Starting phenix.real_space_refine on Mon Jan 20 13:13:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rwk_19549/01_2025/8rwk_19549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rwk_19549/01_2025/8rwk_19549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rwk_19549/01_2025/8rwk_19549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rwk_19549/01_2025/8rwk_19549.map" model { file = "/net/cci-nas-00/data/ceres_data/8rwk_19549/01_2025/8rwk_19549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rwk_19549/01_2025/8rwk_19549.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 44 5.16 5 C 9772 2.51 5 N 2588 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15416 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3806 Classifications: {'peptide': 495} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 473} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 8.03, per 1000 atoms: 0.52 Number of scatterers: 15416 At special positions: 0 Unit cell: (113.3, 115.5, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 12 15.00 O 3000 8.00 N 2588 7.00 C 9772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.92 Conformation dependent library (CDL) restraints added in 2.0 seconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 42.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.589A pdb=" N ARG A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 193 through 207 Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 221 through 227 removed outlier: 3.639A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 247 through 257 removed outlier: 4.057A pdb=" N GLU A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.680A pdb=" N ALA A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 318 Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.875A pdb=" N GLU A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 386 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 105 through 121 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 137 through 156 removed outlier: 3.589A pdb=" N ARG B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 193 through 207 Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.639A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 247 through 257 removed outlier: 4.057A pdb=" N GLU B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 removed outlier: 3.680A pdb=" N ALA B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 318 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.875A pdb=" N GLU B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 386 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 457 through 466 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'C' and resid 80 through 97 Processing helix chain 'C' and resid 105 through 121 Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 137 through 156 removed outlier: 3.590A pdb=" N ARG C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLY C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 193 through 207 Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.639A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 247 through 257 removed outlier: 4.057A pdb=" N GLU C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.680A pdb=" N ALA C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 318 Processing helix chain 'C' and resid 319 through 322 Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.874A pdb=" N GLU C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 386 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 457 through 466 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'D' and resid 80 through 97 Processing helix chain 'D' and resid 105 through 121 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 137 through 156 removed outlier: 3.589A pdb=" N ARG D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 193 through 207 Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.639A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 235 Processing helix chain 'D' and resid 247 through 257 removed outlier: 4.057A pdb=" N GLU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 removed outlier: 3.679A pdb=" N ALA D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 318 Processing helix chain 'D' and resid 319 through 322 Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.875A pdb=" N GLU D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 386 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'D' and resid 500 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 65 removed outlier: 7.179A pdb=" N LYS A 60 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR A 77 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 62 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS A 75 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 64 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 388 through 391 removed outlier: 6.392A pdb=" N VAL B 407 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 330 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE B 432 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 332 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN B 297 " --> pdb=" O TYR B 331 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU B 333 " --> pdb=" O ASN B 297 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL B 299 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA B 451 " --> pdb=" O TRP B 474 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 175 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 175 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL C 473 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LYS D 516 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 475 " --> pdb=" O LYS D 516 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 451 " --> pdb=" O TRP C 474 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASN C 297 " --> pdb=" O TYR C 331 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU C 333 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 299 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 330 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE C 432 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL C 332 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 407 " --> pdb=" O ILE C 390 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 241 through 245 removed outlier: 6.607A pdb=" N CYS A 185 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS A 215 " --> pdb=" O CYS A 185 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN A 187 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 263 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR A 267 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 391 removed outlier: 6.393A pdb=" N VAL A 407 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 330 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 432 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL A 332 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN A 297 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU A 333 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 299 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 451 " --> pdb=" O TRP A 474 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A 473 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS B 516 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 475 " --> pdb=" O LYS B 516 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 175 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 175 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA D 451 " --> pdb=" O TRP D 474 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASN D 297 " --> pdb=" O TYR D 331 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU D 333 " --> pdb=" O ASN D 297 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL D 299 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL D 330 " --> pdb=" O THR D 430 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE D 432 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 332 " --> pdb=" O PHE D 432 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 407 " --> pdb=" O ILE D 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 35 Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 65 removed outlier: 7.179A pdb=" N LYS B 60 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR B 77 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE B 62 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N HIS B 75 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 64 " --> pdb=" O ILE B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.607A pdb=" N CYS B 185 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS B 215 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN B 187 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 263 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR B 267 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 35 Processing sheet with id=AB3, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 65 removed outlier: 7.179A pdb=" N LYS C 60 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR C 77 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 62 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N HIS C 75 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 64 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 241 through 245 removed outlier: 6.606A pdb=" N CYS C 185 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LYS C 215 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN C 187 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 263 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR C 267 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 35 Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AB8, first strand: chain 'D' and resid 60 through 65 removed outlier: 7.179A pdb=" N LYS D 60 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR D 77 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE D 62 " --> pdb=" O HIS D 75 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N HIS D 75 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL D 64 " --> pdb=" O ILE D 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 241 through 245 removed outlier: 6.607A pdb=" N CYS D 185 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS D 215 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN D 187 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 263 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR D 267 " --> pdb=" O ILE D 188 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2016 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: 5.17 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2746 1.31 - 1.45: 4703 1.45 - 1.59: 8191 1.59 - 1.73: 24 1.73 - 1.87: 72 Bond restraints: 15736 Sorted by residual: bond pdb=" C1D NAP D 601 " pdb=" O4D NAP D 601 " ideal model delta sigma weight residual 1.375 1.570 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" C1D NAP C 601 " pdb=" O4D NAP C 601 " ideal model delta sigma weight residual 1.375 1.570 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C1D NAP B 601 " pdb=" O4D NAP B 601 " ideal model delta sigma weight residual 1.375 1.569 -0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" C1D NAP A 601 " pdb=" O4D NAP A 601 " ideal model delta sigma weight residual 1.375 1.569 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C1B NAP A 601 " pdb=" O4B NAP A 601 " ideal model delta sigma weight residual 1.400 1.564 -0.164 2.00e-02 2.50e+03 6.75e+01 ... (remaining 15731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 18111 2.28 - 4.55: 2647 4.55 - 6.83: 473 6.83 - 9.11: 113 9.11 - 11.39: 16 Bond angle restraints: 21360 Sorted by residual: angle pdb=" N PHE D 490 " pdb=" CA PHE D 490 " pdb=" C PHE D 490 " ideal model delta sigma weight residual 111.07 120.82 -9.75 1.07e+00 8.73e-01 8.30e+01 angle pdb=" N PHE C 490 " pdb=" CA PHE C 490 " pdb=" C PHE C 490 " ideal model delta sigma weight residual 111.07 120.80 -9.73 1.07e+00 8.73e-01 8.26e+01 angle pdb=" N PHE B 490 " pdb=" CA PHE B 490 " pdb=" C PHE B 490 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.26e+01 angle pdb=" N PHE A 490 " pdb=" CA PHE A 490 " pdb=" C PHE A 490 " ideal model delta sigma weight residual 111.07 120.78 -9.71 1.07e+00 8.73e-01 8.24e+01 angle pdb=" CA PHE B 432 " pdb=" CB PHE B 432 " pdb=" CG PHE B 432 " ideal model delta sigma weight residual 113.80 121.66 -7.86 1.00e+00 1.00e+00 6.17e+01 ... (remaining 21355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 8946 16.91 - 33.82: 362 33.82 - 50.73: 130 50.73 - 67.65: 98 67.65 - 84.56: 28 Dihedral angle restraints: 9564 sinusoidal: 3912 harmonic: 5652 Sorted by residual: dihedral pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CA PHE A 174 " pdb=" CB PHE A 174 " ideal model delta harmonic sigma weight residual 122.80 107.63 15.17 0 2.50e+00 1.60e-01 3.68e+01 dihedral pdb=" N PHE B 174 " pdb=" C PHE B 174 " pdb=" CA PHE B 174 " pdb=" CB PHE B 174 " ideal model delta harmonic sigma weight residual 122.80 107.66 15.14 0 2.50e+00 1.60e-01 3.67e+01 dihedral pdb=" N PHE C 174 " pdb=" C PHE C 174 " pdb=" CA PHE C 174 " pdb=" CB PHE C 174 " ideal model delta harmonic sigma weight residual 122.80 107.66 15.14 0 2.50e+00 1.60e-01 3.67e+01 ... (remaining 9561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1650 0.095 - 0.190: 617 0.190 - 0.285: 114 0.285 - 0.380: 15 0.380 - 0.475: 4 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CA TYR C 176 " pdb=" N TYR C 176 " pdb=" C TYR C 176 " pdb=" CB TYR C 176 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA TYR B 176 " pdb=" N TYR B 176 " pdb=" C TYR B 176 " pdb=" CB TYR B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA TYR D 176 " pdb=" N TYR D 176 " pdb=" C TYR D 176 " pdb=" CB TYR D 176 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.58e+00 ... (remaining 2397 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 519 " -0.027 2.00e-02 2.50e+03 5.40e-02 2.92e+01 pdb=" C GLU B 519 " 0.093 2.00e-02 2.50e+03 pdb=" O GLU B 519 " -0.034 2.00e-02 2.50e+03 pdb=" OXT GLU B 519 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 519 " 0.027 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C GLU C 519 " -0.093 2.00e-02 2.50e+03 pdb=" O GLU C 519 " 0.033 2.00e-02 2.50e+03 pdb=" OXT GLU C 519 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 519 " -0.027 2.00e-02 2.50e+03 5.37e-02 2.89e+01 pdb=" C GLU A 519 " 0.093 2.00e-02 2.50e+03 pdb=" O GLU A 519 " -0.033 2.00e-02 2.50e+03 pdb=" OXT GLU A 519 " -0.033 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3468 2.77 - 3.31: 14724 3.31 - 3.84: 24282 3.84 - 4.37: 29523 4.37 - 4.90: 48523 Nonbonded interactions: 120520 Sorted by model distance: nonbonded pdb=" NZ LYS C 307 " pdb=" OD2 ASP D 518 " model vdw 2.244 3.120 nonbonded pdb=" OE1 GLU D 218 " pdb=" O3X NAP D 601 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU C 218 " pdb=" O3X NAP C 601 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU A 218 " pdb=" O3X NAP A 601 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLU B 218 " pdb=" O3X NAP B 601 " model vdw 2.304 3.040 ... (remaining 120515 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.970 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 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 : 0.020 0.195 15736 Z= 1.308 Angle : 1.766 11.387 21360 Z= 1.169 Chirality : 0.097 0.475 2400 Planarity : 0.008 0.054 2744 Dihedral : 13.757 84.557 5956 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1972 helix: -0.34 (0.18), residues: 736 sheet: 0.51 (0.23), residues: 432 loop : 0.71 (0.25), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.011 TRP D 100 HIS 0.010 0.003 HIS B 75 PHE 0.027 0.006 PHE C 48 TYR 0.034 0.008 TYR A 230 ARG 0.007 0.001 ARG D 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7907 (mm) cc_final: 0.7669 (mt) REVERT: A 75 HIS cc_start: 0.7077 (m-70) cc_final: 0.6496 (m170) REVERT: A 89 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6636 (mm-40) REVERT: A 161 LYS cc_start: 0.6823 (mmtm) cc_final: 0.5849 (mtpt) REVERT: A 428 THR cc_start: 0.8162 (m) cc_final: 0.7914 (p) REVERT: A 446 GLU cc_start: 0.6794 (mp0) cc_final: 0.6137 (pm20) REVERT: A 498 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6616 (mt-10) REVERT: B 75 HIS cc_start: 0.7260 (m-70) cc_final: 0.6801 (m170) REVERT: B 80 ARG cc_start: 0.6485 (mmm-85) cc_final: 0.4805 (mmm-85) REVERT: B 89 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6676 (mp10) REVERT: B 161 LYS cc_start: 0.6653 (mmtm) cc_final: 0.6128 (mtpt) REVERT: B 166 MET cc_start: 0.7972 (tpt) cc_final: 0.7334 (tpp) REVERT: B 343 GLU cc_start: 0.7840 (tp30) cc_final: 0.7496 (tp30) REVERT: B 428 THR cc_start: 0.8113 (m) cc_final: 0.7854 (p) REVERT: B 446 GLU cc_start: 0.6696 (mp0) cc_final: 0.6119 (pm20) REVERT: B 498 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6623 (mt-10) REVERT: C 29 MET cc_start: 0.5882 (mmp) cc_final: 0.5637 (tmm) REVERT: C 63 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6430 (mt-10) REVERT: C 83 ASP cc_start: 0.6601 (m-30) cc_final: 0.6305 (m-30) REVERT: C 138 ILE cc_start: 0.8060 (tp) cc_final: 0.7785 (tp) REVERT: C 253 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6949 (mm-30) REVERT: C 297 ASN cc_start: 0.8539 (m-40) cc_final: 0.7920 (m-40) REVERT: C 369 GLN cc_start: 0.7175 (pm20) cc_final: 0.6677 (tt0) REVERT: C 497 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7392 (mpt180) REVERT: C 498 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6995 (mm-30) REVERT: C 504 LEU cc_start: 0.7849 (mt) cc_final: 0.7345 (tp) REVERT: D 29 MET cc_start: 0.5608 (mmp) cc_final: 0.5168 (tmm) REVERT: D 40 GLU cc_start: 0.6561 (tp30) cc_final: 0.6175 (pm20) REVERT: D 65 ILE cc_start: 0.7817 (mm) cc_final: 0.7499 (tt) REVERT: D 83 ASP cc_start: 0.6808 (m-30) cc_final: 0.6557 (m-30) REVERT: D 138 ILE cc_start: 0.8088 (tp) cc_final: 0.7817 (tp) REVERT: D 213 VAL cc_start: 0.8532 (t) cc_final: 0.8095 (p) REVERT: D 250 ILE cc_start: 0.6942 (mt) cc_final: 0.6742 (mm) REVERT: D 275 HIS cc_start: 0.6644 (t70) cc_final: 0.6185 (t-170) REVERT: D 369 GLN cc_start: 0.7198 (pm20) cc_final: 0.6737 (tp40) REVERT: D 428 THR cc_start: 0.7965 (m) cc_final: 0.7762 (p) REVERT: D 431 LYS cc_start: 0.7087 (mttt) cc_final: 0.6698 (ptmt) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.3146 time to fit residues: 250.3567 Evaluate side-chains 258 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 371 GLN A 483 HIS A 491 ASN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 75 HIS B 371 GLN B 483 HIS B 491 ASN C 363 GLN C 384 ASN C 491 ASN D 297 ASN D 491 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.159408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139116 restraints weight = 20521.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140085 restraints weight = 17859.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141607 restraints weight = 14589.168| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15736 Z= 0.214 Angle : 0.660 7.634 21360 Z= 0.365 Chirality : 0.047 0.231 2400 Planarity : 0.005 0.037 2744 Dihedral : 12.679 79.906 2376 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.69 % Allowed : 11.19 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1972 helix: 0.93 (0.19), residues: 740 sheet: 0.84 (0.23), residues: 468 loop : 0.33 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 198 HIS 0.004 0.001 HIS C 75 PHE 0.026 0.002 PHE C 340 TYR 0.018 0.002 TYR D 337 ARG 0.009 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7618 (mm) cc_final: 0.7410 (mt) REVERT: A 166 MET cc_start: 0.7911 (tpp) cc_final: 0.7325 (tpp) REVERT: A 179 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7936 (mtt180) REVERT: A 289 LEU cc_start: 0.7948 (pp) cc_final: 0.7571 (mt) REVERT: A 338 ASP cc_start: 0.5961 (OUTLIER) cc_final: 0.5708 (t70) REVERT: B 161 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7552 (tptp) REVERT: B 166 MET cc_start: 0.7662 (tpt) cc_final: 0.7226 (tpp) REVERT: B 179 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7858 (mtt180) REVERT: B 338 ASP cc_start: 0.5946 (OUTLIER) cc_final: 0.5676 (t0) REVERT: C 213 VAL cc_start: 0.8750 (t) cc_final: 0.8478 (p) REVERT: C 253 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6907 (mm-30) REVERT: C 275 HIS cc_start: 0.7556 (m-70) cc_final: 0.6883 (t70) REVERT: C 297 ASN cc_start: 0.8808 (m-40) cc_final: 0.8381 (m-40) REVERT: C 431 LYS cc_start: 0.6638 (mttt) cc_final: 0.6435 (ptmm) REVERT: D 29 MET cc_start: 0.5802 (mmp) cc_final: 0.5416 (tmm) REVERT: D 41 TYR cc_start: 0.4394 (t80) cc_final: 0.3855 (t80) REVERT: D 166 MET cc_start: 0.6768 (tpp) cc_final: 0.5876 (tpp) REVERT: D 213 VAL cc_start: 0.8906 (t) cc_final: 0.8662 (p) REVERT: D 316 ILE cc_start: 0.8511 (tp) cc_final: 0.8300 (tp) REVERT: D 351 ILE cc_start: 0.7475 (tp) cc_final: 0.7149 (mt) REVERT: D 406 THR cc_start: 0.7254 (OUTLIER) cc_final: 0.7033 (p) REVERT: D 415 MET cc_start: 0.8016 (mtp) cc_final: 0.7729 (ttp) outliers start: 44 outliers final: 23 residues processed: 336 average time/residue: 0.2773 time to fit residues: 139.0393 Evaluate side-chains 231 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 459 ASN A 469 ASN B 469 ASN C 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.146817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125834 restraints weight = 21081.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127193 restraints weight = 16749.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128902 restraints weight = 14053.298| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15736 Z= 0.287 Angle : 0.626 5.717 21360 Z= 0.351 Chirality : 0.047 0.160 2400 Planarity : 0.005 0.055 2744 Dihedral : 10.699 77.452 2376 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.18 % Allowed : 14.12 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1972 helix: 0.91 (0.19), residues: 772 sheet: 0.43 (0.24), residues: 480 loop : -0.21 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 200 HIS 0.008 0.001 HIS B 454 PHE 0.020 0.002 PHE D 340 TYR 0.021 0.002 TYR C 230 ARG 0.003 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7589 (mm) cc_final: 0.7261 (mt) REVERT: A 134 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6659 (m110) REVERT: A 166 MET cc_start: 0.8266 (tpp) cc_final: 0.8065 (tpp) REVERT: A 337 TYR cc_start: 0.7402 (t80) cc_final: 0.7007 (t80) REVERT: C 129 ILE cc_start: 0.8707 (mt) cc_final: 0.8026 (mt) REVERT: C 253 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6872 (mm-30) REVERT: C 297 ASN cc_start: 0.9018 (m-40) cc_final: 0.8572 (m-40) REVERT: C 369 GLN cc_start: 0.7394 (pm20) cc_final: 0.6066 (tm-30) REVERT: D 41 TYR cc_start: 0.4552 (t80) cc_final: 0.4139 (t80) REVERT: D 166 MET cc_start: 0.7163 (tpp) cc_final: 0.6878 (tpp) REVERT: D 343 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: D 369 GLN cc_start: 0.7220 (pm20) cc_final: 0.6138 (tm-30) REVERT: D 415 MET cc_start: 0.8047 (mtp) cc_final: 0.7785 (ttp) REVERT: D 431 LYS cc_start: 0.7148 (ptmt) cc_final: 0.6764 (ptmm) outliers start: 52 outliers final: 35 residues processed: 268 average time/residue: 0.2706 time to fit residues: 107.7258 Evaluate side-chains 223 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 93 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 119 optimal weight: 0.0870 chunk 129 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 469 ASN B 440 ASN B 469 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133825 restraints weight = 20582.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134695 restraints weight = 20009.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136215 restraints weight = 17417.781| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15736 Z= 0.165 Angle : 0.511 4.890 21360 Z= 0.285 Chirality : 0.044 0.169 2400 Planarity : 0.004 0.051 2744 Dihedral : 9.227 74.592 2376 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.63 % Allowed : 16.20 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1972 helix: 1.38 (0.20), residues: 744 sheet: 0.56 (0.23), residues: 476 loop : -0.24 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 198 HIS 0.003 0.001 HIS B 454 PHE 0.013 0.001 PHE C 340 TYR 0.019 0.001 TYR C 337 ARG 0.005 0.000 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7440 (mm) cc_final: 0.7068 (mt) REVERT: A 276 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8640 (mm) REVERT: A 337 TYR cc_start: 0.7501 (t80) cc_final: 0.7109 (t80) REVERT: A 469 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7438 (p0) REVERT: B 276 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8571 (mm) REVERT: B 469 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7446 (p0) REVERT: C 41 TYR cc_start: 0.5005 (t80) cc_final: 0.4490 (t80) REVERT: C 129 ILE cc_start: 0.8679 (mt) cc_final: 0.8057 (mt) REVERT: C 166 MET cc_start: 0.6668 (tpp) cc_final: 0.5793 (tpp) REVERT: C 213 VAL cc_start: 0.8912 (t) cc_final: 0.8651 (p) REVERT: C 253 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6589 (mm-30) REVERT: C 257 ASN cc_start: 0.8008 (m-40) cc_final: 0.7717 (m110) REVERT: C 278 GLN cc_start: 0.7133 (mm110) cc_final: 0.6773 (tm-30) REVERT: C 297 ASN cc_start: 0.8953 (m-40) cc_final: 0.8468 (m-40) REVERT: C 369 GLN cc_start: 0.7073 (pm20) cc_final: 0.6069 (tm-30) REVERT: D 41 TYR cc_start: 0.4749 (t80) cc_final: 0.4304 (t80) REVERT: D 166 MET cc_start: 0.6905 (tpp) cc_final: 0.5802 (tpp) REVERT: D 369 GLN cc_start: 0.7200 (pm20) cc_final: 0.6244 (tm-30) REVERT: D 404 LYS cc_start: 0.8212 (mttm) cc_final: 0.7703 (mttt) REVERT: D 415 MET cc_start: 0.7921 (mtp) cc_final: 0.7694 (ttp) REVERT: D 431 LYS cc_start: 0.7143 (ptmt) cc_final: 0.6831 (ptmm) outliers start: 43 outliers final: 22 residues processed: 245 average time/residue: 0.2673 time to fit residues: 99.6577 Evaluate side-chains 217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 29 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN B 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127194 restraints weight = 21080.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128150 restraints weight = 17306.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.129055 restraints weight = 16152.615| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15736 Z= 0.225 Angle : 0.532 4.918 21360 Z= 0.295 Chirality : 0.044 0.160 2400 Planarity : 0.004 0.053 2744 Dihedral : 8.843 73.033 2376 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.57 % Allowed : 16.81 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1972 helix: 1.28 (0.20), residues: 772 sheet: 0.64 (0.24), residues: 468 loop : -0.65 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 198 HIS 0.005 0.001 HIS B 454 PHE 0.013 0.001 PHE A 193 TYR 0.018 0.002 TYR C 337 ARG 0.005 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7610 (mm) cc_final: 0.7291 (mt) REVERT: A 276 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 337 TYR cc_start: 0.7572 (t80) cc_final: 0.7139 (t80) REVERT: B 276 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8581 (mm) REVERT: C 166 MET cc_start: 0.6859 (tpp) cc_final: 0.5710 (tpp) REVERT: C 278 GLN cc_start: 0.7095 (mm110) cc_final: 0.6720 (tm-30) REVERT: C 369 GLN cc_start: 0.7293 (pm20) cc_final: 0.6337 (tm-30) REVERT: D 41 TYR cc_start: 0.4830 (t80) cc_final: 0.4275 (t80) REVERT: D 369 GLN cc_start: 0.7364 (pm20) cc_final: 0.6289 (tm-30) REVERT: D 431 LYS cc_start: 0.7462 (ptmt) cc_final: 0.7137 (ptmm) outliers start: 42 outliers final: 30 residues processed: 231 average time/residue: 0.2492 time to fit residues: 89.7320 Evaluate side-chains 222 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN D 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.146726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126270 restraints weight = 20851.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127429 restraints weight = 16913.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128801 restraints weight = 15432.674| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15736 Z= 0.206 Angle : 0.516 5.974 21360 Z= 0.287 Chirality : 0.044 0.158 2400 Planarity : 0.004 0.049 2744 Dihedral : 8.417 71.417 2376 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.38 % Allowed : 17.79 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1972 helix: 1.40 (0.20), residues: 748 sheet: 0.58 (0.24), residues: 468 loop : -0.76 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.005 0.001 HIS B 454 PHE 0.011 0.001 PHE A 193 TYR 0.017 0.002 TYR D 277 ARG 0.004 0.000 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7674 (mm) cc_final: 0.7324 (mt) REVERT: A 276 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8678 (mm) REVERT: A 337 TYR cc_start: 0.7549 (t80) cc_final: 0.7116 (t80) REVERT: A 383 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6210 (ttpp) REVERT: B 54 VAL cc_start: 0.7686 (m) cc_final: 0.7416 (p) REVERT: B 276 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8570 (mm) REVERT: C 166 MET cc_start: 0.6914 (tpp) cc_final: 0.5629 (tpp) REVERT: C 278 GLN cc_start: 0.7207 (mm110) cc_final: 0.6796 (tm-30) REVERT: C 369 GLN cc_start: 0.7357 (pm20) cc_final: 0.6574 (tm-30) REVERT: D 41 TYR cc_start: 0.4931 (t80) cc_final: 0.4254 (t80) REVERT: D 369 GLN cc_start: 0.7356 (pm20) cc_final: 0.6162 (tm-30) REVERT: D 431 LYS cc_start: 0.7635 (ptmt) cc_final: 0.7404 (ptmm) outliers start: 39 outliers final: 30 residues processed: 231 average time/residue: 0.2510 time to fit residues: 89.8138 Evaluate side-chains 220 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN B 134 ASN B 192 ASN D 278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122482 restraints weight = 21179.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123847 restraints weight = 17235.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125684 restraints weight = 14569.673| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15736 Z= 0.318 Angle : 0.615 5.897 21360 Z= 0.338 Chirality : 0.047 0.358 2400 Planarity : 0.005 0.051 2744 Dihedral : 8.702 74.243 2376 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.18 % Allowed : 18.03 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1972 helix: 1.18 (0.19), residues: 748 sheet: 0.38 (0.25), residues: 456 loop : -1.08 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 474 HIS 0.008 0.001 HIS B 454 PHE 0.019 0.002 PHE A 193 TYR 0.022 0.002 TYR C 230 ARG 0.003 0.001 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7746 (mm) cc_final: 0.7413 (mt) REVERT: A 276 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 337 TYR cc_start: 0.7615 (t80) cc_final: 0.7140 (t80) REVERT: A 383 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.6268 (ttpp) REVERT: B 134 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.6705 (m-40) REVERT: B 276 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8593 (mm) REVERT: C 278 GLN cc_start: 0.7472 (mm110) cc_final: 0.7073 (tm-30) REVERT: C 310 GLN cc_start: 0.6615 (mm-40) cc_final: 0.6121 (tp-100) REVERT: C 369 GLN cc_start: 0.7334 (pm20) cc_final: 0.6467 (tm-30) REVERT: D 369 GLN cc_start: 0.7409 (pm20) cc_final: 0.6149 (tm-30) REVERT: D 517 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7902 (mp) outliers start: 52 outliers final: 37 residues processed: 235 average time/residue: 0.2542 time to fit residues: 91.3866 Evaluate side-chains 223 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN B 134 ASN B 366 GLN D 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.144556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124542 restraints weight = 20775.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.125172 restraints weight = 16827.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126361 restraints weight = 15611.718| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15736 Z= 0.210 Angle : 0.532 5.945 21360 Z= 0.294 Chirality : 0.045 0.315 2400 Planarity : 0.004 0.050 2744 Dihedral : 8.352 72.283 2376 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.44 % Allowed : 18.70 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1972 helix: 1.28 (0.20), residues: 752 sheet: 0.48 (0.25), residues: 464 loop : -1.01 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 198 HIS 0.003 0.001 HIS B 454 PHE 0.014 0.001 PHE A 432 TYR 0.014 0.002 TYR C 447 ARG 0.004 0.000 ARG D 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7726 (mm) cc_final: 0.7384 (mt) REVERT: A 276 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8631 (mm) REVERT: A 337 TYR cc_start: 0.7532 (t80) cc_final: 0.7150 (t80) REVERT: A 383 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6258 (ttpp) REVERT: B 54 VAL cc_start: 0.7726 (m) cc_final: 0.7487 (p) REVERT: B 134 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.6801 (m-40) REVERT: B 276 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8603 (mm) REVERT: C 278 GLN cc_start: 0.7385 (mm110) cc_final: 0.7072 (tm-30) REVERT: C 310 GLN cc_start: 0.6633 (mm-40) cc_final: 0.6096 (tp-100) REVERT: C 369 GLN cc_start: 0.7166 (pm20) cc_final: 0.6590 (tm-30) REVERT: D 369 GLN cc_start: 0.7318 (pm20) cc_final: 0.6016 (tm-30) REVERT: D 517 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7885 (mp) outliers start: 40 outliers final: 31 residues processed: 226 average time/residue: 0.2599 time to fit residues: 89.5365 Evaluate side-chains 225 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 193 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125813 restraints weight = 20781.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126555 restraints weight = 16626.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127971 restraints weight = 15500.947| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15736 Z= 0.179 Angle : 0.511 5.451 21360 Z= 0.283 Chirality : 0.044 0.306 2400 Planarity : 0.004 0.051 2744 Dihedral : 8.082 70.431 2376 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.38 % Allowed : 19.13 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1972 helix: 1.45 (0.20), residues: 748 sheet: 0.55 (0.25), residues: 468 loop : -1.03 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 200 HIS 0.002 0.001 HIS B 454 PHE 0.012 0.001 PHE B 193 TYR 0.012 0.001 TYR C 277 ARG 0.006 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7677 (mm) cc_final: 0.7341 (mt) REVERT: A 276 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 383 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.6115 (ttpp) REVERT: B 54 VAL cc_start: 0.7730 (m) cc_final: 0.7505 (p) REVERT: B 276 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8596 (mm) REVERT: C 278 GLN cc_start: 0.7363 (mm110) cc_final: 0.7036 (tm-30) REVERT: C 310 GLN cc_start: 0.6604 (mm-40) cc_final: 0.6095 (tp-100) REVERT: C 369 GLN cc_start: 0.7153 (pm20) cc_final: 0.6578 (tm-30) REVERT: D 166 MET cc_start: 0.6856 (tpp) cc_final: 0.5733 (tpp) REVERT: D 310 GLN cc_start: 0.6680 (mm-40) cc_final: 0.6438 (tm-30) REVERT: D 369 GLN cc_start: 0.7310 (pm20) cc_final: 0.5835 (tm-30) outliers start: 39 outliers final: 33 residues processed: 227 average time/residue: 0.2545 time to fit residues: 88.2173 Evaluate side-chains 230 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.141243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.121521 restraints weight = 21312.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121654 restraints weight = 17656.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.123666 restraints weight = 15698.257| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15736 Z= 0.358 Angle : 0.644 9.114 21360 Z= 0.352 Chirality : 0.048 0.296 2400 Planarity : 0.005 0.055 2744 Dihedral : 8.595 74.493 2376 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.51 % Allowed : 19.19 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1972 helix: 1.12 (0.19), residues: 748 sheet: 0.24 (0.25), residues: 456 loop : -1.27 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 198 HIS 0.006 0.001 HIS B 454 PHE 0.021 0.002 PHE B 193 TYR 0.021 0.003 TYR B 277 ARG 0.007 0.001 ARG D 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7858 (mm) cc_final: 0.7613 (mt) REVERT: A 166 MET cc_start: 0.7645 (tpp) cc_final: 0.7130 (ttm) REVERT: A 276 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8653 (mm) REVERT: A 337 TYR cc_start: 0.7518 (t80) cc_final: 0.7124 (t80) REVERT: A 383 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6238 (ttpp) REVERT: B 40 GLU cc_start: 0.6065 (tp30) cc_final: 0.5252 (tt0) REVERT: B 166 MET cc_start: 0.7605 (tpp) cc_final: 0.7145 (ttm) REVERT: B 276 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8624 (mm) REVERT: C 65 ILE cc_start: 0.7903 (mm) cc_final: 0.7558 (tt) REVERT: C 78 GLU cc_start: 0.5564 (tp30) cc_final: 0.5271 (tp30) REVERT: C 310 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6102 (tp-100) REVERT: C 369 GLN cc_start: 0.7115 (pm20) cc_final: 0.6432 (tm-30) REVERT: D 369 GLN cc_start: 0.7436 (pm20) cc_final: 0.6073 (tm-30) REVERT: D 416 ARG cc_start: 0.6902 (mtp85) cc_final: 0.6438 (ttp80) REVERT: D 517 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8077 (mp) outliers start: 41 outliers final: 35 residues processed: 221 average time/residue: 0.2591 time to fit residues: 88.2788 Evaluate side-chains 218 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 191 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 0.0010 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125286 restraints weight = 20928.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125999 restraints weight = 16997.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127379 restraints weight = 14849.679| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15736 Z= 0.191 Angle : 0.529 6.672 21360 Z= 0.292 Chirality : 0.045 0.302 2400 Planarity : 0.004 0.059 2744 Dihedral : 8.107 71.058 2376 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 19.80 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1972 helix: 1.36 (0.20), residues: 748 sheet: 0.38 (0.25), residues: 464 loop : -1.16 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 200 HIS 0.002 0.001 HIS C 454 PHE 0.012 0.001 PHE A 62 TYR 0.012 0.001 TYR A 318 ARG 0.006 0.000 ARG D 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3718.17 seconds wall clock time: 68 minutes 15.42 seconds (4095.42 seconds total)