Starting phenix.real_space_refine on Fri Jun 13 17:37:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rwk_19549/06_2025/8rwk_19549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rwk_19549/06_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_19549/06_2025/8rwk_19549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rwk_19549/06_2025/8rwk_19549.map" model { file = "/net/cci-nas-00/data/ceres_data/8rwk_19549/06_2025/8rwk_19549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rwk_19549/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.91, per 1000 atoms: 0.51 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: 3.63 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: 1.94 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: 5.27 Time building geometry restraints manager: 4.31 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: 0.500 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 35.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.680 ------------------------------------------------------------------------------- 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= 1.084 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 Details of bonding type rmsd hydrogen bonds : bond 0.21764 ( 720) hydrogen bonds : angle 7.64217 ( 2016) covalent geometry : bond 0.01999 (15736) covalent geometry : angle 1.76599 (21360) *********************** 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 : 1.777 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: 0.2915 time to fit residues: 232.6686 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 : 1.685 ------------------------------------------------------------------------------- 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 = 0.159407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139112 restraints weight = 20521.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.139974 restraints weight = 17860.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141579 restraints weight = 14600.575| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- 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= 0.163 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 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 720) hydrogen bonds : angle 5.35218 ( 2016) covalent geometry : bond 0.00329 (15736) covalent geometry : angle 0.65988 (21360) *********************** 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 : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7616 (mm) cc_final: 0.7409 (mt) REVERT: A 166 MET cc_start: 0.7909 (tpp) cc_final: 0.7324 (tpp) REVERT: A 179 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7936 (mtt180) REVERT: A 289 LEU cc_start: 0.7945 (pp) cc_final: 0.7570 (mt) REVERT: A 338 ASP cc_start: 0.5960 (OUTLIER) cc_final: 0.5706 (t70) REVERT: B 161 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7552 (tptp) REVERT: B 166 MET cc_start: 0.7658 (tpt) cc_final: 0.7223 (tpp) REVERT: B 179 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7859 (mtt180) REVERT: B 338 ASP cc_start: 0.5944 (OUTLIER) cc_final: 0.5673 (t0) REVERT: C 213 VAL cc_start: 0.8750 (t) cc_final: 0.8477 (p) REVERT: C 253 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6908 (mm-30) REVERT: C 275 HIS cc_start: 0.7554 (m-70) cc_final: 0.6883 (t70) REVERT: C 297 ASN cc_start: 0.8808 (m-40) cc_final: 0.8382 (m-40) REVERT: C 431 LYS cc_start: 0.6635 (mttt) cc_final: 0.6433 (ptmm) REVERT: D 29 MET cc_start: 0.5801 (mmp) cc_final: 0.5418 (tmm) REVERT: D 41 TYR cc_start: 0.4391 (t80) cc_final: 0.3852 (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: 0.8299 (tp) REVERT: D 351 ILE cc_start: 0.7474 (tp) cc_final: 0.7148 (mt) REVERT: D 406 THR cc_start: 0.7254 (OUTLIER) cc_final: 0.7033 (p) REVERT: D 415 MET cc_start: 0.8017 (mtp) cc_final: 0.7730 (ttp) outliers start: 44 outliers final: 23 residues processed: 336 average time/residue: 0.2620 time to fit residues: 131.1147 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 : 1.756 ------------------------------------------------------------------------------- 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: 1.9990 chunk 121 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 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: 0.7980 chunk 63 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.148904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128188 restraints weight = 21010.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129773 restraints weight = 17266.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131096 restraints weight = 14451.543| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15736 Z= 0.174 Angle : 0.596 5.869 21360 Z= 0.334 Chirality : 0.046 0.156 2400 Planarity : 0.004 0.054 2744 Dihedral : 10.529 76.533 2376 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.93 % Allowed : 14.30 % Favored : 82.76 % 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: 0.98 (0.19), residues: 772 sheet: 0.61 (0.23), residues: 476 loop : -0.26 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.006 0.001 HIS B 454 PHE 0.019 0.002 PHE D 340 TYR 0.016 0.002 TYR C 230 ARG 0.002 0.000 ARG D 514 Details of bonding type rmsd hydrogen bonds : bond 0.05477 ( 720) hydrogen bonds : angle 5.06610 ( 2016) covalent geometry : bond 0.00391 (15736) covalent geometry : angle 0.59552 (21360) *********************** 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 277 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7582 (mm) cc_final: 0.7261 (mt) REVERT: A 134 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.6664 (m110) REVERT: A 276 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8638 (mm) REVERT: A 337 TYR cc_start: 0.7517 (t80) cc_final: 0.7157 (t80) REVERT: C 129 ILE cc_start: 0.8724 (mt) cc_final: 0.8100 (mt) REVERT: C 136 LYS cc_start: 0.6839 (tttp) cc_final: 0.6601 (ttpt) REVERT: C 166 MET cc_start: 0.6893 (tpp) cc_final: 0.5727 (tpp) REVERT: C 213 VAL cc_start: 0.8880 (t) cc_final: 0.8570 (p) REVERT: C 253 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6844 (mm-30) REVERT: C 297 ASN cc_start: 0.8982 (m-40) cc_final: 0.8507 (m-40) REVERT: C 369 GLN cc_start: 0.7320 (pm20) cc_final: 0.6022 (tm-30) REVERT: D 41 TYR cc_start: 0.4697 (t80) cc_final: 0.4302 (t80) REVERT: D 166 MET cc_start: 0.7144 (tpp) cc_final: 0.6910 (tpp) REVERT: D 213 VAL cc_start: 0.8934 (t) cc_final: 0.8682 (p) REVERT: D 369 GLN cc_start: 0.7176 (pm20) cc_final: 0.6283 (tm-30) REVERT: D 415 MET cc_start: 0.8023 (mtp) cc_final: 0.7792 (ttp) REVERT: D 431 LYS cc_start: 0.7043 (ptmt) cc_final: 0.6676 (ptmm) outliers start: 48 outliers final: 31 residues processed: 265 average time/residue: 0.2610 time to fit residues: 104.7695 Evaluate side-chains 225 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN 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 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 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: 4.9990 chunk 159 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 62 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 119 optimal weight: 0.0570 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136402 restraints weight = 20554.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.136790 restraints weight = 19938.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.138094 restraints weight = 18463.757| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15736 Z= 0.110 Angle : 0.498 4.856 21360 Z= 0.278 Chirality : 0.043 0.200 2400 Planarity : 0.004 0.049 2744 Dihedral : 8.990 72.904 2376 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.75 % Allowed : 15.34 % Favored : 81.91 % 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: 0.95 (0.20), residues: 1972 helix: 1.45 (0.20), residues: 744 sheet: 0.65 (0.24), residues: 484 loop : -0.11 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 198 HIS 0.002 0.000 HIS B 454 PHE 0.013 0.001 PHE C 340 TYR 0.020 0.001 TYR C 337 ARG 0.003 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 720) hydrogen bonds : angle 4.75858 ( 2016) covalent geometry : bond 0.00233 (15736) covalent geometry : angle 0.49809 (21360) *********************** 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 261 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7435 (mm) cc_final: 0.7071 (mt) REVERT: A 276 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 337 TYR cc_start: 0.7514 (t80) cc_final: 0.7126 (t80) REVERT: B 54 VAL cc_start: 0.7541 (m) cc_final: 0.7303 (p) REVERT: B 276 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8551 (mm) REVERT: C 213 VAL cc_start: 0.8878 (t) cc_final: 0.8659 (p) REVERT: C 253 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6543 (mm-30) REVERT: C 257 ASN cc_start: 0.7975 (m-40) cc_final: 0.7663 (m110) REVERT: C 297 ASN cc_start: 0.8944 (m-40) cc_final: 0.8431 (m-40) REVERT: C 369 GLN cc_start: 0.7068 (pm20) cc_final: 0.6545 (tt0) REVERT: D 41 TYR cc_start: 0.4801 (t80) cc_final: 0.4418 (t80) REVERT: D 166 MET cc_start: 0.6803 (tpp) cc_final: 0.5793 (tpp) REVERT: D 257 ASN cc_start: 0.7922 (m-40) cc_final: 0.7490 (m110) REVERT: D 369 GLN cc_start: 0.7200 (pm20) cc_final: 0.6268 (tm-30) REVERT: D 404 LYS cc_start: 0.8166 (mttm) cc_final: 0.7625 (mttt) REVERT: D 415 MET cc_start: 0.7943 (mtp) cc_final: 0.7697 (ttp) REVERT: D 431 LYS cc_start: 0.6969 (ptmt) cc_final: 0.6614 (ptmm) outliers start: 45 outliers final: 22 residues processed: 250 average time/residue: 0.2522 time to fit residues: 95.9025 Evaluate side-chains 218 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP 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 479 ASN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 502 ASP 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 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: 8.9990 chunk 190 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.130108 restraints weight = 20933.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131343 restraints weight = 17179.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132749 restraints weight = 15273.235| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15736 Z= 0.121 Angle : 0.497 4.884 21360 Z= 0.276 Chirality : 0.043 0.157 2400 Planarity : 0.004 0.049 2744 Dihedral : 8.410 70.302 2376 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.26 % Allowed : 16.93 % Favored : 80.81 % 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: 1.02 (0.20), residues: 1972 helix: 1.62 (0.20), residues: 744 sheet: 0.78 (0.24), residues: 468 loop : -0.25 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 198 HIS 0.004 0.001 HIS B 454 PHE 0.013 0.001 PHE C 340 TYR 0.019 0.002 TYR C 337 ARG 0.011 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 720) hydrogen bonds : angle 4.64848 ( 2016) covalent geometry : bond 0.00272 (15736) covalent geometry : angle 0.49717 (21360) *********************** 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 252 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7559 (mm) cc_final: 0.7175 (mt) REVERT: A 166 MET cc_start: 0.7449 (tpp) cc_final: 0.7202 (ttm) REVERT: A 276 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8652 (mm) REVERT: A 337 TYR cc_start: 0.7583 (t80) cc_final: 0.7111 (t80) REVERT: B 54 VAL cc_start: 0.7625 (m) cc_final: 0.7371 (p) REVERT: B 276 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8549 (mm) REVERT: C 166 MET cc_start: 0.6503 (tpp) cc_final: 0.5647 (tpp) REVERT: C 213 VAL cc_start: 0.8899 (t) cc_final: 0.8639 (p) REVERT: C 253 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6592 (mm-30) REVERT: C 257 ASN cc_start: 0.8103 (m-40) cc_final: 0.7638 (m110) REVERT: C 278 GLN cc_start: 0.7067 (mm110) cc_final: 0.6698 (tm-30) REVERT: C 297 ASN cc_start: 0.8999 (m-40) cc_final: 0.8495 (m-40) REVERT: C 369 GLN cc_start: 0.7321 (pm20) cc_final: 0.6228 (tm-30) REVERT: D 41 TYR cc_start: 0.4771 (t80) cc_final: 0.4330 (t80) REVERT: D 257 ASN cc_start: 0.7971 (m-40) cc_final: 0.7499 (m110) REVERT: D 278 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6793 (mp10) REVERT: D 369 GLN cc_start: 0.7333 (pm20) cc_final: 0.6267 (tm-30) REVERT: D 415 MET cc_start: 0.8013 (mtp) cc_final: 0.7709 (ttp) REVERT: D 431 LYS cc_start: 0.7254 (ptmt) cc_final: 0.6935 (ptmm) outliers start: 37 outliers final: 28 residues processed: 239 average time/residue: 0.2618 time to fit residues: 94.1857 Evaluate side-chains 226 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 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 A residue 502 ASP 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 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 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: 7.9990 chunk 171 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129517 restraints weight = 20686.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130883 restraints weight = 17150.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132570 restraints weight = 14790.246| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15736 Z= 0.116 Angle : 0.486 5.752 21360 Z= 0.270 Chirality : 0.043 0.157 2400 Planarity : 0.004 0.048 2744 Dihedral : 8.185 68.664 2376 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.51 % Allowed : 17.73 % Favored : 79.77 % 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: 0.95 (0.20), residues: 1972 helix: 1.64 (0.20), residues: 744 sheet: 0.63 (0.24), residues: 484 loop : -0.34 (0.24), residues: 744 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 0.015 0.001 PHE C 340 TYR 0.015 0.001 TYR C 337 ARG 0.009 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 720) hydrogen bonds : angle 4.59795 ( 2016) covalent geometry : bond 0.00262 (15736) covalent geometry : angle 0.48637 (21360) *********************** 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 251 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7576 (mm) cc_final: 0.7197 (mt) REVERT: A 276 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8635 (mm) REVERT: A 337 TYR cc_start: 0.7588 (t80) cc_final: 0.7182 (t80) REVERT: A 383 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.6135 (ttpp) REVERT: B 54 VAL cc_start: 0.7674 (m) cc_final: 0.7415 (p) REVERT: B 276 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8561 (mm) REVERT: B 469 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7576 (p0) REVERT: C 166 MET cc_start: 0.6604 (tpp) cc_final: 0.5569 (tpp) REVERT: C 253 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6446 (mm-30) REVERT: C 257 ASN cc_start: 0.8101 (m-40) cc_final: 0.7668 (m110) REVERT: C 278 GLN cc_start: 0.7037 (mm110) cc_final: 0.6587 (tm-30) REVERT: C 297 ASN cc_start: 0.9002 (m-40) cc_final: 0.8524 (m-40) REVERT: C 369 GLN cc_start: 0.7285 (pm20) cc_final: 0.6438 (tm-30) REVERT: D 41 TYR cc_start: 0.4911 (t80) cc_final: 0.4347 (t80) REVERT: D 166 MET cc_start: 0.6651 (tpp) cc_final: 0.5880 (tpp) REVERT: D 369 GLN cc_start: 0.7329 (pm20) cc_final: 0.6243 (tm-30) REVERT: D 415 MET cc_start: 0.7987 (mtp) cc_final: 0.7748 (ttp) REVERT: D 431 LYS cc_start: 0.7446 (ptmt) cc_final: 0.7105 (ptmm) outliers start: 41 outliers final: 29 residues processed: 239 average time/residue: 0.2474 time to fit residues: 90.4539 Evaluate side-chains 229 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 479 ASN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 502 ASP 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 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 438 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 45 THR 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: 4.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 469 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 = 0.3557 r_free = 0.3557 target = 0.142150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121598 restraints weight = 21216.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122504 restraints weight = 17121.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.124055 restraints weight = 14983.487| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15736 Z= 0.229 Angle : 0.649 6.142 21360 Z= 0.358 Chirality : 0.048 0.171 2400 Planarity : 0.005 0.052 2744 Dihedral : 8.829 74.407 2376 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.36 % Allowed : 17.79 % 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: 0.12 (0.19), residues: 1972 helix: 1.06 (0.19), residues: 752 sheet: 0.41 (0.25), residues: 460 loop : -1.09 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 474 HIS 0.008 0.002 HIS B 454 PHE 0.022 0.002 PHE B 344 TYR 0.028 0.003 TYR C 41 ARG 0.004 0.001 ARG B 467 Details of bonding type rmsd hydrogen bonds : bond 0.06078 ( 720) hydrogen bonds : angle 5.02723 ( 2016) covalent geometry : bond 0.00543 (15736) covalent geometry : angle 0.64906 (21360) *********************** 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 258 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7753 (mm) cc_final: 0.7426 (mt) REVERT: A 337 TYR cc_start: 0.7679 (t80) cc_final: 0.7220 (t80) REVERT: A 383 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6289 (ttpp) REVERT: B 89 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6352 (mp10) REVERT: B 166 MET cc_start: 0.7943 (tpp) cc_final: 0.7060 (ttm) REVERT: B 276 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8618 (mm) REVERT: B 463 LYS cc_start: 0.7762 (tttt) cc_final: 0.7478 (ttpt) REVERT: C 310 GLN cc_start: 0.6751 (mm-40) cc_final: 0.6155 (tp-100) REVERT: C 369 GLN cc_start: 0.7447 (pm20) cc_final: 0.6484 (tm-30) REVERT: D 369 GLN cc_start: 0.7416 (pm20) cc_final: 0.6209 (tm-30) REVERT: D 394 GLU cc_start: 0.6435 (mp0) cc_final: 0.6148 (mp0) REVERT: D 431 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7608 (ptmm) outliers start: 55 outliers final: 40 residues processed: 240 average time/residue: 0.2515 time to fit residues: 94.1271 Evaluate side-chains 227 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 418 VAL 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 69 THR Chi-restraints excluded: chain B residue 89 GLN 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 316 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 255 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 427 VAL 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 287 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 184 optimal weight: 0.0980 chunk 52 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN B 134 ASN D 278 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 = 0.3588 r_free = 0.3588 target = 0.144767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124487 restraints weight = 20758.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125304 restraints weight = 17175.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126789 restraints weight = 15801.907| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15736 Z= 0.155 Angle : 0.552 7.774 21360 Z= 0.304 Chirality : 0.045 0.180 2400 Planarity : 0.004 0.053 2744 Dihedral : 8.420 72.161 2376 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.69 % Allowed : 19.13 % Favored : 78.18 % 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: 0.41 (0.19), residues: 1972 helix: 1.41 (0.20), residues: 724 sheet: 0.41 (0.24), residues: 468 loop : -0.86 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 198 HIS 0.004 0.001 HIS B 454 PHE 0.014 0.001 PHE A 432 TYR 0.022 0.002 TYR C 41 ARG 0.005 0.000 ARG D 467 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 720) hydrogen bonds : angle 4.78495 ( 2016) covalent geometry : bond 0.00361 (15736) covalent geometry : angle 0.55170 (21360) *********************** 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 243 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7749 (mm) cc_final: 0.7399 (mt) REVERT: A 166 MET cc_start: 0.7631 (tpp) cc_final: 0.7080 (ttm) REVERT: A 276 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 337 TYR cc_start: 0.7572 (t80) cc_final: 0.7140 (t80) REVERT: B 134 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.6679 (m-40) REVERT: B 276 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 463 LYS cc_start: 0.7723 (tttt) cc_final: 0.7513 (ttpt) REVERT: C 310 GLN cc_start: 0.6762 (mm-40) cc_final: 0.6169 (tp-100) REVERT: C 369 GLN cc_start: 0.7226 (pm20) cc_final: 0.6537 (tm-30) REVERT: D 310 GLN cc_start: 0.6678 (mm-40) cc_final: 0.6436 (tm-30) REVERT: D 369 GLN cc_start: 0.7349 (pm20) cc_final: 0.5972 (tm-30) REVERT: D 394 GLU cc_start: 0.6179 (mp0) cc_final: 0.5878 (mp0) outliers start: 44 outliers final: 34 residues processed: 229 average time/residue: 0.2519 time to fit residues: 89.9123 Evaluate side-chains 219 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 411 VAL Chi-restraints excluded: chain A residue 418 VAL 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 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 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 304 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 415 MET 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN B 134 ASN B 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125710 restraints weight = 20726.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126763 restraints weight = 16856.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128531 restraints weight = 14567.568| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15736 Z= 0.128 Angle : 0.525 6.133 21360 Z= 0.289 Chirality : 0.044 0.158 2400 Planarity : 0.004 0.052 2744 Dihedral : 8.157 70.921 2376 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.63 % Allowed : 19.38 % Favored : 78.00 % 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: 0.58 (0.20), residues: 1972 helix: 1.54 (0.20), residues: 724 sheet: 0.52 (0.25), residues: 464 loop : -0.76 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 200 HIS 0.003 0.001 HIS B 454 PHE 0.013 0.001 PHE A 193 TYR 0.020 0.001 TYR C 41 ARG 0.005 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 720) hydrogen bonds : angle 4.69211 ( 2016) covalent geometry : bond 0.00290 (15736) covalent geometry : angle 0.52487 (21360) *********************** 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 246 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7655 (mm) cc_final: 0.7390 (mt) REVERT: A 166 MET cc_start: 0.7564 (tpp) cc_final: 0.7055 (ttm) REVERT: A 276 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8588 (mm) REVERT: B 54 VAL cc_start: 0.7733 (m) cc_final: 0.7519 (p) REVERT: B 134 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.6722 (m-40) REVERT: B 166 MET cc_start: 0.7495 (tpp) cc_final: 0.7098 (ttm) REVERT: B 276 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 463 LYS cc_start: 0.7771 (tttt) cc_final: 0.7546 (ttpt) REVERT: C 310 GLN cc_start: 0.6672 (mm-40) cc_final: 0.6109 (tp-100) REVERT: C 369 GLN cc_start: 0.7198 (pm20) cc_final: 0.6556 (tm-30) REVERT: D 278 GLN cc_start: 0.7063 (mm110) cc_final: 0.6750 (tt0) REVERT: D 310 GLN cc_start: 0.6626 (mm-40) cc_final: 0.6400 (tm-30) REVERT: D 369 GLN cc_start: 0.7323 (pm20) cc_final: 0.5886 (tm-30) REVERT: D 394 GLU cc_start: 0.6243 (mp0) cc_final: 0.6011 (mp0) outliers start: 43 outliers final: 34 residues processed: 228 average time/residue: 0.2984 time to fit residues: 105.9027 Evaluate side-chains 227 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 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 391 THR 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 A residue 502 ASP 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 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 304 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 415 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 160 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124641 restraints weight = 20997.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.125373 restraints weight = 17186.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126990 restraints weight = 15238.213| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15736 Z= 0.148 Angle : 0.549 6.984 21360 Z= 0.301 Chirality : 0.045 0.161 2400 Planarity : 0.004 0.052 2744 Dihedral : 8.129 70.952 2376 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.38 % Allowed : 19.56 % Favored : 78.06 % 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: 0.53 (0.19), residues: 1972 helix: 1.55 (0.20), residues: 720 sheet: 0.49 (0.25), residues: 464 loop : -0.84 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.004 0.001 HIS B 454 PHE 0.015 0.001 PHE B 193 TYR 0.021 0.002 TYR C 41 ARG 0.004 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 720) hydrogen bonds : angle 4.73256 ( 2016) covalent geometry : bond 0.00349 (15736) covalent geometry : angle 0.54912 (21360) ********************** 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 236 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7958 (mm) cc_final: 0.7622 (mt) REVERT: A 54 VAL cc_start: 0.8145 (m) cc_final: 0.7905 (p) REVERT: A 166 MET cc_start: 0.7708 (tpp) cc_final: 0.7119 (ttm) REVERT: A 276 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8593 (mm) REVERT: A 337 TYR cc_start: 0.7506 (t80) cc_final: 0.7189 (t80) REVERT: B 54 VAL cc_start: 0.7768 (m) cc_final: 0.7529 (p) REVERT: B 134 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6647 (m-40) REVERT: B 166 MET cc_start: 0.7574 (tpp) cc_final: 0.7066 (ttm) REVERT: B 276 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8616 (mm) REVERT: B 463 LYS cc_start: 0.7848 (tttt) cc_final: 0.7585 (ttpt) REVERT: C 310 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6146 (tp-100) REVERT: C 369 GLN cc_start: 0.7216 (pm20) cc_final: 0.6544 (tm-30) REVERT: D 278 GLN cc_start: 0.7000 (mm110) cc_final: 0.6773 (tt0) REVERT: D 310 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6464 (tm-30) REVERT: D 369 GLN cc_start: 0.7323 (pm20) cc_final: 0.6026 (tm-30) REVERT: D 394 GLU cc_start: 0.6358 (mp0) cc_final: 0.6130 (mp0) outliers start: 39 outliers final: 36 residues processed: 220 average time/residue: 0.2439 time to fit residues: 82.9914 Evaluate side-chains 228 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 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 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 391 THR 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 A residue 502 ASP 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 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 304 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 427 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 191 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 0.1980 chunk 182 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 371 GLN B 134 ASN B 371 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.147550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127342 restraints weight = 20723.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.128421 restraints weight = 16641.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130232 restraints weight = 14362.245| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15736 Z= 0.104 Angle : 0.496 5.680 21360 Z= 0.272 Chirality : 0.043 0.152 2400 Planarity : 0.004 0.050 2744 Dihedral : 7.774 68.193 2376 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.83 % Allowed : 20.42 % Favored : 77.75 % 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: 0.78 (0.20), residues: 1972 helix: 1.70 (0.20), residues: 724 sheet: 0.65 (0.25), residues: 472 loop : -0.66 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 200 HIS 0.002 0.000 HIS B 26 PHE 0.010 0.001 PHE C 340 TYR 0.017 0.001 TYR C 41 ARG 0.009 0.000 ARG D 416 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 720) hydrogen bonds : angle 4.53925 ( 2016) covalent geometry : bond 0.00222 (15736) covalent geometry : angle 0.49619 (21360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4180.05 seconds wall clock time: 75 minutes 36.55 seconds (4536.55 seconds total)