Starting phenix.real_space_refine on Wed Feb 4 10:46:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4k_47513/02_2026/9e4k_47513.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4k_47513/02_2026/9e4k_47513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e4k_47513/02_2026/9e4k_47513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4k_47513/02_2026/9e4k_47513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e4k_47513/02_2026/9e4k_47513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4k_47513/02_2026/9e4k_47513.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 87 5.16 5 C 6330 2.51 5 N 1632 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9915 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "B" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Time building chain proxies: 2.60, per 1000 atoms: 0.26 Number of scatterers: 9915 At special positions: 0 Unit cell: (96.759, 102.548, 133.974, 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 87 16.00 O 1866 8.00 N 1632 7.00 C 6330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 412.8 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 41.3% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 40 through 69 removed outlier: 4.398A pdb=" N PHE A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.859A pdb=" N ASP A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A 203 " --> pdb=" O GLY A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 203' Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.785A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.972A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.537A pdb=" N LYS A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 3.537A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 452 removed outlier: 3.537A pdb=" N LEU A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 69 Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.734A pdb=" N VAL B 103 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.711A pdb=" N ASP B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B 203 " --> pdb=" O GLY B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 203' Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.636A pdb=" N GLY B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.946A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 383 through 394 removed outlier: 4.714A pdb=" N LYS B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.746A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 452 removed outlier: 4.029A pdb=" N LEU B 441 " --> pdb=" O GLY B 437 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 69 removed outlier: 3.795A pdb=" N LEU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.742A pdb=" N VAL C 103 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 131 through 142 removed outlier: 3.748A pdb=" N ILE C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.813A pdb=" N GLY C 203 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.824A pdb=" N GLY C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.976A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.873A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 452 removed outlier: 3.658A pdb=" N LEU C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 13.070A pdb=" N ASN A 416 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N CYS A 275 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 171 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP A 223 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU A 169 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS A 172 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 81 removed outlier: 13.070A pdb=" N ASN A 416 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N CYS A 275 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 6.724A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 245 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 81 removed outlier: 13.198A pdb=" N ASN B 416 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N CYS B 275 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 171 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 81 removed outlier: 13.198A pdb=" N ASN B 416 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N CYS B 275 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 6.835A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 245 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 81 removed outlier: 3.501A pdb=" N GLU C 421 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 171 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 81 removed outlier: 3.501A pdb=" N GLU C 421 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 6.716A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR C 195 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 245 " --> pdb=" O VAL C 265 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1440 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: 1.68 Time building geometry restraints manager: 1.03 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: 3237 1.35 - 1.47: 2425 1.47 - 1.59: 4361 1.59 - 1.71: 0 1.71 - 1.83: 120 Bond restraints: 10143 Sorted by residual: bond pdb=" CB CYS B 179 " pdb=" SG CYS B 179 " ideal model delta sigma weight residual 1.808 1.829 -0.021 3.30e-02 9.18e+02 4.08e-01 bond pdb=" CB CYS C 179 " pdb=" SG CYS C 179 " ideal model delta sigma weight residual 1.808 1.826 -0.018 3.30e-02 9.18e+02 2.96e-01 bond pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " ideal model delta sigma weight residual 1.808 1.826 -0.018 3.30e-02 9.18e+02 2.83e-01 bond pdb=" N ASP B 126 " pdb=" CA ASP B 126 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.29e-02 6.01e+03 2.61e-01 bond pdb=" CA CYS B 179 " pdb=" CB CYS B 179 " ideal model delta sigma weight residual 1.530 1.538 -0.008 1.52e-02 4.33e+03 2.56e-01 ... (remaining 10138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 13418 1.08 - 2.15: 210 2.15 - 3.23: 60 3.23 - 4.31: 13 4.31 - 5.38: 12 Bond angle restraints: 13713 Sorted by residual: angle pdb=" CA CYS B 172 " pdb=" CB CYS B 172 " pdb=" SG CYS B 172 " ideal model delta sigma weight residual 114.40 119.78 -5.38 2.30e+00 1.89e-01 5.48e+00 angle pdb=" CA CYS A 172 " pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " ideal model delta sigma weight residual 114.40 119.23 -4.83 2.30e+00 1.89e-01 4.42e+00 angle pdb=" CA CYS B 179 " pdb=" CB CYS B 179 " pdb=" SG CYS B 179 " ideal model delta sigma weight residual 114.40 119.21 -4.81 2.30e+00 1.89e-01 4.37e+00 angle pdb=" CA CYS C 172 " pdb=" CB CYS C 172 " pdb=" SG CYS C 172 " ideal model delta sigma weight residual 114.40 119.11 -4.71 2.30e+00 1.89e-01 4.19e+00 angle pdb=" CA CYS C 179 " pdb=" CB CYS C 179 " pdb=" SG CYS C 179 " ideal model delta sigma weight residual 114.40 118.73 -4.33 2.30e+00 1.89e-01 3.55e+00 ... (remaining 13708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 5526 16.94 - 33.87: 472 33.87 - 50.81: 116 50.81 - 67.75: 23 67.75 - 84.69: 16 Dihedral angle restraints: 6153 sinusoidal: 2535 harmonic: 3618 Sorted by residual: dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual -86.00 -162.01 76.01 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS B 290 " pdb=" SG CYS B 290 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual -86.00 -160.56 74.56 1 1.00e+01 1.00e-02 7.04e+01 dihedral pdb=" CB CYS C 290 " pdb=" SG CYS C 290 " pdb=" SG CYS C 367 " pdb=" CB CYS C 367 " ideal model delta sinusoidal sigma weight residual -86.00 -155.71 69.71 1 1.00e+01 1.00e-02 6.27e+01 ... (remaining 6150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 844 0.026 - 0.052: 423 0.052 - 0.079: 130 0.079 - 0.105: 58 0.105 - 0.131: 21 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE B 381 " pdb=" N ILE B 381 " pdb=" C ILE B 381 " pdb=" CB ILE B 381 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1473 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 233 " 0.006 2.00e-02 2.50e+03 6.97e-03 1.22e+00 pdb=" CG TRP C 233 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP C 233 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 233 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 233 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 233 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 233 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 233 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 233 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 233 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 284 " -0.016 5.00e-02 4.00e+02 2.40e-02 9.24e-01 pdb=" N PRO A 285 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 284 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.69e-01 pdb=" N PRO C 285 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " 0.013 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2500 2.80 - 3.32: 8783 3.32 - 3.85: 15744 3.85 - 4.37: 18956 4.37 - 4.90: 32948 Nonbonded interactions: 78931 Sorted by model distance: nonbonded pdb=" OH TYR A 389 " pdb=" OE1 GLU C 235 " model vdw 2.275 3.040 nonbonded pdb=" OE1 GLU A 235 " pdb=" OH TYR B 389 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLU B 113 " pdb=" NZ LYS B 343 " model vdw 2.286 3.120 nonbonded pdb=" ND2 ASN A 96 " pdb=" O PHE A 98 " model vdw 2.334 3.120 nonbonded pdb=" NH1 ARG B 155 " pdb=" OH TYR B 336 " model vdw 2.341 3.120 ... (remaining 78926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.810 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 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 : 0.002 0.021 10164 Z= 0.089 Angle : 0.427 5.383 13755 Z= 0.214 Chirality : 0.037 0.131 1476 Planarity : 0.002 0.024 1788 Dihedral : 13.820 84.687 3768 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.37 (0.24), residues: 1233 helix: 1.72 (0.26), residues: 366 sheet: 0.17 (0.29), residues: 303 loop : 1.00 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 121 TYR 0.007 0.001 TYR B 342 PHE 0.011 0.001 PHE A 257 TRP 0.018 0.001 TRP C 233 HIS 0.002 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00207 (10143) covalent geometry : angle 0.42024 (13713) SS BOND : bond 0.00203 ( 21) SS BOND : angle 1.38565 ( 42) hydrogen bonds : bond 0.22637 ( 479) hydrogen bonds : angle 8.11751 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8745 (t80) cc_final: 0.8464 (t80) REVERT: A 358 GLN cc_start: 0.9179 (pt0) cc_final: 0.8778 (pm20) REVERT: A 384 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8663 (mtmm) REVERT: A 399 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 418 GLU cc_start: 0.8409 (pt0) cc_final: 0.8122 (pt0) REVERT: B 57 LEU cc_start: 0.9010 (tp) cc_final: 0.8302 (tm) REVERT: B 143 ASN cc_start: 0.8953 (t0) cc_final: 0.8720 (t0) REVERT: B 327 MET cc_start: 0.9121 (mtm) cc_final: 0.8882 (mtt) REVERT: B 355 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8460 (mp0) REVERT: B 375 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8136 (mt-10) REVERT: B 435 ILE cc_start: 0.9154 (pt) cc_final: 0.8931 (pt) REVERT: B 438 GLN cc_start: 0.8994 (mm110) cc_final: 0.8632 (mt0) REVERT: B 439 MET cc_start: 0.8976 (tpp) cc_final: 0.8724 (mmm) REVERT: C 134 GLN cc_start: 0.8287 (mt0) cc_final: 0.7459 (pp30) REVERT: C 136 GLU cc_start: 0.8830 (tt0) cc_final: 0.8497 (tm-30) REVERT: C 204 ARG cc_start: 0.8160 (ptp-170) cc_final: 0.7723 (ptm160) REVERT: C 347 ASP cc_start: 0.8857 (m-30) cc_final: 0.8591 (m-30) REVERT: C 358 GLN cc_start: 0.8791 (pt0) cc_final: 0.8340 (pm20) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.7206 time to fit residues: 137.0378 Evaluate side-chains 100 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084340 restraints weight = 16838.720| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.06 r_work: 0.2814 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10164 Z= 0.175 Angle : 0.586 8.817 13755 Z= 0.308 Chirality : 0.043 0.158 1476 Planarity : 0.003 0.034 1788 Dihedral : 4.071 26.093 1350 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.48 % Allowed : 9.70 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.37 (0.23), residues: 1233 helix: 1.58 (0.26), residues: 402 sheet: 0.11 (0.28), residues: 300 loop : 1.11 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 201 TYR 0.009 0.001 TYR B 195 PHE 0.016 0.001 PHE B 442 TRP 0.008 0.001 TRP B 233 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00400 (10143) covalent geometry : angle 0.58141 (13713) SS BOND : bond 0.00428 ( 21) SS BOND : angle 1.42781 ( 42) hydrogen bonds : bond 0.05394 ( 479) hydrogen bonds : angle 5.63356 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 TYR cc_start: 0.9446 (t80) cc_final: 0.9228 (t80) REVERT: A 384 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8636 (mtmm) REVERT: A 392 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9150 (tptp) REVERT: A 399 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 418 GLU cc_start: 0.8400 (pt0) cc_final: 0.8193 (pt0) REVERT: B 64 ARG cc_start: 0.8113 (mmt180) cc_final: 0.7882 (mmp80) REVERT: B 327 MET cc_start: 0.8866 (mtm) cc_final: 0.8565 (mtt) REVERT: B 344 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: B 355 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8368 (mp0) REVERT: B 375 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7934 (mt-10) REVERT: C 66 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8709 (tm-30) REVERT: C 134 GLN cc_start: 0.8274 (mt0) cc_final: 0.7388 (pp30) REVERT: C 136 GLU cc_start: 0.8877 (tt0) cc_final: 0.8614 (tm-30) REVERT: C 358 GLN cc_start: 0.8831 (pt0) cc_final: 0.8317 (pm20) REVERT: C 421 GLU cc_start: 0.8473 (tt0) cc_final: 0.8074 (tt0) outliers start: 16 outliers final: 5 residues processed: 110 average time/residue: 0.5949 time to fit residues: 69.5980 Evaluate side-chains 101 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 171 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 63 optimal weight: 0.0070 chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS B 143 ASN C 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085171 restraints weight = 16781.068| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.09 r_work: 0.2837 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10164 Z= 0.115 Angle : 0.521 8.504 13755 Z= 0.270 Chirality : 0.041 0.242 1476 Planarity : 0.003 0.034 1788 Dihedral : 4.078 27.679 1350 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.48 % Allowed : 12.28 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.32 (0.24), residues: 1233 helix: 1.62 (0.26), residues: 402 sheet: 0.00 (0.28), residues: 300 loop : 1.07 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 201 TYR 0.009 0.001 TYR C 318 PHE 0.023 0.001 PHE B 50 TRP 0.009 0.001 TRP A 46 HIS 0.002 0.000 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00247 (10143) covalent geometry : angle 0.51723 (13713) SS BOND : bond 0.00290 ( 21) SS BOND : angle 1.22065 ( 42) hydrogen bonds : bond 0.04606 ( 479) hydrogen bonds : angle 5.20592 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8343 (t80) cc_final: 0.8024 (t80) REVERT: A 54 LEU cc_start: 0.8778 (tp) cc_final: 0.8501 (mm) REVERT: A 67 TYR cc_start: 0.9406 (t80) cc_final: 0.9172 (t80) REVERT: A 384 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8598 (mtmm) REVERT: A 392 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9148 (tptm) REVERT: A 399 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 409 ASP cc_start: 0.8357 (t0) cc_final: 0.8147 (t0) REVERT: A 442 PHE cc_start: 0.8426 (t80) cc_final: 0.8145 (t80) REVERT: B 64 ARG cc_start: 0.8104 (mmt180) cc_final: 0.7887 (mmp80) REVERT: B 201 ARG cc_start: 0.8298 (ptm160) cc_final: 0.7729 (ptm-80) REVERT: B 355 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8277 (mp0) REVERT: B 375 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7911 (mt-10) REVERT: C 66 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8700 (tm-30) REVERT: C 134 GLN cc_start: 0.8267 (mt0) cc_final: 0.7387 (pp30) REVERT: C 136 GLU cc_start: 0.8873 (tt0) cc_final: 0.8632 (tm-30) REVERT: C 204 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7839 (ptm160) REVERT: C 358 GLN cc_start: 0.8800 (pt0) cc_final: 0.8291 (pm20) REVERT: C 421 GLU cc_start: 0.8453 (tt0) cc_final: 0.8113 (tt0) outliers start: 16 outliers final: 5 residues processed: 115 average time/residue: 0.5217 time to fit residues: 64.2594 Evaluate side-chains 104 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 204 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 22 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.116381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.084975 restraints weight = 16830.820| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.07 r_work: 0.2826 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10164 Z= 0.136 Angle : 0.517 7.876 13755 Z= 0.265 Chirality : 0.042 0.221 1476 Planarity : 0.003 0.026 1788 Dihedral : 3.961 24.701 1350 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.22 % Allowed : 13.48 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.36 (0.24), residues: 1233 helix: 1.70 (0.26), residues: 405 sheet: -0.06 (0.28), residues: 300 loop : 1.10 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 121 TYR 0.009 0.001 TYR C 318 PHE 0.020 0.001 PHE B 442 TRP 0.010 0.001 TRP A 46 HIS 0.002 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00312 (10143) covalent geometry : angle 0.51351 (13713) SS BOND : bond 0.00288 ( 21) SS BOND : angle 1.16604 ( 42) hydrogen bonds : bond 0.04120 ( 479) hydrogen bonds : angle 5.02742 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8372 (t80) cc_final: 0.7910 (t80) REVERT: A 54 LEU cc_start: 0.8787 (tp) cc_final: 0.8538 (mm) REVERT: A 67 TYR cc_start: 0.9412 (t80) cc_final: 0.9108 (t80) REVERT: A 392 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9147 (tptm) REVERT: A 399 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 57 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8340 (tm) REVERT: B 64 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7902 (mmp80) REVERT: B 201 ARG cc_start: 0.8274 (ptm160) cc_final: 0.7716 (ptm-80) REVERT: B 355 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8313 (mp0) REVERT: B 375 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7932 (mt-10) REVERT: C 66 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8680 (tm-30) REVERT: C 134 GLN cc_start: 0.8283 (mt0) cc_final: 0.7398 (pp30) REVERT: C 136 GLU cc_start: 0.8843 (tt0) cc_final: 0.8618 (tm-30) REVERT: C 204 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7811 (ptm160) REVERT: C 358 GLN cc_start: 0.8807 (pt0) cc_final: 0.8296 (pm20) REVERT: C 421 GLU cc_start: 0.8444 (tt0) cc_final: 0.8117 (tt0) outliers start: 24 outliers final: 8 residues processed: 116 average time/residue: 0.5637 time to fit residues: 69.8906 Evaluate side-chains 108 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 204 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS B 143 ASN C 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085188 restraints weight = 16866.488| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.08 r_work: 0.2828 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10164 Z= 0.123 Angle : 0.506 7.738 13755 Z= 0.260 Chirality : 0.041 0.189 1476 Planarity : 0.003 0.040 1788 Dihedral : 3.965 23.519 1350 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.66 % Allowed : 15.24 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.37 (0.24), residues: 1233 helix: 1.77 (0.26), residues: 405 sheet: -0.10 (0.28), residues: 300 loop : 1.08 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 121 TYR 0.008 0.001 TYR C 318 PHE 0.024 0.001 PHE B 50 TRP 0.010 0.001 TRP A 46 HIS 0.002 0.000 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00280 (10143) covalent geometry : angle 0.50251 (13713) SS BOND : bond 0.00260 ( 21) SS BOND : angle 1.20096 ( 42) hydrogen bonds : bond 0.03893 ( 479) hydrogen bonds : angle 4.92491 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8387 (t80) cc_final: 0.8162 (t80) REVERT: A 67 TYR cc_start: 0.9388 (t80) cc_final: 0.9180 (t80) REVERT: A 384 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8606 (mtmm) REVERT: A 392 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9141 (tptm) REVERT: A 399 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8259 (tm-30) REVERT: B 57 LEU cc_start: 0.8671 (tt) cc_final: 0.8417 (tm) REVERT: B 201 ARG cc_start: 0.8285 (ptm160) cc_final: 0.7745 (ptm-80) REVERT: B 345 CYS cc_start: 0.6324 (OUTLIER) cc_final: 0.6054 (t) REVERT: B 355 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8290 (mp0) REVERT: B 375 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7939 (mt-10) REVERT: C 66 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8657 (tm-30) REVERT: C 134 GLN cc_start: 0.8285 (mt0) cc_final: 0.7413 (pp30) REVERT: C 136 GLU cc_start: 0.8848 (tt0) cc_final: 0.8617 (tm-30) REVERT: C 201 ARG cc_start: 0.8206 (ptp-110) cc_final: 0.7854 (ptp90) REVERT: C 204 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7816 (ptm160) REVERT: C 358 GLN cc_start: 0.8802 (pt0) cc_final: 0.8282 (pm20) REVERT: C 421 GLU cc_start: 0.8440 (tt0) cc_final: 0.8110 (tt0) outliers start: 18 outliers final: 7 residues processed: 111 average time/residue: 0.5334 time to fit residues: 63.0436 Evaluate side-chains 107 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 204 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 0.9990 chunk 107 optimal weight: 0.0070 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.115741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084277 restraints weight = 16857.293| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.06 r_work: 0.2811 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10164 Z= 0.157 Angle : 0.538 8.521 13755 Z= 0.273 Chirality : 0.043 0.316 1476 Planarity : 0.003 0.035 1788 Dihedral : 4.004 22.771 1350 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.22 % Allowed : 16.16 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.43 (0.24), residues: 1233 helix: 1.83 (0.26), residues: 405 sheet: -0.09 (0.28), residues: 297 loop : 1.10 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 64 TYR 0.009 0.001 TYR B 195 PHE 0.018 0.001 PHE B 442 TRP 0.010 0.001 TRP A 46 HIS 0.002 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00369 (10143) covalent geometry : angle 0.53504 (13713) SS BOND : bond 0.00296 ( 21) SS BOND : angle 1.20418 ( 42) hydrogen bonds : bond 0.03847 ( 479) hydrogen bonds : angle 4.81997 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8427 (t80) cc_final: 0.8210 (t80) REVERT: A 67 TYR cc_start: 0.9385 (t80) cc_final: 0.9084 (t80) REVERT: A 392 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9146 (tptm) REVERT: A 399 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 57 LEU cc_start: 0.8648 (tt) cc_final: 0.8359 (tm) REVERT: B 345 CYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6085 (t) REVERT: B 375 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7946 (mt-10) REVERT: C 66 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8680 (tm-30) REVERT: C 134 GLN cc_start: 0.8265 (mt0) cc_final: 0.7413 (pp30) REVERT: C 136 GLU cc_start: 0.8869 (tt0) cc_final: 0.8659 (tm-30) REVERT: C 201 ARG cc_start: 0.8230 (ptp-110) cc_final: 0.7906 (ptp90) REVERT: C 204 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7822 (ptm160) REVERT: C 358 GLN cc_start: 0.8815 (pt0) cc_final: 0.8272 (pm20) REVERT: C 421 GLU cc_start: 0.8438 (tt0) cc_final: 0.8114 (tt0) outliers start: 24 outliers final: 12 residues processed: 110 average time/residue: 0.5186 time to fit residues: 60.9057 Evaluate side-chains 107 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 204 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084953 restraints weight = 16859.052| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.06 r_work: 0.2835 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10164 Z= 0.117 Angle : 0.523 9.646 13755 Z= 0.264 Chirality : 0.042 0.308 1476 Planarity : 0.003 0.032 1788 Dihedral : 3.916 22.051 1350 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.03 % Allowed : 16.71 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.49 (0.24), residues: 1233 helix: 1.91 (0.26), residues: 405 sheet: -0.05 (0.28), residues: 297 loop : 1.12 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 121 TYR 0.008 0.001 TYR B 195 PHE 0.025 0.001 PHE B 50 TRP 0.010 0.001 TRP A 46 HIS 0.002 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00266 (10143) covalent geometry : angle 0.52039 (13713) SS BOND : bond 0.00248 ( 21) SS BOND : angle 1.07658 ( 42) hydrogen bonds : bond 0.03637 ( 479) hydrogen bonds : angle 4.71508 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8393 (t80) cc_final: 0.8162 (t80) REVERT: A 67 TYR cc_start: 0.9383 (t80) cc_final: 0.9146 (t80) REVERT: A 210 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8025 (mpp) REVERT: A 378 MET cc_start: 0.8729 (ptp) cc_final: 0.8429 (mtm) REVERT: A 392 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9146 (tptm) REVERT: A 399 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 57 LEU cc_start: 0.8643 (tt) cc_final: 0.8431 (tm) REVERT: B 345 CYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6135 (t) REVERT: B 375 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7943 (mt-10) REVERT: C 66 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 134 GLN cc_start: 0.8278 (mt0) cc_final: 0.7413 (pp30) REVERT: C 136 GLU cc_start: 0.8865 (tt0) cc_final: 0.8633 (tm-30) REVERT: C 201 ARG cc_start: 0.8222 (ptp-110) cc_final: 0.7916 (ptp90) REVERT: C 204 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7829 (ptm160) REVERT: C 421 GLU cc_start: 0.8429 (tt0) cc_final: 0.8100 (tt0) outliers start: 22 outliers final: 11 residues processed: 115 average time/residue: 0.4945 time to fit residues: 60.9911 Evaluate side-chains 116 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 204 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084684 restraints weight = 16829.122| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.06 r_work: 0.2819 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10164 Z= 0.153 Angle : 0.551 10.262 13755 Z= 0.275 Chirality : 0.042 0.278 1476 Planarity : 0.003 0.052 1788 Dihedral : 3.962 21.766 1350 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.75 % Allowed : 17.27 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.51 (0.24), residues: 1233 helix: 1.82 (0.26), residues: 411 sheet: 0.09 (0.28), residues: 291 loop : 1.11 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 121 TYR 0.009 0.001 TYR B 195 PHE 0.016 0.001 PHE B 442 TRP 0.011 0.001 TRP A 46 HIS 0.002 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00360 (10143) covalent geometry : angle 0.54896 (13713) SS BOND : bond 0.00284 ( 21) SS BOND : angle 1.10267 ( 42) hydrogen bonds : bond 0.03650 ( 479) hydrogen bonds : angle 4.70240 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8433 (t80) cc_final: 0.8202 (t80) REVERT: A 67 TYR cc_start: 0.9400 (t80) cc_final: 0.9137 (t80) REVERT: A 210 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8033 (mpp) REVERT: A 378 MET cc_start: 0.8746 (ptp) cc_final: 0.8447 (mtm) REVERT: A 392 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9160 (tptm) REVERT: A 399 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8263 (tm-30) REVERT: B 345 CYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6199 (t) REVERT: B 375 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7960 (mt-10) REVERT: C 57 LEU cc_start: 0.8980 (tt) cc_final: 0.8615 (pp) REVERT: C 66 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8668 (tm-30) REVERT: C 134 GLN cc_start: 0.8273 (mt0) cc_final: 0.7465 (pp30) REVERT: C 136 GLU cc_start: 0.8863 (tt0) cc_final: 0.8637 (tm-30) REVERT: C 201 ARG cc_start: 0.8224 (ptp-110) cc_final: 0.7923 (ptp90) REVERT: C 204 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7820 (ptm160) REVERT: C 421 GLU cc_start: 0.8440 (tt0) cc_final: 0.8060 (tt0) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 0.5144 time to fit residues: 60.9445 Evaluate side-chains 107 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 204 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 35 optimal weight: 0.0040 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.3130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS B 120 ASN C 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.117544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086314 restraints weight = 16781.852| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.06 r_work: 0.2856 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10164 Z= 0.098 Angle : 0.548 11.181 13755 Z= 0.267 Chirality : 0.042 0.278 1476 Planarity : 0.003 0.053 1788 Dihedral : 3.814 21.109 1350 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.39 % Allowed : 18.01 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.55 (0.24), residues: 1233 helix: 1.98 (0.26), residues: 402 sheet: 0.00 (0.28), residues: 297 loop : 1.12 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 121 TYR 0.010 0.001 TYR C 195 PHE 0.029 0.001 PHE B 50 TRP 0.011 0.001 TRP A 46 HIS 0.002 0.000 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00217 (10143) covalent geometry : angle 0.54632 (13713) SS BOND : bond 0.00213 ( 21) SS BOND : angle 0.99051 ( 42) hydrogen bonds : bond 0.03384 ( 479) hydrogen bonds : angle 4.60407 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8389 (t80) cc_final: 0.8144 (t80) REVERT: A 210 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8019 (mpp) REVERT: A 378 MET cc_start: 0.8696 (ptp) cc_final: 0.8428 (mtm) REVERT: A 392 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9168 (tptm) REVERT: A 399 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 345 CYS cc_start: 0.6423 (OUTLIER) cc_final: 0.6134 (t) REVERT: B 375 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7970 (mt-10) REVERT: C 57 LEU cc_start: 0.8967 (tt) cc_final: 0.8632 (pp) REVERT: C 66 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8667 (tm-30) REVERT: C 134 GLN cc_start: 0.8266 (mt0) cc_final: 0.7450 (pp30) REVERT: C 136 GLU cc_start: 0.8855 (tt0) cc_final: 0.8623 (tm-30) REVERT: C 204 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7851 (ptm160) REVERT: C 421 GLU cc_start: 0.8429 (tt0) cc_final: 0.8068 (tt0) outliers start: 15 outliers final: 7 residues processed: 115 average time/residue: 0.5181 time to fit residues: 64.1043 Evaluate side-chains 112 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 204 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.0060 chunk 121 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.0020 overall best weight: 0.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.120059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088793 restraints weight = 16836.747| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.11 r_work: 0.2874 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10164 Z= 0.095 Angle : 0.557 11.357 13755 Z= 0.269 Chirality : 0.041 0.233 1476 Planarity : 0.003 0.056 1788 Dihedral : 3.738 20.813 1350 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.57 % Allowed : 17.82 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.51 (0.24), residues: 1233 helix: 1.91 (0.26), residues: 402 sheet: 0.03 (0.28), residues: 297 loop : 1.10 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 121 TYR 0.010 0.001 TYR C 195 PHE 0.021 0.001 PHE B 442 TRP 0.010 0.001 TRP A 46 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00205 (10143) covalent geometry : angle 0.55576 (13713) SS BOND : bond 0.00190 ( 21) SS BOND : angle 0.94499 ( 42) hydrogen bonds : bond 0.03294 ( 479) hydrogen bonds : angle 4.57558 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8406 (t80) cc_final: 0.8178 (t80) REVERT: A 210 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.7999 (mpp) REVERT: A 378 MET cc_start: 0.8596 (ptp) cc_final: 0.8357 (mtm) REVERT: A 392 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9182 (tptm) REVERT: A 399 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 327 MET cc_start: 0.8635 (mmm) cc_final: 0.8294 (mtt) REVERT: B 345 CYS cc_start: 0.6420 (OUTLIER) cc_final: 0.6116 (t) REVERT: B 354 VAL cc_start: 0.8930 (t) cc_final: 0.8488 (p) REVERT: B 355 GLU cc_start: 0.7942 (mp0) cc_final: 0.7283 (mp0) REVERT: B 375 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7983 (mt-10) REVERT: B 380 LYS cc_start: 0.8645 (tttm) cc_final: 0.8420 (ttmm) REVERT: C 57 LEU cc_start: 0.8966 (tt) cc_final: 0.8672 (pp) REVERT: C 66 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8654 (tm-30) REVERT: C 134 GLN cc_start: 0.8257 (mt0) cc_final: 0.7434 (pp30) REVERT: C 136 GLU cc_start: 0.8853 (tt0) cc_final: 0.8625 (tm-30) REVERT: C 204 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7874 (ptm160) REVERT: C 421 GLU cc_start: 0.8409 (tt0) cc_final: 0.8119 (tt0) REVERT: C 438 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8259 (mt0) outliers start: 17 outliers final: 7 residues processed: 121 average time/residue: 0.4817 time to fit residues: 62.5846 Evaluate side-chains 112 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain C residue 438 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 0.0010 chunk 77 optimal weight: 0.5980 overall best weight: 0.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.119332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.087051 restraints weight = 16783.466| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.07 r_work: 0.2870 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 10164 Z= 0.165 Angle : 0.880 59.196 13755 Z= 0.502 Chirality : 0.041 0.250 1476 Planarity : 0.004 0.054 1788 Dihedral : 3.749 20.782 1350 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.29 % Allowed : 18.65 % Favored : 80.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 11.11 % 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: 1.51 (0.24), residues: 1233 helix: 1.90 (0.26), residues: 402 sheet: 0.04 (0.28), residues: 297 loop : 1.10 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 145 TYR 0.010 0.001 TYR C 195 PHE 0.021 0.001 PHE B 442 TRP 0.010 0.001 TRP A 46 HIS 0.002 0.000 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00342 (10143) covalent geometry : angle 0.87972 (13713) SS BOND : bond 0.00191 ( 21) SS BOND : angle 0.93391 ( 42) hydrogen bonds : bond 0.03282 ( 479) hydrogen bonds : angle 4.57317 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2812.86 seconds wall clock time: 48 minutes 31.50 seconds (2911.50 seconds total)