVERT: A 329 MET cc_start: 0.8427 (mtt) cc_final: 0.7997 (mtp) REVERT: C 57 LEU cc_start: 0.8318 (tp) cc_final: 0.8019 (tp) REVERT: C 329 MET cc_start: 0.8384 (mtt) cc_final: 0.8009 (mtp) REVERT: B 57 LEU cc_start: 0.8346 (tp) cc_final: 0.8096 (tp) REVERT: B 78 LEU cc_start: 0.9116 (mm) cc_final: 0.8882 (mm) REVERT: B 101 PHE cc_start: 0.8049 (t80) cc_final: 0.7789 (t80) REVERT: B 329 MET cc_start: 0.8418 (mtt) cc_final: 0.7997 (mtp) outliers start: 39 outliers final: 31 residues processed: 132 average time/residue: 0.0745 time to fit residues: 15.5265 Evaluate side-chains 129 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 364 MET 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 291 CYS 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 418 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.167984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.129477 restraints weight = 21043.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.130022 restraints weight = 13703.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.132043 restraints weight = 9553.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.132246 restraints weight = 8338.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.132628 restraints weight = 7597.197| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10509 Z= 0.168 Angle : 0.600 8.471 14316 Z= 0.298 Chirality : 0.043 0.182 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.838 22.621 1446 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.34 % Allowed : 17.01 % Favored : 79.65 % 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: -2.28 (0.23), residues: 1332 helix: -1.06 (0.24), residues: 450 sheet: -2.84 (0.27), residues: 291 loop : -0.92 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.025 0.001 TYR B 416 PHE 0.012 0.001 PHE C 264 TRP 0.011 0.002 TRP A 47 HIS 0.004 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (10482) covalent geometry : angle 0.59285 / 0.30 (14256) SS BOND : bond 0.00391 / 0.27 ( 21) SS BOND : angle 1.49180 / 1.13 ( 42) hydrogen bonds : bond 0.03263 / 2.18 ( 387) hydrogen bonds : angle 5.61563 / 3.82 ( 1179) link_NAG-ASN : bond 0.00184 / 0.10 ( 6) link_NAG-ASN : angle 1.63830 / 0.93 ( 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 138 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.403 Fit side-chains REVERT: A 57 LEU cc_start: 0.8308 (tp) cc_final: 0.8078 (tp) REVERT: A 78 LEU cc_start: 0.9116 (mm) cc_final: 0.8890 (mm) REVERT: A 329 MET cc_start: 0.8519 (mtt) cc_final: 0.8184 (mtp) REVERT: C 57 LEU cc_start: 0.8292 (tp) cc_final: 0.8062 (tp) REVERT: C 329 MET cc_start: 0.8489 (mtt) cc_final: 0.8181 (mtp) REVERT: B 57 LEU cc_start: 0.8354 (tp) cc_final: 0.8139 (tp) REVERT: B 78 LEU cc_start: 0.9105 (mm) cc_final: 0.8851 (mm) REVERT: B 101 PHE cc_start: 0.7997 (t80) cc_final: 0.7760 (t80) REVERT: B 329 MET cc_start: 0.8491 (mtt) cc_final: 0.8170 (mtp) outliers start: 34 outliers final: 28 residues processed: 129 average time/residue: 0.0701 time to fit residues: 14.9115 Evaluate side-chains 127 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 MET 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 180 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 262 LEU 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 405 LEU 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 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 405 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 5.9990 chunk 78 optimal weight: 0.0060 chunk 43 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.0060 chunk 69 optimal weight: 1.9990 overall best weight: 0.5212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.171561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.135624 restraints weight = 19756.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.137540 restraints weight = 11339.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.139045 restraints weight = 9220.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.139873 restraints weight = 6842.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.140405 restraints weight = 6472.625| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10509 Z= 0.101 Angle : 0.558 7.390 14316 Z= 0.274 Chirality : 0.041 0.201 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.452 20.747 1446 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.95 % Allowed : 17.99 % Favored : 79.06 % 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: -1.84 (0.23), residues: 1332 helix: -0.74 (0.24), residues: 462 sheet: -2.45 (0.28), residues: 285 loop : -0.72 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.022 0.001 TYR B 416 PHE 0.011 0.001 PHE A 264 TRP 0.019 0.002 TRP A 47 HIS 0.002 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (10482) covalent geometry : angle 0.55402 / 0.27 (14256) SS BOND : bond 0.00206 / 0.14 ( 21) SS BOND : angle 1.01937 / 0.77 ( 42) hydrogen bonds : bond 0.02941 / 1.97 ( 387) hydrogen bonds : angle 5.34056 / 3.65 ( 1179) link_NAG-ASN : bond 0.00134 / 0.08 ( 6) link_NAG-ASN : angle 1.46716 / 0.81 ( 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 140 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.483 Fit side-chains REVERT: A 78 LEU cc_start: 0.9055 (mm) cc_final: 0.8794 (mm) REVERT: A 329 MET cc_start: 0.8549 (mtt) cc_final: 0.8284 (mtp) REVERT: C 329 MET cc_start: 0.8532 (mtt) cc_final: 0.8294 (mtp) REVERT: B 78 LEU cc_start: 0.9076 (mm) cc_final: 0.8755 (mm) REVERT: B 101 PHE cc_start: 0.7932 (t80) cc_final: 0.7712 (t80) REVERT: B 329 MET cc_start: 0.8475 (mtt) cc_final: 0.8244 (mtp) REVERT: B 417 GLU cc_start: 0.8386 (mp0) cc_final: 0.8183 (mp0) outliers start: 30 outliers final: 22 residues processed: 129 average time/residue: 0.0728 time to fit residues: 15.3633 Evaluate side-chains 125 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain C residue 99 PHE 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 262 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain B residue 139 LEU 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 Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 405 LEU 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: 0.5980 chunk 84 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.168482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.124324 restraints weight = 20981.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.128268 restraints weight = 11871.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.130874 restraints weight = 8553.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.131477 restraints weight = 7179.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.132497 restraints weight = 6704.971| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10509 Z= 0.188 Angle : 0.607 13.070 14316 Z= 0.296 Chirality : 0.044 0.397 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.612 19.331 1446 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.64 % Allowed : 18.29 % Favored : 78.07 % 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: -1.79 (0.23), residues: 1332 helix: -0.55 (0.24), residues: 459 sheet: -2.55 (0.28), residues: 285 loop : -0.77 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.019 0.001 TYR B 416 PHE 0.011 0.001 PHE B 273 TRP 0.015 0.002 TRP A 47 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (10482) covalent geometry : angle 0.60285 / 0.29 (14256) SS BOND : bond 0.00311 / 0.20 ( 21) SS BOND : angle 1.06682 / 0.74 ( 42) hydrogen bonds : bond 0.03156 / 2.10 ( 387) hydrogen bonds : angle 5.40053 / 3.69 ( 1179) link_NAG-ASN : bond 0.00151 / 0.09 ( 6) link_NAG-ASN : angle 1.47416 / 0.82 ( 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 138 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.439 Fit side-chains REVERT: A 78 LEU cc_start: 0.9068 (mm) cc_final: 0.8825 (mm) REVERT: A 329 MET cc_start: 0.8480 (mtt) cc_final: 0.8104 (mtp) REVERT: C 329 MET cc_start: 0.8437 (mtt) cc_final: 0.8100 (mtp) REVERT: B 78 LEU cc_start: 0.9104 (mm) cc_final: 0.8809 (mm) REVERT: B 101 PHE cc_start: 0.8014 (t80) cc_final: 0.7787 (t80) REVERT: B 329 MET cc_start: 0.8400 (mtt) cc_final: 0.8072 (mtp) outliers start: 37 outliers final: 29 residues processed: 129 average time/residue: 0.0691 time to fit residues: 14.8054 Evaluate side-chains 128 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL 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 262 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 389 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 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 376 SER 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: 6.9990 chunk 22 optimal weight: 0.0000 chunk 107 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS C 74 HIS C 111 HIS B 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.173069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.128901 restraints weight = 20811.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.133496 restraints weight = 10757.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.136397 restraints weight = 7451.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.137768 restraints weight = 6127.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.138699 restraints weight = 5559.826| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10509 Z= 0.099 Angle : 0.574 14.366 14316 Z= 0.274 Chirality : 0.042 0.329 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.288 18.145 1446 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.65 % Allowed : 19.37 % Favored : 77.97 % 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: -1.44 (0.24), residues: 1332 helix: -0.30 (0.25), residues: 450 sheet: -2.37 (0.28), residues: 291 loop : -0.49 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.021 0.001 TYR B 416 PHE 0.009 0.001 PHE B 264 TRP 0.016 0.002 TRP A 47 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (10482) covalent geometry : angle 0.57188 / 0.27 (14256) SS BOND : bond 0.00142 / 0.09 ( 21) SS BOND : angle 0.79101 / 0.57 ( 42) hydrogen bonds : bond 0.02841 / 1.91 ( 387) hydrogen bonds : angle 5.19638 / 3.57 ( 1179) link_NAG-ASN : bond 0.00179 / 0.10 ( 6) link_NAG-ASN : angle 1.40189 / 0.77 ( 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 130 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.437 Fit side-chains REVERT: A 78 LEU cc_start: 0.9030 (mm) cc_final: 0.8741 (mm) REVERT: A 329 MET cc_start: 0.8456 (mtt) cc_final: 0.8155 (mtp) REVERT: C 329 MET cc_start: 0.8450 (mtt) cc_final: 0.8160 (mtp) REVERT: B 78 LEU cc_start: 0.9047 (mm) cc_final: 0.8719 (mm) REVERT: B 101 PHE cc_start: 0.7938 (t80) cc_final: 0.7732 (t80) REVERT: B 329 MET cc_start: 0.8386 (mtt) cc_final: 0.8124 (mtp) outliers start: 27 outliers final: 22 residues processed: 122 average time/residue: 0.0713 time to fit residues: 14.3189 Evaluate side-chains 122 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 364 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 364 MET 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 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 376 SER Chi-restraints excluded: chain B residue 405 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4642 r_free = 0.4642 target = 0.170385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.126569 restraints weight = 20700.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.130430 restraints weight = 11713.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.132473 restraints weight = 8473.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.134583 restraints weight = 7191.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.134796 restraints weight = 6460.141| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10509 Z= 0.145 Angle : 0.599 14.338 14316 Z= 0.287 Chirality : 0.043 0.341 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.362 17.260 1446 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.05 % Allowed : 19.17 % Favored : 77.78 % 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: -1.44 (0.24), residues: 1332 helix: -0.21 (0.25), residues: 453 sheet: -2.40 (0.28), residues: 291 loop : -0.54 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.019 0.001 TYR B 416 PHE 0.012 0.001 PHE C 441 TRP 0.017 0.002 TRP C 47 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10482) covalent geometry : angle 0.59586 / 0.29 (14256) SS BOND : bond 0.00233 / 0.15 ( 21) SS BOND : angle 1.05819 / 0.69 ( 42) hydrogen bonds : bond 0.02972 / 1.98 ( 387) hydrogen bonds : angle 5.24249 / 3.60 ( 1179) link_NAG-ASN : bond 0.00128 / 0.07 ( 6) link_NAG-ASN : angle 1.37508 / 0.76 ( 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 133 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.494 Fit side-chains REVERT: A 78 LEU cc_start: 0.9043 (mm) cc_final: 0.8773 (mm) REVERT: A 329 MET cc_start: 0.8423 (mtt) cc_final: 0.8129 (mtp) REVERT: C 329 MET cc_start: 0.8427 (mtt) cc_final: 0.8119 (mtp) REVERT: B 78 LEU cc_start: 0.9090 (mm) cc_final: 0.8784 (mm) REVERT: B 101 PHE cc_start: 0.7989 (t80) cc_final: 0.7772 (t80) REVERT: B 329 MET cc_start: 0.8405 (mtt) cc_final: 0.8138 (mtp) outliers start: 31 outliers final: 27 residues processed: 124 average time/residue: 0.0712 time to fit residues: 14.5711 Evaluate side-chains 127 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 364 MET 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 262 LEU 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 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 376 SER 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: 0.9990 chunk 127 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS C 111 HIS B 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.172400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.128159 restraints weight = 20956.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.132699 restraints weight = 10886.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.135601 restraints weight = 7550.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.136953 restraints weight = 6177.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.138510 restraints weight = 5608.590| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10509 Z= 0.106 Angle : 0.579 13.945 14316 Z= 0.274 Chirality : 0.042 0.308 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.242 17.011 1446 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.95 % Allowed : 19.57 % Favored : 77.48 % 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: -1.28 (0.24), residues: 1332 helix: -0.16 (0.25), residues: 456 sheet: -2.31 (0.28), residues: 291 loop : -0.37 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.019 0.001 TYR B 416 PHE 0.013 0.001 PHE C 441 TRP 0.016 0.002 TRP C 47 HIS 0.002 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10482) covalent geometry : angle 0.57684 / 0.27 (14256) SS BOND : bond 0.00179 / 0.11 ( 21) SS BOND : angle 0.82250 / 0.56 ( 42) hydrogen bonds : bond 0.02834 / 1.90 ( 387) hydrogen bonds : angle 5.19931 / 3.58 ( 1179) link_NAG-ASN : bond 0.00129 / 0.08 ( 6) link_NAG-ASN : angle 1.31587 / 0.72 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.41 seconds wall clock time: 33 minutes 11.50 seconds (1991.50 seconds total)