Starting phenix.real_space_refine on Sun Oct 13 15:56:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rwk_19549/10_2024/8rwk_19549.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rwk_19549/10_2024/8rwk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rwk_19549/10_2024/8rwk_19549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rwk_19549/10_2024/8rwk_19549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rwk_19549/10_2024/8rwk_19549.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rwk_19549/10_2024/8rwk_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 15416 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3806 Classifications: {'peptide': 495} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 473} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 8.36, per 1000 atoms: 0.54 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: 3.99 Conformation dependent library (CDL) restraints added in 2.1 seconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 42.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 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: 5.16 Time building geometry restraints manager: 4.60 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.190 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.195 15736 Z= 1.308 Angle : 1.766 11.387 21360 Z= 1.169 Chirality : 0.097 0.475 2400 Planarity : 0.008 0.054 2744 Dihedral : 13.757 84.557 5956 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1972 helix: -0.34 (0.18), residues: 736 sheet: 0.51 (0.23), residues: 432 loop : 0.71 (0.25), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.011 TRP D 100 HIS 0.010 0.003 HIS B 75 PHE 0.027 0.006 PHE C 48 TYR 0.034 0.008 TYR A 230 ARG 0.007 0.001 ARG D 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 1.633 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: 0.3397 time to fit residues: 269.4954 Evaluate side-chains 258 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15736 Z= 0.214 Angle : 0.660 7.634 21360 Z= 0.365 Chirality : 0.047 0.231 2400 Planarity : 0.005 0.037 2744 Dihedral : 12.679 79.906 2376 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.69 % Allowed : 11.19 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1972 helix: 0.93 (0.19), residues: 740 sheet: 0.84 (0.23), residues: 468 loop : 0.33 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 198 HIS 0.004 0.001 HIS C 75 PHE 0.026 0.002 PHE C 340 TYR 0.018 0.002 TYR D 337 ARG 0.009 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 302 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7695 (mm) cc_final: 0.7472 (mt) REVERT: A 89 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6549 (mp10) REVERT: A 166 MET cc_start: 0.7764 (tpp) cc_final: 0.7206 (tpp) REVERT: A 179 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7594 (mtt180) REVERT: A 218 GLU cc_start: 0.6183 (pp20) cc_final: 0.5786 (tp30) REVERT: A 289 LEU cc_start: 0.7648 (pp) cc_final: 0.7182 (mt) REVERT: A 338 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6195 (t70) REVERT: A 498 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 43 GLN cc_start: 0.7079 (tp-100) cc_final: 0.6812 (tp-100) REVERT: B 89 GLN cc_start: 0.6949 (mm-40) cc_final: 0.6531 (mp10) REVERT: B 166 MET cc_start: 0.7280 (tpt) cc_final: 0.6869 (tpp) REVERT: B 179 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7533 (mtt180) REVERT: B 337 TYR cc_start: 0.7108 (t80) cc_final: 0.6838 (t80) REVERT: B 338 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.6092 (t0) REVERT: B 498 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6826 (mm-30) REVERT: C 213 VAL cc_start: 0.8598 (t) cc_final: 0.8370 (p) REVERT: C 253 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6925 (mm-30) REVERT: C 275 HIS cc_start: 0.7872 (m-70) cc_final: 0.6782 (t70) REVERT: C 297 ASN cc_start: 0.8616 (m-40) cc_final: 0.8183 (m-40) REVERT: C 415 MET cc_start: 0.8095 (mtp) cc_final: 0.7727 (ttp) REVERT: C 431 LYS cc_start: 0.6826 (mttt) cc_final: 0.6350 (ptmm) REVERT: D 29 MET cc_start: 0.5837 (mmp) cc_final: 0.5093 (tmm) REVERT: D 41 TYR cc_start: 0.4193 (t80) cc_final: 0.3742 (t80) REVERT: D 166 MET cc_start: 0.6724 (tpp) cc_final: 0.5777 (tpp) REVERT: D 253 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6925 (mm-30) REVERT: D 351 ILE cc_start: 0.7551 (tp) cc_final: 0.7157 (mt) REVERT: D 406 THR cc_start: 0.7124 (OUTLIER) cc_final: 0.6884 (p) REVERT: D 415 MET cc_start: 0.8053 (mtp) cc_final: 0.7627 (ttp) outliers start: 44 outliers final: 23 residues processed: 336 average time/residue: 0.3189 time to fit residues: 161.2547 Evaluate side-chains 233 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 192 ASN A 454 HIS A 459 ASN A 469 ASN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 469 ASN C 311 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 15736 Z= 0.491 Angle : 0.801 6.902 21360 Z= 0.447 Chirality : 0.052 0.178 2400 Planarity : 0.006 0.064 2744 Dihedral : 11.835 81.968 2376 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.79 % Allowed : 14.49 % Favored : 81.72 % 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: -0.09 (0.19), residues: 1972 helix: 0.51 (0.18), residues: 772 sheet: 0.49 (0.24), residues: 452 loop : -0.91 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 474 HIS 0.011 0.002 HIS B 454 PHE 0.027 0.003 PHE B 344 TYR 0.039 0.004 TYR C 230 ARG 0.005 0.001 ARG A 329 *********************** 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 286 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 224 time to evaluate : 1.741 Fit side-chains revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7744 (mm) cc_final: 0.7402 (mt) REVERT: A 40 GLU cc_start: 0.5958 (tp30) cc_final: 0.5670 (tt0) REVERT: A 134 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6057 (m110) REVERT: A 166 MET cc_start: 0.8032 (tpp) cc_final: 0.7824 (tpp) REVERT: A 179 ARG cc_start: 0.8315 (mtt-85) cc_final: 0.7873 (mtp180) REVERT: A 197 MET cc_start: 0.8318 (mmm) cc_final: 0.8015 (mmm) REVERT: A 337 TYR cc_start: 0.7317 (t80) cc_final: 0.6560 (t80) REVERT: A 404 LYS cc_start: 0.7312 (ttmt) cc_final: 0.7055 (tptm) REVERT: A 463 LYS cc_start: 0.7762 (tttt) cc_final: 0.7393 (ttpt) REVERT: B 40 GLU cc_start: 0.6056 (tp30) cc_final: 0.5830 (tt0) REVERT: B 166 MET cc_start: 0.7866 (tpt) cc_final: 0.7603 (tpp) REVERT: B 179 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.7830 (mtp180) REVERT: B 197 MET cc_start: 0.8350 (mmm) cc_final: 0.8058 (mmm) REVERT: B 337 TYR cc_start: 0.7097 (t80) cc_final: 0.6424 (t80) REVERT: B 404 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6926 (tptp) REVERT: B 463 LYS cc_start: 0.7796 (tttt) cc_final: 0.7409 (ttpt) REVERT: C 136 LYS cc_start: 0.7347 (tttp) cc_final: 0.6995 (mtpt) REVERT: C 166 MET cc_start: 0.7171 (tpp) cc_final: 0.5779 (tpp) REVERT: C 253 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7089 (mm-30) REVERT: C 278 GLN cc_start: 0.6736 (mm110) cc_final: 0.6398 (tm-30) REVERT: C 369 GLN cc_start: 0.7870 (pm20) cc_final: 0.6420 (tm-30) REVERT: C 431 LYS cc_start: 0.7326 (mttt) cc_final: 0.6801 (ptmm) REVERT: D 41 TYR cc_start: 0.4609 (t80) cc_final: 0.4044 (t80) REVERT: D 166 MET cc_start: 0.7226 (tpp) cc_final: 0.5973 (tpp) REVERT: D 253 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6904 (mm-30) REVERT: D 278 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6451 (mp10) REVERT: D 343 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: D 369 GLN cc_start: 0.7464 (pm20) cc_final: 0.6376 (tm-30) REVERT: D 431 LYS cc_start: 0.7684 (ptmt) cc_final: 0.7355 (ptmm) outliers start: 62 outliers final: 44 residues processed: 274 average time/residue: 0.3026 time to fit residues: 122.9558 Evaluate side-chains 224 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 276 ILE 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 429 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 64 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 216 THR 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 295 SER 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 30 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 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 176 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 469 ASN B 242 ASN B 469 ASN D 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15736 Z= 0.257 Angle : 0.587 5.571 21360 Z= 0.327 Chirality : 0.045 0.163 2400 Planarity : 0.005 0.054 2744 Dihedral : 10.526 80.556 2376 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.67 % Allowed : 16.44 % Favored : 79.89 % 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: 0.14 (0.19), residues: 1972 helix: 1.03 (0.19), residues: 748 sheet: 0.34 (0.23), residues: 460 loop : -0.95 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 198 HIS 0.004 0.001 HIS B 454 PHE 0.015 0.002 PHE B 193 TYR 0.018 0.002 TYR C 230 ARG 0.005 0.001 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 205 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7741 (mm) cc_final: 0.7352 (mt) REVERT: A 40 GLU cc_start: 0.5904 (tp30) cc_final: 0.5632 (tt0) REVERT: A 89 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6420 (mp10) REVERT: A 179 ARG cc_start: 0.8316 (mtt-85) cc_final: 0.7920 (mtt180) REVERT: A 197 MET cc_start: 0.8296 (mmm) cc_final: 0.7968 (mmm) REVERT: A 202 ILE cc_start: 0.8170 (mm) cc_final: 0.7966 (mm) REVERT: A 337 TYR cc_start: 0.7362 (t80) cc_final: 0.6523 (t80) REVERT: A 449 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8314 (tp) REVERT: A 463 LYS cc_start: 0.7743 (tttt) cc_final: 0.7326 (ttpt) REVERT: B 40 GLU cc_start: 0.5979 (tp30) cc_final: 0.5776 (tt0) REVERT: B 89 GLN cc_start: 0.6812 (mm-40) cc_final: 0.6390 (mp10) REVERT: B 166 MET cc_start: 0.7873 (tpt) cc_final: 0.7494 (tpp) REVERT: B 179 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.7907 (mtt180) REVERT: B 197 MET cc_start: 0.8317 (mmm) cc_final: 0.8000 (mmm) REVERT: B 337 TYR cc_start: 0.7020 (t80) cc_final: 0.6299 (t80) REVERT: B 463 LYS cc_start: 0.7689 (tttt) cc_final: 0.7453 (ttpt) REVERT: C 166 MET cc_start: 0.7066 (tpp) cc_final: 0.6862 (tpp) REVERT: C 253 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6943 (mm-30) REVERT: C 278 GLN cc_start: 0.6897 (mm110) cc_final: 0.6373 (tm-30) REVERT: C 369 GLN cc_start: 0.7771 (pm20) cc_final: 0.6519 (tm-30) REVERT: C 431 LYS cc_start: 0.7457 (mttt) cc_final: 0.7181 (ptmm) REVERT: D 41 TYR cc_start: 0.4814 (t80) cc_final: 0.4239 (t80) REVERT: D 78 GLU cc_start: 0.6234 (tp30) cc_final: 0.6013 (tp30) REVERT: D 253 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6790 (mm-30) REVERT: D 369 GLN cc_start: 0.7579 (pm20) cc_final: 0.6247 (tm-30) REVERT: D 415 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7784 (ttp) REVERT: D 431 LYS cc_start: 0.7702 (ptmt) cc_final: 0.7433 (ptmm) outliers start: 60 outliers final: 36 residues processed: 250 average time/residue: 0.2877 time to fit residues: 108.6753 Evaluate side-chains 218 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 320 SER 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 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 320 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 163 ASP Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 493 SER 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 287 VAL 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 415 MET 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 157 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 78 optimal weight: 0.3980 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 278 GLN D 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15736 Z= 0.155 Angle : 0.496 5.122 21360 Z= 0.276 Chirality : 0.044 0.299 2400 Planarity : 0.004 0.049 2744 Dihedral : 8.855 73.800 2376 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.81 % Allowed : 17.79 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1972 helix: 1.40 (0.20), residues: 748 sheet: 0.61 (0.24), residues: 456 loop : -0.75 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 200 HIS 0.003 0.001 HIS D 482 PHE 0.010 0.001 PHE C 340 TYR 0.016 0.001 TYR C 337 ARG 0.005 0.000 ARG C 467 *********************** 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 260 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 1.734 Fit side-chains revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7615 (mm) cc_final: 0.7241 (mt) REVERT: A 40 GLU cc_start: 0.5861 (tp30) cc_final: 0.5618 (tt0) REVERT: A 89 GLN cc_start: 0.6664 (mm-40) cc_final: 0.6225 (mp10) REVERT: A 179 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.7896 (mtt180) REVERT: A 197 MET cc_start: 0.8223 (mmm) cc_final: 0.7972 (mmm) REVERT: A 202 ILE cc_start: 0.8166 (mm) cc_final: 0.7956 (mm) REVERT: A 337 TYR cc_start: 0.7250 (t80) cc_final: 0.6477 (t80) REVERT: A 463 LYS cc_start: 0.7667 (tttt) cc_final: 0.7263 (ttpt) REVERT: B 40 GLU cc_start: 0.6002 (tp30) cc_final: 0.5680 (tt0) REVERT: B 89 GLN cc_start: 0.6701 (mm-40) cc_final: 0.6332 (mp10) REVERT: B 166 MET cc_start: 0.7708 (tpt) cc_final: 0.6940 (tpp) REVERT: B 179 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.7901 (mtt180) REVERT: B 197 MET cc_start: 0.8198 (mmm) cc_final: 0.7976 (mmm) REVERT: B 337 TYR cc_start: 0.6937 (t80) cc_final: 0.6210 (t80) REVERT: B 463 LYS cc_start: 0.7709 (tttt) cc_final: 0.7457 (ttpt) REVERT: C 78 GLU cc_start: 0.6364 (tp30) cc_final: 0.6103 (tp30) REVERT: C 253 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6846 (mm-30) REVERT: C 278 GLN cc_start: 0.6962 (mm110) cc_final: 0.6214 (tm-30) REVERT: C 369 GLN cc_start: 0.7657 (pm20) cc_final: 0.6618 (tm-30) REVERT: C 431 LYS cc_start: 0.7305 (mttt) cc_final: 0.6992 (ptmm) REVERT: D 41 TYR cc_start: 0.4784 (t80) cc_final: 0.4112 (t80) REVERT: D 153 LYS cc_start: 0.8398 (mttt) cc_final: 0.8138 (mttm) REVERT: D 166 MET cc_start: 0.6620 (tpp) cc_final: 0.5795 (tpp) REVERT: D 253 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6702 (mm-30) REVERT: D 310 GLN cc_start: 0.6033 (mm110) cc_final: 0.5640 (tm-30) REVERT: D 369 GLN cc_start: 0.7542 (pm20) cc_final: 0.6156 (tm-30) REVERT: D 431 LYS cc_start: 0.7714 (ptmt) cc_final: 0.7481 (ptmm) outliers start: 46 outliers final: 25 residues processed: 246 average time/residue: 0.2974 time to fit residues: 110.8426 Evaluate side-chains 214 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 411 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 418 VAL 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 406 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 411 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.5702 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= 0.188 Angle : 0.506 5.359 21360 Z= 0.278 Chirality : 0.044 0.208 2400 Planarity : 0.004 0.048 2744 Dihedral : 8.446 71.796 2376 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.69 % Allowed : 18.22 % Favored : 79.10 % 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 (0.20), residues: 1972 helix: 1.46 (0.20), residues: 752 sheet: 0.68 (0.25), residues: 456 loop : -0.83 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 198 HIS 0.003 0.001 HIS B 454 PHE 0.013 0.001 PHE A 247 TYR 0.015 0.002 TYR A 41 ARG 0.003 0.000 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7686 (mm) cc_final: 0.7275 (mt) REVERT: A 40 GLU cc_start: 0.5888 (tp30) cc_final: 0.5636 (tt0) REVERT: A 89 GLN cc_start: 0.6810 (mm-40) cc_final: 0.6352 (mp10) REVERT: A 166 MET cc_start: 0.7495 (tpp) cc_final: 0.7168 (ttm) REVERT: A 179 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7898 (mtt180) REVERT: A 197 MET cc_start: 0.8184 (mmm) cc_final: 0.7939 (mmm) REVERT: A 337 TYR cc_start: 0.7325 (t80) cc_final: 0.6509 (t80) REVERT: B 40 GLU cc_start: 0.6077 (tp30) cc_final: 0.5722 (tt0) REVERT: B 89 GLN cc_start: 0.6766 (mm-40) cc_final: 0.6393 (mp10) REVERT: B 93 ARG cc_start: 0.7495 (mtp-110) cc_final: 0.6953 (ttp80) REVERT: B 166 MET cc_start: 0.7734 (tpt) cc_final: 0.7372 (tpp) REVERT: B 179 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.7936 (mtt180) REVERT: B 197 MET cc_start: 0.8214 (mmm) cc_final: 0.7991 (mmm) REVERT: B 202 ILE cc_start: 0.8161 (mm) cc_final: 0.7952 (mm) REVERT: B 337 TYR cc_start: 0.6998 (t80) cc_final: 0.6256 (t80) REVERT: B 338 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.6125 (t0) REVERT: B 463 LYS cc_start: 0.7691 (tttt) cc_final: 0.7442 (ttpt) REVERT: C 122 ASP cc_start: 0.6986 (m-30) cc_final: 0.6697 (m-30) REVERT: C 253 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6736 (mm-30) REVERT: C 278 GLN cc_start: 0.7158 (mm110) cc_final: 0.6403 (tm-30) REVERT: C 369 GLN cc_start: 0.7740 (pm20) cc_final: 0.6600 (tm-30) REVERT: C 421 GLU cc_start: 0.7355 (tt0) cc_final: 0.7133 (tt0) REVERT: C 431 LYS cc_start: 0.7339 (mttt) cc_final: 0.6989 (ptmm) REVERT: C 495 LEU cc_start: 0.6905 (tp) cc_final: 0.6700 (tp) REVERT: D 120 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6190 (tt0) REVERT: D 130 GLU cc_start: 0.7636 (tp30) cc_final: 0.7428 (tp30) REVERT: D 166 MET cc_start: 0.6882 (tpp) cc_final: 0.5835 (tpp) REVERT: D 253 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6684 (mm-30) REVERT: D 310 GLN cc_start: 0.6040 (mm110) cc_final: 0.5658 (tm-30) REVERT: D 369 GLN cc_start: 0.7586 (pm20) cc_final: 0.6210 (tm-30) REVERT: D 431 LYS cc_start: 0.7757 (ptmt) cc_final: 0.7536 (ptmm) outliers start: 44 outliers final: 31 residues processed: 237 average time/residue: 0.2930 time to fit residues: 104.6589 Evaluate side-chains 222 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 468 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 411 VAL Chi-restraints excluded: chain D residue 438 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 138 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN A 371 GLN B 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15736 Z= 0.143 Angle : 0.473 5.544 21360 Z= 0.261 Chirality : 0.043 0.182 2400 Planarity : 0.004 0.049 2744 Dihedral : 7.978 68.230 2376 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.38 % Allowed : 18.95 % Favored : 78.67 % 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: 0.93 (0.20), residues: 1972 helix: 1.80 (0.20), residues: 724 sheet: 0.78 (0.25), residues: 456 loop : -0.56 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 198 HIS 0.001 0.000 HIS B 173 PHE 0.012 0.001 PHE A 432 TYR 0.015 0.001 TYR B 41 ARG 0.003 0.000 ARG C 467 *********************** 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 253 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 1.904 Fit side-chains REVERT: A 33 ILE cc_start: 0.7627 (mm) cc_final: 0.7207 (mt) REVERT: A 40 GLU cc_start: 0.5757 (tp30) cc_final: 0.5492 (tt0) REVERT: A 89 GLN cc_start: 0.6640 (mm-40) cc_final: 0.6183 (mp10) REVERT: A 93 ARG cc_start: 0.7388 (mtp-110) cc_final: 0.6861 (ttp80) REVERT: A 179 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7904 (mtt180) REVERT: A 197 MET cc_start: 0.8063 (mmm) cc_final: 0.7840 (mmm) REVERT: A 337 TYR cc_start: 0.7303 (t80) cc_final: 0.6542 (t80) REVERT: A 385 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.5120 (tt0) REVERT: A 463 LYS cc_start: 0.7412 (tttp) cc_final: 0.6745 (ttpt) REVERT: B 54 VAL cc_start: 0.7386 (m) cc_final: 0.7144 (p) REVERT: B 89 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6306 (mp10) REVERT: B 93 ARG cc_start: 0.7506 (mtp-110) cc_final: 0.6964 (ttp80) REVERT: B 166 MET cc_start: 0.7701 (tpt) cc_final: 0.7049 (tpp) REVERT: B 179 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7922 (mtt180) REVERT: B 337 TYR cc_start: 0.6990 (t80) cc_final: 0.6274 (t80) REVERT: B 463 LYS cc_start: 0.7692 (tttt) cc_final: 0.7397 (ttpt) REVERT: C 153 LYS cc_start: 0.8387 (mttt) cc_final: 0.8119 (mttm) REVERT: C 253 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6743 (tp30) REVERT: C 257 ASN cc_start: 0.7861 (m-40) cc_final: 0.6888 (m110) REVERT: C 278 GLN cc_start: 0.7076 (mm110) cc_final: 0.6388 (tm-30) REVERT: C 369 GLN cc_start: 0.7543 (pm20) cc_final: 0.6568 (tm-30) REVERT: C 431 LYS cc_start: 0.7351 (mttt) cc_final: 0.7043 (ptmm) REVERT: D 41 TYR cc_start: 0.4843 (t80) cc_final: 0.4252 (t80) REVERT: D 120 GLU cc_start: 0.6590 (tm-30) cc_final: 0.6158 (tt0) REVERT: D 130 GLU cc_start: 0.7601 (tp30) cc_final: 0.7341 (tp30) REVERT: D 253 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6587 (mm-30) REVERT: D 310 GLN cc_start: 0.5924 (mm110) cc_final: 0.5553 (tm-30) REVERT: D 369 GLN cc_start: 0.7520 (pm20) cc_final: 0.5943 (tm-30) REVERT: D 431 LYS cc_start: 0.7765 (ptmt) cc_final: 0.7550 (ptmm) outliers start: 39 outliers final: 31 residues processed: 241 average time/residue: 0.2960 time to fit residues: 107.2303 Evaluate side-chains 230 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 136 LYS 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 406 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 468 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 338 ASP Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 438 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 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 : 0.005 0.041 15736 Z= 0.306 Angle : 0.584 5.141 21360 Z= 0.320 Chirality : 0.046 0.169 2400 Planarity : 0.005 0.050 2744 Dihedral : 8.416 72.070 2376 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.06 % Allowed : 18.95 % 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: 0.39 (0.19), residues: 1972 helix: 1.36 (0.20), residues: 752 sheet: 0.60 (0.25), residues: 448 loop : -1.04 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 474 HIS 0.006 0.001 HIS A 454 PHE 0.019 0.002 PHE A 193 TYR 0.020 0.002 TYR B 277 ARG 0.004 0.001 ARG D 416 *********************** 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 246 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 196 time to evaluate : 1.783 Fit side-chains REVERT: A 33 ILE cc_start: 0.7791 (mm) cc_final: 0.7391 (mt) REVERT: A 40 GLU cc_start: 0.5852 (tp30) cc_final: 0.5581 (tt0) REVERT: A 89 GLN cc_start: 0.6840 (mm-40) cc_final: 0.6328 (mp10) REVERT: A 179 ARG cc_start: 0.8358 (mtt-85) cc_final: 0.7962 (mtt180) REVERT: A 197 MET cc_start: 0.8296 (mmm) cc_final: 0.8011 (mmm) REVERT: A 202 ILE cc_start: 0.8158 (mm) cc_final: 0.7899 (mm) REVERT: A 337 TYR cc_start: 0.7466 (t80) cc_final: 0.6696 (t80) REVERT: B 89 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6374 (mp10) REVERT: B 93 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7047 (ttp80) REVERT: B 134 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6200 (m-40) REVERT: B 166 MET cc_start: 0.7966 (tpt) cc_final: 0.6979 (tpp) REVERT: B 179 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.7984 (mtt180) REVERT: B 197 MET cc_start: 0.8233 (mmm) cc_final: 0.7997 (mmm) REVERT: B 337 TYR cc_start: 0.7206 (t80) cc_final: 0.6452 (t80) REVERT: B 463 LYS cc_start: 0.7783 (tttt) cc_final: 0.7443 (ttpt) REVERT: C 65 ILE cc_start: 0.7985 (mm) cc_final: 0.7675 (tt) REVERT: C 78 GLU cc_start: 0.6283 (tp30) cc_final: 0.5609 (tp30) REVERT: C 253 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6902 (mm-30) REVERT: C 278 GLN cc_start: 0.7211 (mm110) cc_final: 0.6634 (tm-30) REVERT: C 310 GLN cc_start: 0.6416 (mm-40) cc_final: 0.5653 (tp-100) REVERT: C 369 GLN cc_start: 0.7502 (pm20) cc_final: 0.6489 (tm-30) REVERT: C 421 GLU cc_start: 0.7371 (tt0) cc_final: 0.7158 (tt0) REVERT: C 431 LYS cc_start: 0.7498 (mttt) cc_final: 0.7111 (ptmm) REVERT: D 130 GLU cc_start: 0.7727 (tp30) cc_final: 0.7470 (tp30) REVERT: D 253 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6718 (mm-30) REVERT: D 369 GLN cc_start: 0.7622 (pm20) cc_final: 0.6031 (tm-30) REVERT: D 415 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7932 (ttp) REVERT: D 431 LYS cc_start: 0.7892 (ptmt) cc_final: 0.7674 (ptmm) outliers start: 50 outliers final: 39 residues processed: 232 average time/residue: 0.2674 time to fit residues: 93.5511 Evaluate side-chains 231 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 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 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 155 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 432 PHE 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 136 LYS 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 439 ILE Chi-restraints excluded: chain C residue 468 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 415 MET Chi-restraints excluded: chain D residue 438 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN D 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15736 Z= 0.165 Angle : 0.495 5.767 21360 Z= 0.274 Chirality : 0.044 0.160 2400 Planarity : 0.004 0.043 2744 Dihedral : 8.009 69.234 2376 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 19.99 % Favored : 77.87 % 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: 0.79 (0.20), residues: 1972 helix: 1.75 (0.20), residues: 724 sheet: 0.68 (0.25), residues: 456 loop : -0.70 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.002 0.001 HIS C 454 PHE 0.012 0.001 PHE A 432 TYR 0.012 0.001 TYR C 277 ARG 0.004 0.000 ARG D 416 *********************** 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 238 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.857 Fit side-chains REVERT: A 33 ILE cc_start: 0.7729 (mm) cc_final: 0.7074 (mt) REVERT: A 89 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6249 (mp10) REVERT: A 93 ARG cc_start: 0.7483 (mtp-110) cc_final: 0.6945 (ttp80) REVERT: A 179 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.7996 (mtt180) REVERT: A 197 MET cc_start: 0.8192 (mmm) cc_final: 0.7951 (mmm) REVERT: A 202 ILE cc_start: 0.8116 (mm) cc_final: 0.7864 (mm) REVERT: A 289 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7387 (pp) REVERT: A 337 TYR cc_start: 0.7319 (t80) cc_final: 0.6486 (t80) REVERT: A 463 LYS cc_start: 0.7396 (tttp) cc_final: 0.6731 (ttpt) REVERT: B 89 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6343 (mp10) REVERT: B 93 ARG cc_start: 0.7518 (mtp-110) cc_final: 0.6991 (ttp80) REVERT: B 134 ASN cc_start: 0.7012 (OUTLIER) cc_final: 0.6276 (m-40) REVERT: B 166 MET cc_start: 0.7837 (tpt) cc_final: 0.7009 (tpp) REVERT: B 179 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.7948 (mtt180) REVERT: B 197 MET cc_start: 0.8181 (mmm) cc_final: 0.7950 (mmm) REVERT: B 202 ILE cc_start: 0.8129 (mm) cc_final: 0.7878 (mm) REVERT: B 337 TYR cc_start: 0.7074 (t80) cc_final: 0.6313 (t80) REVERT: B 463 LYS cc_start: 0.7743 (tttt) cc_final: 0.7413 (ttpt) REVERT: C 65 ILE cc_start: 0.7949 (mm) cc_final: 0.7653 (tt) REVERT: C 278 GLN cc_start: 0.7181 (mm110) cc_final: 0.6689 (tm-30) REVERT: C 310 GLN cc_start: 0.6390 (mm-40) cc_final: 0.5632 (tp-100) REVERT: C 369 GLN cc_start: 0.7533 (pm20) cc_final: 0.6601 (tm-30) REVERT: C 421 GLU cc_start: 0.7366 (tt0) cc_final: 0.7147 (tt0) REVERT: C 431 LYS cc_start: 0.7546 (mttt) cc_final: 0.7193 (ptmm) REVERT: D 120 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6291 (tt0) REVERT: D 130 GLU cc_start: 0.7600 (tp30) cc_final: 0.7337 (tp30) REVERT: D 253 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6634 (mm-30) REVERT: D 310 GLN cc_start: 0.6095 (mm110) cc_final: 0.5704 (tm-30) REVERT: D 369 GLN cc_start: 0.7542 (pm20) cc_final: 0.6036 (tm-30) outliers start: 35 outliers final: 30 residues processed: 227 average time/residue: 0.3137 time to fit residues: 105.6786 Evaluate side-chains 225 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 136 LYS 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 338 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 468 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 88 optimal weight: 0.0470 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN B 371 GLN D 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15736 Z= 0.140 Angle : 0.471 5.732 21360 Z= 0.260 Chirality : 0.043 0.155 2400 Planarity : 0.004 0.041 2744 Dihedral : 7.698 67.055 2376 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.02 % Allowed : 19.93 % 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: 0.94 (0.20), residues: 1972 helix: 1.87 (0.20), residues: 724 sheet: 0.79 (0.25), residues: 456 loop : -0.64 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.001 0.000 HIS B 173 PHE 0.010 0.001 PHE A 432 TYR 0.012 0.001 TYR C 277 ARG 0.004 0.000 ARG D 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 2.263 Fit side-chains REVERT: A 33 ILE cc_start: 0.7595 (mm) cc_final: 0.7247 (mt) REVERT: A 89 GLN cc_start: 0.6656 (mm-40) cc_final: 0.6219 (mp10) REVERT: A 179 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.8006 (mtt180) REVERT: A 202 ILE cc_start: 0.8052 (mm) cc_final: 0.7803 (mm) REVERT: A 289 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7354 (pp) REVERT: A 337 TYR cc_start: 0.7344 (t80) cc_final: 0.6554 (t80) REVERT: B 54 VAL cc_start: 0.7489 (m) cc_final: 0.7264 (p) REVERT: B 89 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6319 (mp10) REVERT: B 93 ARG cc_start: 0.7521 (mtp-110) cc_final: 0.7017 (ttp80) REVERT: B 134 ASN cc_start: 0.6607 (OUTLIER) cc_final: 0.6064 (m-40) REVERT: B 166 MET cc_start: 0.7716 (tpt) cc_final: 0.7021 (tpp) REVERT: B 179 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7961 (mtt180) REVERT: B 197 MET cc_start: 0.8162 (mmm) cc_final: 0.7923 (mmm) REVERT: B 202 ILE cc_start: 0.8109 (mm) cc_final: 0.7908 (mm) REVERT: B 257 ASN cc_start: 0.6063 (m-40) cc_final: 0.5596 (m-40) REVERT: B 337 TYR cc_start: 0.7056 (t80) cc_final: 0.6429 (t80) REVERT: B 463 LYS cc_start: 0.7751 (tttt) cc_final: 0.7426 (ttpt) REVERT: C 136 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7488 (mtpp) REVERT: C 153 LYS cc_start: 0.8348 (mttt) cc_final: 0.8100 (mttm) REVERT: C 257 ASN cc_start: 0.7633 (m-40) cc_final: 0.7217 (m110) REVERT: C 278 GLN cc_start: 0.7073 (mm110) cc_final: 0.6637 (tm-30) REVERT: C 310 GLN cc_start: 0.6359 (mm-40) cc_final: 0.5618 (tp-100) REVERT: C 369 GLN cc_start: 0.7515 (pm20) cc_final: 0.6576 (tm-30) REVERT: C 431 LYS cc_start: 0.7511 (mttt) cc_final: 0.7205 (ptmm) REVERT: D 120 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6149 (tt0) REVERT: D 130 GLU cc_start: 0.7593 (tp30) cc_final: 0.7313 (tp30) REVERT: D 253 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6560 (mm-30) REVERT: D 310 GLN cc_start: 0.6019 (mm110) cc_final: 0.5677 (tm-30) REVERT: D 369 GLN cc_start: 0.7488 (pm20) cc_final: 0.6006 (tm-30) REVERT: D 404 LYS cc_start: 0.7701 (mttt) cc_final: 0.7343 (mttt) outliers start: 33 outliers final: 25 residues processed: 228 average time/residue: 0.3026 time to fit residues: 105.4727 Evaluate side-chains 227 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 136 LYS 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 338 ASP Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 468 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.143877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124610 restraints weight = 20977.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124681 restraints weight = 16370.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126623 restraints weight = 14792.748| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15736 Z= 0.249 Angle : 0.545 9.987 21360 Z= 0.296 Chirality : 0.045 0.295 2400 Planarity : 0.004 0.042 2744 Dihedral : 7.946 68.910 2376 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.14 % Allowed : 20.48 % Favored : 77.38 % 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: 1.77 (0.20), residues: 724 sheet: 0.77 (0.25), residues: 448 loop : -0.80 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 200 HIS 0.008 0.001 HIS A 26 PHE 0.016 0.002 PHE A 193 TYR 0.016 0.002 TYR B 277 ARG 0.011 0.000 ARG D 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.63 seconds wall clock time: 59 minutes 23.73 seconds (3563.73 seconds total)