Starting phenix.real_space_refine on Wed Oct 28 16:36:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11bt_75608/10_2026/11bt_75608.cif Found real_map, /net/cci-nas-00/data/ceres_data/11bt_75608/10_2026/11bt_75608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11bt_75608/10_2026/11bt_75608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11bt_75608/10_2026/11bt_75608.map" model { file = "/net/cci-nas-00/data/ceres_data/11bt_75608/10_2026/11bt_75608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11bt_75608/10_2026/11bt_75608.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 17634 2.51 5 N 4854 2.21 5 O 5316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27906 Number of models: 1 Model: "" Number of chains: 6 Chain: "Ar" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4651 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 23, 'TRANS': 559} Chain: "As" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4651 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 23, 'TRANS': 559} Chain: "At" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4651 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 23, 'TRANS': 559} Chain: "Au" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4651 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 23, 'TRANS': 559} Chain: "Av" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4651 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 23, 'TRANS': 559} Chain: "Aw" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4651 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 23, 'TRANS': 559} Time building chain proxies: 5.45, per 1000 atoms: 0.20 Number of scatterers: 27906 At special positions: 0 Unit cell: (187.6, 180.6, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 5316 8.00 N 4854 7.00 C 17634 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6660 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 60 sheets defined 24.4% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'Ar' and resid 182 through 189 Processing helix chain 'Ar' and resid 231 through 235 Processing helix chain 'Ar' and resid 291 through 296 removed outlier: 3.646A pdb=" N ILEAr 295 " --> pdb=" O ASPAr 291 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALAAr 296 " --> pdb=" O METAr 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ar' and resid 291 through 296' Processing helix chain 'Ar' and resid 298 through 303 removed outlier: 3.614A pdb=" N LEUAr 302 " --> pdb=" O ASPAr 298 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 386 through 393 Processing helix chain 'Ar' and resid 437 through 446 removed outlier: 3.502A pdb=" N GLUAr 445 " --> pdb=" O LYSAr 441 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASPAr 446 " --> pdb=" O GLNAr 442 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 500 through 534 removed outlier: 3.967A pdb=" N PHEAr 515 " --> pdb=" O ALAAr 511 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASPAr 516 " --> pdb=" O ASNAr 512 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASNAr 517 " --> pdb=" O ALAAr 513 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALAAr 534 " --> pdb=" O LEUAr 530 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 548 through 553 removed outlier: 3.652A pdb=" N ARGAr 551 " --> pdb=" O GLYAr 548 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYRAr 552 " --> pdb=" O PHEAr 549 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 566 through 568 No H-bonds generated for 'chain 'Ar' and resid 566 through 568' Processing helix chain 'Ar' and resid 573 through 575 No H-bonds generated for 'chain 'Ar' and resid 573 through 575' Processing helix chain 'Ar' and resid 576 through 600 removed outlier: 3.640A pdb=" N SERAr 582 " --> pdb=" O ARGAr 578 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 601 through 610 removed outlier: 4.010A pdb=" N ALAAr 605 " --> pdb=" O GLYAr 601 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 626 through 630 removed outlier: 3.586A pdb=" N GLNAr 629 " --> pdb=" O TYRAr 626 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 653 through 657 Processing helix chain 'Ar' and resid 725 through 731 removed outlier: 3.566A pdb=" N THRAr 730 " --> pdb=" O ARGAr 726 " (cutoff:3.500A) Processing helix chain 'As' and resid 182 through 189 Processing helix chain 'As' and resid 231 through 235 Processing helix chain 'As' and resid 291 through 296 removed outlier: 3.646A pdb=" N ILEAs 295 " --> pdb=" O ASPAs 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAAs 296 " --> pdb=" O METAs 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'As' and resid 291 through 296' Processing helix chain 'As' and resid 298 through 303 removed outlier: 3.613A pdb=" N LEUAs 302 " --> pdb=" O ASPAs 298 " (cutoff:3.500A) Processing helix chain 'As' and resid 386 through 393 Processing helix chain 'As' and resid 437 through 446 removed outlier: 3.501A pdb=" N GLUAs 445 " --> pdb=" O LYSAs 441 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASPAs 446 " --> pdb=" O GLNAs 442 " (cutoff:3.500A) Processing helix chain 'As' and resid 500 through 534 removed outlier: 3.966A pdb=" N PHEAs 515 " --> pdb=" O ALAAs 511 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASPAs 516 " --> pdb=" O ASNAs 512 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASNAs 517 " --> pdb=" O ALAAs 513 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALAAs 534 " --> pdb=" O LEUAs 530 " (cutoff:3.500A) Processing helix chain 'As' and resid 548 through 553 removed outlier: 3.651A pdb=" N ARGAs 551 " --> pdb=" O GLYAs 548 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYRAs 552 " --> pdb=" O PHEAs 549 " (cutoff:3.500A) Processing helix chain 'As' and resid 566 through 568 No H-bonds generated for 'chain 'As' and resid 566 through 568' Processing helix chain 'As' and resid 573 through 575 No H-bonds generated for 'chain 'As' and resid 573 through 575' Processing helix chain 'As' and resid 576 through 600 removed outlier: 3.640A pdb=" N SERAs 582 " --> pdb=" O ARGAs 578 " (cutoff:3.500A) Processing helix chain 'As' and resid 601 through 610 removed outlier: 4.011A pdb=" N ALAAs 605 " --> pdb=" O GLYAs 601 " (cutoff:3.500A) Processing helix chain 'As' and resid 626 through 630 removed outlier: 3.587A pdb=" N GLNAs 629 " --> pdb=" O TYRAs 626 " (cutoff:3.500A) Processing helix chain 'As' and resid 653 through 657 Processing helix chain 'As' and resid 725 through 731 removed outlier: 3.566A pdb=" N THRAs 730 " --> pdb=" O ARGAs 726 " (cutoff:3.500A) Processing helix chain 'At' and resid 182 through 189 Processing helix chain 'At' and resid 231 through 235 Processing helix chain 'At' and resid 291 through 296 removed outlier: 3.645A pdb=" N ILEAt 295 " --> pdb=" O ASPAt 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAAt 296 " --> pdb=" O METAt 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'At' and resid 291 through 296' Processing helix chain 'At' and resid 298 through 303 removed outlier: 3.614A pdb=" N LEUAt 302 " --> pdb=" O ASPAt 298 " (cutoff:3.500A) Processing helix chain 'At' and resid 386 through 393 Processing helix chain 'At' and resid 437 through 446 removed outlier: 3.501A pdb=" N GLUAt 445 " --> pdb=" O LYSAt 441 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASPAt 446 " --> pdb=" O GLNAt 442 " (cutoff:3.500A) Processing helix chain 'At' and resid 500 through 534 removed outlier: 3.967A pdb=" N PHEAt 515 " --> pdb=" O ALAAt 511 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASPAt 516 " --> pdb=" O ASNAt 512 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASNAt 517 " --> pdb=" O ALAAt 513 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALAAt 534 " --> pdb=" O LEUAt 530 " (cutoff:3.500A) Processing helix chain 'At' and resid 548 through 553 removed outlier: 3.651A pdb=" N ARGAt 551 " --> pdb=" O GLYAt 548 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYRAt 552 " --> pdb=" O PHEAt 549 " (cutoff:3.500A) Processing helix chain 'At' and resid 566 through 568 No H-bonds generated for 'chain 'At' and resid 566 through 568' Processing helix chain 'At' and resid 573 through 575 No H-bonds generated for 'chain 'At' and resid 573 through 575' Processing helix chain 'At' and resid 576 through 600 removed outlier: 3.639A pdb=" N SERAt 582 " --> pdb=" O ARGAt 578 " (cutoff:3.500A) Processing helix chain 'At' and resid 601 through 610 removed outlier: 4.010A pdb=" N ALAAt 605 " --> pdb=" O GLYAt 601 " (cutoff:3.500A) Processing helix chain 'At' and resid 626 through 630 removed outlier: 3.586A pdb=" N GLNAt 629 " --> pdb=" O TYRAt 626 " (cutoff:3.500A) Processing helix chain 'At' and resid 653 through 657 Processing helix chain 'At' and resid 725 through 731 removed outlier: 3.566A pdb=" N THRAt 730 " --> pdb=" O ARGAt 726 " (cutoff:3.500A) Processing helix chain 'Au' and resid 182 through 189 Processing helix chain 'Au' and resid 231 through 235 Processing helix chain 'Au' and resid 291 through 296 removed outlier: 3.646A pdb=" N ILEAu 295 " --> pdb=" O ASPAu 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAAu 296 " --> pdb=" O METAu 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'Au' and resid 291 through 296' Processing helix chain 'Au' and resid 298 through 303 removed outlier: 3.614A pdb=" N LEUAu 302 " --> pdb=" O ASPAu 298 " (cutoff:3.500A) Processing helix chain 'Au' and resid 386 through 393 Processing helix chain 'Au' and resid 437 through 446 removed outlier: 3.502A pdb=" N GLUAu 445 " --> pdb=" O LYSAu 441 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASPAu 446 " --> pdb=" O GLNAu 442 " (cutoff:3.500A) Processing helix chain 'Au' and resid 500 through 534 removed outlier: 3.966A pdb=" N PHEAu 515 " --> pdb=" O ALAAu 511 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASPAu 516 " --> pdb=" O ASNAu 512 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASNAu 517 " --> pdb=" O ALAAu 513 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALAAu 534 " --> pdb=" O LEUAu 530 " (cutoff:3.500A) Processing helix chain 'Au' and resid 548 through 553 removed outlier: 3.651A pdb=" N ARGAu 551 " --> pdb=" O GLYAu 548 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYRAu 552 " --> pdb=" O PHEAu 549 " (cutoff:3.500A) Processing helix chain 'Au' and resid 566 through 568 No H-bonds generated for 'chain 'Au' and resid 566 through 568' Processing helix chain 'Au' and resid 573 through 575 No H-bonds generated for 'chain 'Au' and resid 573 through 575' Processing helix chain 'Au' and resid 576 through 600 removed outlier: 3.639A pdb=" N SERAu 582 " --> pdb=" O ARGAu 578 " (cutoff:3.500A) Processing helix chain 'Au' and resid 601 through 610 removed outlier: 4.010A pdb=" N ALAAu 605 " --> pdb=" O GLYAu 601 " (cutoff:3.500A) Processing helix chain 'Au' and resid 626 through 631 removed outlier: 3.587A pdb=" N GLNAu 629 " --> pdb=" O TYRAu 626 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEUAu 631 " --> pdb=" O PROAu 628 " (cutoff:3.500A) Processing helix chain 'Au' and resid 653 through 657 Processing helix chain 'Au' and resid 725 through 731 removed outlier: 3.566A pdb=" N THRAu 730 " --> pdb=" O ARGAu 726 " (cutoff:3.500A) Processing helix chain 'Av' and resid 182 through 189 Processing helix chain 'Av' and resid 231 through 235 Processing helix chain 'Av' and resid 291 through 296 removed outlier: 3.647A pdb=" N ILEAv 295 " --> pdb=" O ASPAv 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAAv 296 " --> pdb=" O METAv 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'Av' and resid 291 through 296' Processing helix chain 'Av' and resid 298 through 303 removed outlier: 3.613A pdb=" N LEUAv 302 " --> pdb=" O ASPAv 298 " (cutoff:3.500A) Processing helix chain 'Av' and resid 386 through 393 Processing helix chain 'Av' and resid 437 through 446 removed outlier: 3.502A pdb=" N GLUAv 445 " --> pdb=" O LYSAv 441 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASPAv 446 " --> pdb=" O GLNAv 442 " (cutoff:3.500A) Processing helix chain 'Av' and resid 500 through 534 removed outlier: 3.966A pdb=" N PHEAv 515 " --> pdb=" O ALAAv 511 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASPAv 516 " --> pdb=" O ASNAv 512 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASNAv 517 " --> pdb=" O ALAAv 513 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALAAv 534 " --> pdb=" O LEUAv 530 " (cutoff:3.500A) Processing helix chain 'Av' and resid 548 through 553 removed outlier: 3.652A pdb=" N ARGAv 551 " --> pdb=" O GLYAv 548 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYRAv 552 " --> pdb=" O PHEAv 549 " (cutoff:3.500A) Processing helix chain 'Av' and resid 566 through 568 No H-bonds generated for 'chain 'Av' and resid 566 through 568' Processing helix chain 'Av' and resid 573 through 575 No H-bonds generated for 'chain 'Av' and resid 573 through 575' Processing helix chain 'Av' and resid 576 through 600 removed outlier: 3.639A pdb=" N SERAv 582 " --> pdb=" O ARGAv 578 " (cutoff:3.500A) Processing helix chain 'Av' and resid 601 through 610 removed outlier: 4.010A pdb=" N ALAAv 605 " --> pdb=" O GLYAv 601 " (cutoff:3.500A) Processing helix chain 'Av' and resid 626 through 630 removed outlier: 3.588A pdb=" N GLNAv 629 " --> pdb=" O TYRAv 626 " (cutoff:3.500A) Processing helix chain 'Av' and resid 653 through 657 Processing helix chain 'Av' and resid 725 through 731 removed outlier: 3.566A pdb=" N THRAv 730 " --> pdb=" O ARGAv 726 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 182 through 189 Processing helix chain 'Aw' and resid 231 through 235 Processing helix chain 'Aw' and resid 291 through 296 removed outlier: 3.646A pdb=" N ILEAw 295 " --> pdb=" O ASPAw 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAAw 296 " --> pdb=" O METAw 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aw' and resid 291 through 296' Processing helix chain 'Aw' and resid 298 through 303 removed outlier: 3.614A pdb=" N LEUAw 302 " --> pdb=" O ASPAw 298 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 386 through 393 Processing helix chain 'Aw' and resid 437 through 446 removed outlier: 3.502A pdb=" N GLUAw 445 " --> pdb=" O LYSAw 441 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASPAw 446 " --> pdb=" O GLNAw 442 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 500 through 534 removed outlier: 3.967A pdb=" N PHEAw 515 " --> pdb=" O ALAAw 511 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASPAw 516 " --> pdb=" O ASNAw 512 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASNAw 517 " --> pdb=" O ALAAw 513 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALAAw 534 " --> pdb=" O LEUAw 530 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 548 through 553 removed outlier: 3.652A pdb=" N ARGAw 551 " --> pdb=" O GLYAw 548 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYRAw 552 " --> pdb=" O PHEAw 549 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 566 through 568 No H-bonds generated for 'chain 'Aw' and resid 566 through 568' Processing helix chain 'Aw' and resid 573 through 575 No H-bonds generated for 'chain 'Aw' and resid 573 through 575' Processing helix chain 'Aw' and resid 576 through 600 removed outlier: 3.639A pdb=" N SERAw 582 " --> pdb=" O ARGAw 578 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 601 through 610 removed outlier: 4.010A pdb=" N ALAAw 605 " --> pdb=" O GLYAw 601 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 626 through 631 removed outlier: 3.587A pdb=" N GLNAw 629 " --> pdb=" O TYRAw 626 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEUAw 631 " --> pdb=" O PROAw 628 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 653 through 657 Processing helix chain 'Aw' and resid 725 through 731 removed outlier: 3.565A pdb=" N THRAw 730 " --> pdb=" O ARGAw 726 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Ar' and resid 190 through 193 removed outlier: 5.772A pdb=" N ASNAr 190 " --> pdb=" O PHEAr 680 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYRAr 682 " --> pdb=" O ASNAr 190 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILEAr 192 " --> pdb=" O TYRAr 682 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ar' and resid 228 through 229 Processing sheet with id=AA3, first strand: chain 'Ar' and resid 228 through 229 Processing sheet with id=AA4, first strand: chain 'Ar' and resid 270 through 274 Processing sheet with id=AA5, first strand: chain 'Ar' and resid 312 through 313 removed outlier: 4.597A pdb=" N ALAAr 312 " --> pdb=" O ASNAr 461 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASNAr 461 " --> pdb=" O ALAAr 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Ar' and resid 333 through 340 removed outlier: 6.972A pdb=" N LEUAr 319 " --> pdb=" O LEUAr 456 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEUAr 456 " --> pdb=" O LEUAr 319 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYSAr 321 " --> pdb=" O TYRAr 454 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYRAr 454 " --> pdb=" O LYSAr 321 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEUAr 323 " --> pdb=" O VALAr 452 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ar' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAr 366 " --> pdb=" O ILEAr 400 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SERAr 368 " --> pdb=" O LEUAr 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAr 398 " --> pdb=" O SERAr 368 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHEAr 370 " --> pdb=" O ALAAr 396 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAAr 396 " --> pdb=" O PHEAr 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ar' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAr 366 " --> pdb=" O ILEAr 400 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SERAr 368 " --> pdb=" O LEUAr 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAr 398 " --> pdb=" O SERAr 368 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHEAr 370 " --> pdb=" O ALAAr 396 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAAr 396 " --> pdb=" O PHEAr 370 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALAAr 395 " --> pdb=" O LEUAr 425 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEUAr 425 " --> pdb=" O ALAAr 395 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLNAr 397 " --> pdb=" O TYRAr 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ar' and resid 489 through 490 removed outlier: 3.538A pdb=" N SERAr 699 " --> pdb=" O VALAr 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Ar' and resid 560 through 564 Processing sheet with id=AB2, first strand: chain 'Ar' and resid 735 through 740 removed outlier: 3.878A pdb=" N LEUAs 735 " --> pdb=" O PROAr 736 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLNAr 738 " --> pdb=" O LEUAs 735 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VALAs 737 " --> pdb=" O GLNAr 738 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASNAr 740 " --> pdb=" O VALAs 737 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THRAs 739 " --> pdb=" O ASNAr 740 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VALAt 737 " --> pdb=" O GLNAs 738 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THRAt 739 " --> pdb=" O ASNAs 740 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEUAu 735 " --> pdb=" O PROAt 736 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VALAu 737 " --> pdb=" O GLNAt 738 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THRAu 739 " --> pdb=" O ASNAt 740 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THRAv 739 " --> pdb=" O ASNAu 740 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VALAw 737 " --> pdb=" O GLNAv 738 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THRAw 739 " --> pdb=" O ASNAv 740 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEUAr 735 " --> pdb=" O GLNAw 738 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASNAw 740 " --> pdb=" O LEUAr 735 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VALAr 737 " --> pdb=" O ASNAw 740 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'As' and resid 190 through 193 removed outlier: 5.773A pdb=" N ASNAs 190 " --> pdb=" O PHEAs 680 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYRAs 682 " --> pdb=" O ASNAs 190 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILEAs 192 " --> pdb=" O TYRAs 682 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'As' and resid 228 through 229 Processing sheet with id=AB5, first strand: chain 'As' and resid 228 through 229 removed outlier: 3.586A pdb=" N ARGAs 206 " --> pdb=" O VALAt 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'As' and resid 270 through 274 Processing sheet with id=AB7, first strand: chain 'As' and resid 312 through 313 removed outlier: 4.596A pdb=" N ALAAs 312 " --> pdb=" O ASNAs 461 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASNAs 461 " --> pdb=" O ALAAs 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'As' and resid 333 through 340 removed outlier: 6.972A pdb=" N LEUAs 319 " --> pdb=" O LEUAs 456 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEUAs 456 " --> pdb=" O LEUAs 319 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYSAs 321 " --> pdb=" O TYRAs 454 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYRAs 454 " --> pdb=" O LYSAs 321 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEUAs 323 " --> pdb=" O VALAs 452 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'As' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAs 366 " --> pdb=" O ILEAs 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERAs 368 " --> pdb=" O LEUAs 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAs 398 " --> pdb=" O SERAs 368 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHEAs 370 " --> pdb=" O ALAAs 396 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAAs 396 " --> pdb=" O PHEAs 370 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'As' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAs 366 " --> pdb=" O ILEAs 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERAs 368 " --> pdb=" O LEUAs 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAs 398 " --> pdb=" O SERAs 368 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHEAs 370 " --> pdb=" O ALAAs 396 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAAs 396 " --> pdb=" O PHEAs 370 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALAAs 395 " --> pdb=" O LEUAs 425 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEUAs 425 " --> pdb=" O ALAAs 395 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLNAs 397 " --> pdb=" O TYRAs 423 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'As' and resid 489 through 490 removed outlier: 3.538A pdb=" N SERAs 699 " --> pdb=" O VALAs 692 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'As' and resid 560 through 564 Processing sheet with id=AC4, first strand: chain 'At' and resid 190 through 193 removed outlier: 5.773A pdb=" N ASNAt 190 " --> pdb=" O PHEAt 680 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYRAt 682 " --> pdb=" O ASNAt 190 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILEAt 192 " --> pdb=" O TYRAt 682 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'At' and resid 228 through 229 Processing sheet with id=AC6, first strand: chain 'At' and resid 228 through 229 Processing sheet with id=AC7, first strand: chain 'At' and resid 270 through 274 Processing sheet with id=AC8, first strand: chain 'At' and resid 312 through 313 removed outlier: 4.596A pdb=" N ALAAt 312 " --> pdb=" O ASNAt 461 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASNAt 461 " --> pdb=" O ALAAt 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'At' and resid 333 through 340 removed outlier: 6.972A pdb=" N LEUAt 319 " --> pdb=" O LEUAt 456 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEUAt 456 " --> pdb=" O LEUAt 319 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYSAt 321 " --> pdb=" O TYRAt 454 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYRAt 454 " --> pdb=" O LYSAt 321 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEUAt 323 " --> pdb=" O VALAt 452 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'At' and resid 350 through 351 removed outlier: 3.536A pdb=" N THRAt 366 " --> pdb=" O ILEAt 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERAt 368 " --> pdb=" O LEUAt 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAt 398 " --> pdb=" O SERAt 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHEAt 370 " --> pdb=" O ALAAt 396 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALAAt 396 " --> pdb=" O PHEAt 370 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'At' and resid 350 through 351 removed outlier: 3.536A pdb=" N THRAt 366 " --> pdb=" O ILEAt 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERAt 368 " --> pdb=" O LEUAt 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAt 398 " --> pdb=" O SERAt 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHEAt 370 " --> pdb=" O ALAAt 396 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALAAt 396 " --> pdb=" O PHEAt 370 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALAAt 395 " --> pdb=" O LEUAt 425 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEUAt 425 " --> pdb=" O ALAAt 395 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLNAt 397 " --> pdb=" O TYRAt 423 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'At' and resid 489 through 490 removed outlier: 3.538A pdb=" N SERAt 699 " --> pdb=" O VALAt 692 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'At' and resid 560 through 564 Processing sheet with id=AD5, first strand: chain 'Au' and resid 190 through 193 removed outlier: 5.773A pdb=" N ASNAu 190 " --> pdb=" O PHEAu 680 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYRAu 682 " --> pdb=" O ASNAu 190 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILEAu 192 " --> pdb=" O TYRAu 682 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Au' and resid 228 through 229 Processing sheet with id=AD7, first strand: chain 'Au' and resid 228 through 229 Processing sheet with id=AD8, first strand: chain 'Au' and resid 270 through 274 Processing sheet with id=AD9, first strand: chain 'Au' and resid 312 through 313 removed outlier: 4.597A pdb=" N ALAAu 312 " --> pdb=" O ASNAu 461 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNAu 461 " --> pdb=" O ALAAu 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'Au' and resid 333 through 340 removed outlier: 6.972A pdb=" N LEUAu 319 " --> pdb=" O LEUAu 456 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEUAu 456 " --> pdb=" O LEUAu 319 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYSAu 321 " --> pdb=" O TYRAu 454 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYRAu 454 " --> pdb=" O LYSAu 321 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEUAu 323 " --> pdb=" O VALAu 452 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Au' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAu 366 " --> pdb=" O ILEAu 400 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SERAu 368 " --> pdb=" O LEUAu 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAu 398 " --> pdb=" O SERAu 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHEAu 370 " --> pdb=" O ALAAu 396 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAAu 396 " --> pdb=" O PHEAu 370 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARGAu 414 " --> pdb=" O SERAu 405 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Au' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAu 366 " --> pdb=" O ILEAu 400 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SERAu 368 " --> pdb=" O LEUAu 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAu 398 " --> pdb=" O SERAu 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHEAu 370 " --> pdb=" O ALAAu 396 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAAu 396 " --> pdb=" O PHEAu 370 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALAAu 395 " --> pdb=" O LEUAu 425 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEUAu 425 " --> pdb=" O ALAAu 395 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLNAu 397 " --> pdb=" O TYRAu 423 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Au' and resid 489 through 490 removed outlier: 3.538A pdb=" N SERAu 699 " --> pdb=" O VALAu 692 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Au' and resid 560 through 564 Processing sheet with id=AE6, first strand: chain 'Av' and resid 190 through 193 removed outlier: 5.773A pdb=" N ASNAv 190 " --> pdb=" O PHEAv 680 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYRAv 682 " --> pdb=" O ASNAv 190 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILEAv 192 " --> pdb=" O TYRAv 682 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Av' and resid 228 through 229 Processing sheet with id=AE8, first strand: chain 'Av' and resid 228 through 229 Processing sheet with id=AE9, first strand: chain 'Av' and resid 270 through 274 Processing sheet with id=AF1, first strand: chain 'Av' and resid 312 through 313 removed outlier: 4.596A pdb=" N ALAAv 312 " --> pdb=" O ASNAv 461 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNAv 461 " --> pdb=" O ALAAv 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'Av' and resid 333 through 340 removed outlier: 6.972A pdb=" N LEUAv 319 " --> pdb=" O LEUAv 456 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEUAv 456 " --> pdb=" O LEUAv 319 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYSAv 321 " --> pdb=" O TYRAv 454 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYRAv 454 " --> pdb=" O LYSAv 321 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEUAv 323 " --> pdb=" O VALAv 452 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Av' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAv 366 " --> pdb=" O ILEAv 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERAv 368 " --> pdb=" O LEUAv 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAv 398 " --> pdb=" O SERAv 368 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHEAv 370 " --> pdb=" O ALAAv 396 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAAv 396 " --> pdb=" O PHEAv 370 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Av' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAv 366 " --> pdb=" O ILEAv 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERAv 368 " --> pdb=" O LEUAv 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAv 398 " --> pdb=" O SERAv 368 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHEAv 370 " --> pdb=" O ALAAv 396 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAAv 396 " --> pdb=" O PHEAv 370 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALAAv 395 " --> pdb=" O LEUAv 425 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEUAv 425 " --> pdb=" O ALAAv 395 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLNAv 397 " --> pdb=" O TYRAv 423 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Av' and resid 489 through 490 removed outlier: 3.539A pdb=" N SERAv 699 " --> pdb=" O VALAv 692 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Av' and resid 560 through 564 Processing sheet with id=AF7, first strand: chain 'Aw' and resid 190 through 193 removed outlier: 5.773A pdb=" N ASNAw 190 " --> pdb=" O PHEAw 680 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYRAw 682 " --> pdb=" O ASNAw 190 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILEAw 192 " --> pdb=" O TYRAw 682 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Aw' and resid 228 through 229 Processing sheet with id=AF9, first strand: chain 'Aw' and resid 270 through 274 Processing sheet with id=AG1, first strand: chain 'Aw' and resid 312 through 313 removed outlier: 4.596A pdb=" N ALAAw 312 " --> pdb=" O ASNAw 461 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNAw 461 " --> pdb=" O ALAAw 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'Aw' and resid 333 through 340 removed outlier: 6.972A pdb=" N LEUAw 319 " --> pdb=" O LEUAw 456 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEUAw 456 " --> pdb=" O LEUAw 319 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYSAw 321 " --> pdb=" O TYRAw 454 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYRAw 454 " --> pdb=" O LYSAw 321 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEUAw 323 " --> pdb=" O VALAw 452 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Aw' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAw 366 " --> pdb=" O ILEAw 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERAw 368 " --> pdb=" O LEUAw 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAw 398 " --> pdb=" O SERAw 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHEAw 370 " --> pdb=" O ALAAw 396 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALAAw 396 " --> pdb=" O PHEAw 370 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Aw' and resid 350 through 351 removed outlier: 3.535A pdb=" N THRAw 366 " --> pdb=" O ILEAw 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERAw 368 " --> pdb=" O LEUAw 398 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAw 398 " --> pdb=" O SERAw 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHEAw 370 " --> pdb=" O ALAAw 396 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALAAw 396 " --> pdb=" O PHEAw 370 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALAAw 395 " --> pdb=" O LEUAw 425 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEUAw 425 " --> pdb=" O ALAAw 395 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLNAw 397 " --> pdb=" O TYRAw 423 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Aw' and resid 489 through 490 removed outlier: 3.538A pdb=" N SERAw 699 " --> pdb=" O VALAw 692 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Aw' and resid 560 through 564 977 hydrogen bonds defined for protein. 2565 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: 5.59 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9450 1.34 - 1.46: 5404 1.46 - 1.57: 13370 1.57 - 1.69: 0 1.69 - 1.81: 186 Bond restraints: 28410 Sorted by residual: bond pdb=" C ARGAv 514 " pdb=" O ARGAv 514 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.25e-02 6.40e+03 7.11e-01 bond pdb=" C ARGAs 514 " pdb=" O ARGAs 514 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.25e-02 6.40e+03 6.32e-01 bond pdb=" C ARGAr 514 " pdb=" O ARGAr 514 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.25e-02 6.40e+03 6.11e-01 bond pdb=" C ARGAu 514 " pdb=" O ARGAu 514 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.25e-02 6.40e+03 6.00e-01 bond pdb=" C VALAw 581 " pdb=" O VALAw 581 " ideal model delta sigma weight residual 1.237 1.245 -0.009 1.13e-02 7.83e+03 5.91e-01 ... (remaining 28405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 37104 1.00 - 2.01: 1189 2.01 - 3.01: 138 3.01 - 4.01: 23 4.01 - 5.01: 12 Bond angle restraints: 38466 Sorted by residual: angle pdb=" N SERAt 598 " pdb=" CA SERAt 598 " pdb=" C SERAt 598 " ideal model delta sigma weight residual 111.40 113.30 -1.90 1.22e+00 6.72e-01 2.44e+00 angle pdb=" N SERAw 598 " pdb=" CA SERAw 598 " pdb=" C SERAw 598 " ideal model delta sigma weight residual 111.40 113.30 -1.90 1.22e+00 6.72e-01 2.42e+00 angle pdb=" N SERAr 598 " pdb=" CA SERAr 598 " pdb=" C SERAr 598 " ideal model delta sigma weight residual 111.40 113.27 -1.87 1.22e+00 6.72e-01 2.35e+00 angle pdb=" N SERAv 598 " pdb=" CA SERAv 598 " pdb=" C SERAv 598 " ideal model delta sigma weight residual 111.40 113.26 -1.86 1.22e+00 6.72e-01 2.33e+00 angle pdb=" N SERAu 598 " pdb=" CA SERAu 598 " pdb=" C SERAu 598 " ideal model delta sigma weight residual 111.40 113.26 -1.86 1.22e+00 6.72e-01 2.32e+00 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 16495 11.72 - 23.44: 689 23.44 - 35.16: 138 35.16 - 46.88: 36 46.88 - 58.60: 12 Dihedral angle restraints: 17370 sinusoidal: 7080 harmonic: 10290 Sorted by residual: dihedral pdb=" CA ARGAw 657 " pdb=" C ARGAw 657 " pdb=" N ASPAw 658 " pdb=" CA ASPAw 658 " ideal model delta harmonic sigma weight residual 180.00 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ARGAu 657 " pdb=" C ARGAu 657 " pdb=" N ASPAu 658 " pdb=" CA ASPAu 658 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ARGAt 657 " pdb=" C ARGAt 657 " pdb=" N ASPAt 658 " pdb=" CA ASPAt 658 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 17367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2751 0.028 - 0.055: 926 0.055 - 0.083: 295 0.083 - 0.111: 252 0.111 - 0.138: 90 Chirality restraints: 4314 Sorted by residual: chirality pdb=" CA VALAv 683 " pdb=" N VALAv 683 " pdb=" C VALAv 683 " pdb=" CB VALAv 683 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA VALAt 683 " pdb=" N VALAt 683 " pdb=" C VALAt 683 " pdb=" CB VALAt 683 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VALAr 683 " pdb=" N VALAr 683 " pdb=" C VALAr 683 " pdb=" CB VALAr 683 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 4311 not shown) Planarity restraints: 5064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARGAs 207 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PROAs 208 " 0.053 5.00e-02 4.00e+02 pdb=" CA PROAs 208 " -0.016 5.00e-02 4.00e+02 pdb=" CD PROAs 208 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARGAr 207 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PROAr 208 " 0.053 5.00e-02 4.00e+02 pdb=" CA PROAr 208 " -0.016 5.00e-02 4.00e+02 pdb=" CD PROAr 208 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARGAv 207 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PROAv 208 " 0.053 5.00e-02 4.00e+02 pdb=" CA PROAv 208 " -0.016 5.00e-02 4.00e+02 pdb=" CD PROAv 208 " -0.017 5.00e-02 4.00e+02 ... (remaining 5061 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 189 2.56 - 3.15: 20845 3.15 - 3.73: 36142 3.73 - 4.32: 49750 4.32 - 4.90: 86909 Nonbonded interactions: 193835 Sorted by model distance: nonbonded pdb=" ND2 ASNAr 625 " pdb=" OE1 GLNAw 603 " model vdw 1.975 3.120 nonbonded pdb=" OE1 GLNAs 603 " pdb=" ND2 ASNAt 625 " model vdw 2.182 3.120 nonbonded pdb=" OE1 GLNAr 603 " pdb=" ND2 ASNAs 625 " model vdw 2.250 3.120 nonbonded pdb=" O GLYAr 548 " pdb=" NH1 ARGAr 551 " model vdw 2.291 3.120 nonbonded pdb=" O GLYAs 548 " pdb=" NH1 ARGAs 551 " model vdw 2.291 3.120 ... (remaining 193830 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: 0.10 Found NCS groups: ncs_group { reference = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' } 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: 9.590 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.070 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 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 : 0.003 0.027 28410 Z= 0.145 Angle : 0.437 5.014 38466 Z= 0.240 Chirality : 0.041 0.138 4314 Planarity : 0.003 0.031 5064 Dihedral : 7.479 58.604 10710 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.96 % Allowed : 1.38 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 3486 helix: 1.79 (0.22), residues: 666 sheet: 0.76 (0.18), residues: 930 loop : -0.54 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAu 590 TYR 0.008 0.001 TYRAs 626 PHE 0.008 0.001 PHEAr 357 TRP 0.004 0.001 TRPAr 225 HIS 0.001 0.000 HISAt 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (28410) covalent geometry : angle 0.43737 / 0.24 (38466) hydrogen bonds : bond 0.25088 / 16.86 ( 913) hydrogen bonds : angle 7.27972 / 4.94 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 379 time to evaluate : 1.074 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ar 224 ASP cc_start: 0.9115 (t0) cc_final: 0.8822 (t0) REVERT: Ar 321 LYS cc_start: 0.9251 (mttt) cc_final: 0.9020 (mtpp) REVERT: Ar 354 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7151 (mm-30) REVERT: Ar 393 LYS cc_start: 0.9176 (mttt) cc_final: 0.8847 (tptp) REVERT: Ar 413 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9052 (mt) REVERT: Ar 438 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8475 (tm-30) REVERT: Ar 439 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8197 (mp0) REVERT: Ar 456 LEU cc_start: 0.9051 (mt) cc_final: 0.8836 (mt) REVERT: Ar 517 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.8514 (m-40) REVERT: Ar 521 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8723 (mp0) REVERT: Ar 615 GLU cc_start: 0.8749 (tt0) cc_final: 0.8505 (tt0) REVERT: As 177 LYS cc_start: 0.9105 (mttt) cc_final: 0.8856 (mmmt) REVERT: As 235 MET cc_start: 0.9483 (mtt) cc_final: 0.9207 (mtm) REVERT: As 360 MET cc_start: 0.8983 (mtt) cc_final: 0.8768 (mtp) REVERT: As 455 GLU cc_start: 0.9057 (tt0) cc_final: 0.8412 (mt-10) REVERT: As 476 MET cc_start: 0.8884 (ttp) cc_final: 0.7995 (pmm) REVERT: As 519 MET cc_start: 0.9208 (tmm) cc_final: 0.8992 (ppp) REVERT: As 580 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8433 (mm-30) REVERT: As 586 MET cc_start: 0.9172 (mmm) cc_final: 0.8901 (mmm) REVERT: As 655 MET cc_start: 0.9212 (mtp) cc_final: 0.8964 (mtp) REVERT: At 165 ARG cc_start: 0.8626 (ttp-170) cc_final: 0.8405 (ttp80) REVERT: At 354 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7822 (tp30) REVERT: At 455 GLU cc_start: 0.8678 (tt0) cc_final: 0.8050 (tm-30) REVERT: At 519 MET cc_start: 0.9382 (tmm) cc_final: 0.9148 (tmm) REVERT: At 521 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8908 (mt-10) REVERT: At 547 GLU cc_start: 0.8894 (tt0) cc_final: 0.8641 (tt0) REVERT: At 566 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8362 (mp0) REVERT: At 616 LYS cc_start: 0.9418 (mttt) cc_final: 0.9184 (mtpp) REVERT: Au 235 MET cc_start: 0.9233 (mtt) cc_final: 0.8838 (mtp) REVERT: Au 292 MET cc_start: 0.8994 (mmm) cc_final: 0.8782 (mmm) REVERT: Au 360 MET cc_start: 0.8881 (mtt) cc_final: 0.8401 (mtp) REVERT: Au 455 GLU cc_start: 0.9092 (tt0) cc_final: 0.8809 (mm-30) REVERT: Au 476 MET cc_start: 0.8978 (ttp) cc_final: 0.7846 (pmm) REVERT: Au 517 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8091 (m-40) REVERT: Au 521 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8881 (mt-10) REVERT: Au 580 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8327 (mm-30) REVERT: Au 642 VAL cc_start: 0.9655 (OUTLIER) cc_final: 0.9449 (p) REVERT: Au 658 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8633 (p0) REVERT: Av 165 ARG cc_start: 0.9194 (ttp-170) cc_final: 0.8901 (ttp80) REVERT: Av 354 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7672 (tp30) REVERT: Av 375 THR cc_start: 0.8960 (m) cc_final: 0.8513 (p) REVERT: Av 427 ASP cc_start: 0.9346 (t0) cc_final: 0.8510 (p0) REVERT: Av 455 GLU cc_start: 0.8768 (tt0) cc_final: 0.8354 (tm-30) REVERT: Av 476 MET cc_start: 0.8929 (ttp) cc_final: 0.7352 (pmm) REVERT: Av 547 GLU cc_start: 0.8950 (tt0) cc_final: 0.8735 (tt0) REVERT: Av 580 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8397 (mm-30) REVERT: Av 616 LYS cc_start: 0.9523 (mttt) cc_final: 0.9247 (mtpp) REVERT: Aw 177 LYS cc_start: 0.9328 (mttt) cc_final: 0.8915 (mmmt) REVERT: Aw 184 MET cc_start: 0.8783 (ttp) cc_final: 0.8581 (ttp) REVERT: Aw 235 MET cc_start: 0.9078 (mtt) cc_final: 0.8865 (mtm) REVERT: Aw 292 MET cc_start: 0.8844 (mmm) cc_final: 0.8635 (mmm) REVERT: Aw 473 ASP cc_start: 0.8046 (t0) cc_final: 0.7592 (p0) REVERT: Aw 476 MET cc_start: 0.9038 (ttp) cc_final: 0.8159 (pmm) REVERT: Aw 518 LEU cc_start: 0.9498 (mt) cc_final: 0.9205 (mt) REVERT: Aw 521 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8922 (mt-10) REVERT: Aw 580 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8334 (mm-30) REVERT: Aw 616 LYS cc_start: 0.9402 (mttt) cc_final: 0.8969 (mtpp) REVERT: Aw 697 GLN cc_start: 0.8570 (pt0) cc_final: 0.8213 (mm-40) outliers start: 60 outliers final: 18 residues processed: 431 average time/residue: 0.2013 time to fit residues: 131.7496 Evaluate side-chains 250 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 262 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 517 ASN Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain As residue 413 LEU Chi-restraints excluded: chain As residue 415 VAL Chi-restraints excluded: chain As residue 464 ASN Chi-restraints excluded: chain At residue 262 VAL Chi-restraints excluded: chain At residue 415 VAL Chi-restraints excluded: chain At residue 464 ASN Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain Au residue 262 VAL Chi-restraints excluded: chain Au residue 413 LEU Chi-restraints excluded: chain Au residue 415 VAL Chi-restraints excluded: chain Au residue 464 ASN Chi-restraints excluded: chain Au residue 517 ASN Chi-restraints excluded: chain Au residue 642 VAL Chi-restraints excluded: chain Au residue 658 ASP Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 464 ASN Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 642 VAL Chi-restraints excluded: chain Aw residue 415 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ar 629 GLN Ar 651 ASN As 629 GLN At 331 HIS At 442 GLN At 629 GLN At 651 ASN Au 433 GLN Au 629 GLN Au 697 GLN Av 331 HIS Av 629 GLN Av 651 ASN Aw 433 GLN Aw 464 ASN Aw 629 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.059162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.047840 restraints weight = 87747.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.049807 restraints weight = 42348.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.051146 restraints weight = 26013.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.052083 restraints weight = 18358.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.052711 restraints weight = 14210.039| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 28410 Z= 0.285 Angle : 0.658 6.590 38466 Z= 0.349 Chirality : 0.047 0.221 4314 Planarity : 0.004 0.037 5064 Dihedral : 5.042 58.759 3903 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.10 % Allowed : 5.27 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3486 helix: 1.17 (0.21), residues: 660 sheet: 0.55 (0.18), residues: 840 loop : -0.79 (0.15), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARGAr 480 TYR 0.021 0.002 TYRAr 602 PHE 0.020 0.002 PHEAw 680 TRP 0.014 0.002 TRPAt 225 HIS 0.003 0.001 HISAu 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 (28410) covalent geometry : angle 0.65783 / 0.35 (38466) hydrogen bonds : bond 0.06983 / 4.68 ( 913) hydrogen bonds : angle 5.25564 / 3.59 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 1.103 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ar 224 ASP cc_start: 0.8836 (t0) cc_final: 0.8555 (t0) REVERT: Ar 360 MET cc_start: 0.9278 (mmm) cc_final: 0.8373 (mmm) REVERT: Ar 393 LYS cc_start: 0.9388 (mttt) cc_final: 0.8588 (tptp) REVERT: Ar 413 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9094 (mt) REVERT: Ar 455 GLU cc_start: 0.8480 (tp30) cc_final: 0.8161 (tp30) REVERT: As 177 LYS cc_start: 0.9127 (mttt) cc_final: 0.8883 (mmmt) REVERT: As 235 MET cc_start: 0.9547 (mtt) cc_final: 0.9304 (mtm) REVERT: As 360 MET cc_start: 0.8977 (mtt) cc_final: 0.8738 (mtp) REVERT: As 455 GLU cc_start: 0.8847 (tt0) cc_final: 0.8373 (mt-10) REVERT: As 476 MET cc_start: 0.8689 (ttp) cc_final: 0.8027 (pmm) REVERT: As 580 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8057 (mm-30) REVERT: At 165 ARG cc_start: 0.9107 (ttp-170) cc_final: 0.8597 (ttp80) REVERT: At 360 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9196 (mmm) REVERT: At 421 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8154 (mm-30) REVERT: At 455 GLU cc_start: 0.8448 (tt0) cc_final: 0.8090 (tm-30) REVERT: At 519 MET cc_start: 0.9414 (tmm) cc_final: 0.9098 (tmm) REVERT: At 521 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8704 (mt-10) REVERT: At 547 GLU cc_start: 0.8596 (tt0) cc_final: 0.8132 (tt0) REVERT: Au 167 MET cc_start: 0.9159 (mtt) cc_final: 0.8674 (mtm) REVERT: Au 314 ASP cc_start: 0.9018 (t0) cc_final: 0.8815 (t0) REVERT: Au 580 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8488 (mm-30) REVERT: Au 679 MET cc_start: 0.9379 (ptt) cc_final: 0.9123 (ptt) REVERT: Av 167 MET cc_start: 0.8769 (mtm) cc_final: 0.8408 (mtm) REVERT: Av 214 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9079 (pt) REVERT: Av 292 MET cc_start: 0.9239 (mmm) cc_final: 0.8976 (mmm) REVERT: Av 360 MET cc_start: 0.9446 (mtp) cc_final: 0.8022 (mmm) REVERT: Av 414 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7976 (ttm170) REVERT: Av 427 ASP cc_start: 0.9051 (t0) cc_final: 0.8410 (p0) REVERT: Av 455 GLU cc_start: 0.8546 (tt0) cc_final: 0.8294 (tm-30) REVERT: Av 519 MET cc_start: 0.9406 (tmm) cc_final: 0.9039 (tmm) REVERT: Av 596 MET cc_start: 0.8726 (mtp) cc_final: 0.8386 (mtp) REVERT: Av 616 LYS cc_start: 0.9445 (mttt) cc_final: 0.9202 (mtpp) REVERT: Aw 518 LEU cc_start: 0.9562 (mt) cc_final: 0.9352 (mt) REVERT: Aw 519 MET cc_start: 0.9286 (ppp) cc_final: 0.8898 (ppp) REVERT: Aw 580 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8372 (mm-30) REVERT: Aw 616 LYS cc_start: 0.9243 (mttt) cc_final: 0.8866 (mtpp) outliers start: 64 outliers final: 31 residues processed: 256 average time/residue: 0.1761 time to fit residues: 72.2515 Evaluate side-chains 204 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 203 VAL Chi-restraints excluded: chain Ar residue 262 VAL Chi-restraints excluded: chain Ar residue 290 ILE Chi-restraints excluded: chain Ar residue 398 LEU Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 476 MET Chi-restraints excluded: chain Ar residue 504 LEU Chi-restraints excluded: chain Ar residue 518 LEU Chi-restraints excluded: chain Ar residue 546 ILE Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain Ar residue 702 THR Chi-restraints excluded: chain Ar residue 711 VAL Chi-restraints excluded: chain As residue 413 LEU Chi-restraints excluded: chain As residue 483 ILE Chi-restraints excluded: chain At residue 262 VAL Chi-restraints excluded: chain At residue 360 MET Chi-restraints excluded: chain At residue 415 VAL Chi-restraints excluded: chain At residue 546 ILE Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain Au residue 262 VAL Chi-restraints excluded: chain Au residue 530 LEU Chi-restraints excluded: chain Au residue 546 ILE Chi-restraints excluded: chain Av residue 214 LEU Chi-restraints excluded: chain Av residue 414 ARG Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 642 VAL Chi-restraints excluded: chain Aw residue 290 ILE Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 413 LEU Chi-restraints excluded: chain Aw residue 483 ILE Chi-restraints excluded: chain Aw residue 546 ILE Chi-restraints excluded: chain Aw residue 655 MET Chi-restraints excluded: chain Aw residue 679 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [253, 95, 28, 147, 217, 114, 250, 302, 196, 20, 156] chunk 253 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ar 562 ASN At 713 ASN Au 433 GLN Au 697 GLN Au 740 ASN Aw 433 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.060865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.049583 restraints weight = 86604.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.051616 restraints weight = 41345.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.052993 restraints weight = 25240.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.053929 restraints weight = 17698.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.054616 restraints weight = 13632.159| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28410 Z= 0.141 Angle : 0.497 7.228 38466 Z= 0.269 Chirality : 0.043 0.149 4314 Planarity : 0.004 0.036 5064 Dihedral : 4.521 58.438 3883 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.60 % Allowed : 6.75 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3486 helix: 1.57 (0.21), residues: 660 sheet: 0.36 (0.17), residues: 888 loop : -0.80 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAr 638 TYR 0.014 0.001 TYRAr 602 PHE 0.012 0.001 PHEAw 680 TRP 0.006 0.001 TRPAr 557 HIS 0.002 0.000 HISAr 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (28410) covalent geometry : angle 0.49704 / 0.27 (38466) hydrogen bonds : bond 0.05659 / 3.79 ( 913) hydrogen bonds : angle 4.75791 / 3.25 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.850 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ar 224 ASP cc_start: 0.8861 (t0) cc_final: 0.8563 (t0) REVERT: Ar 360 MET cc_start: 0.9313 (mmm) cc_final: 0.8712 (mmm) REVERT: Ar 413 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8940 (mt) REVERT: Ar 455 GLU cc_start: 0.8539 (tp30) cc_final: 0.8116 (tp30) REVERT: Ar 521 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8788 (mt-10) REVERT: Ar 566 GLU cc_start: 0.7944 (mp0) cc_final: 0.7691 (mp0) REVERT: As 177 LYS cc_start: 0.9149 (mttt) cc_final: 0.8824 (mmmt) REVERT: As 235 MET cc_start: 0.9524 (mtt) cc_final: 0.9307 (mtm) REVERT: As 314 ASP cc_start: 0.8995 (t0) cc_final: 0.8646 (t70) REVERT: As 455 GLU cc_start: 0.8801 (tt0) cc_final: 0.8289 (mt-10) REVERT: As 476 MET cc_start: 0.8674 (ttp) cc_final: 0.8005 (pmm) REVERT: As 580 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8150 (mm-30) REVERT: At 165 ARG cc_start: 0.9092 (ttp-170) cc_final: 0.8666 (ttp80) REVERT: At 421 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8220 (mm-30) REVERT: At 521 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8878 (mt-10) REVERT: At 547 GLU cc_start: 0.8579 (tt0) cc_final: 0.7884 (tt0) REVERT: Au 167 MET cc_start: 0.9153 (mtt) cc_final: 0.8783 (mtm) REVERT: Au 235 MET cc_start: 0.9461 (mtp) cc_final: 0.9161 (mtp) REVERT: Au 314 ASP cc_start: 0.9026 (t0) cc_final: 0.8811 (t0) REVERT: Au 476 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7643 (pmm) REVERT: Au 521 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8578 (mt-10) REVERT: Au 566 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7939 (mp0) REVERT: Au 580 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8418 (mm-30) REVERT: Au 709 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.6783 (tmt90) REVERT: Av 167 MET cc_start: 0.8778 (mtm) cc_final: 0.8379 (mtm) REVERT: Av 214 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9128 (pt) REVERT: Av 292 MET cc_start: 0.9250 (mmm) cc_final: 0.8946 (mmm) REVERT: Av 360 MET cc_start: 0.9354 (mtp) cc_final: 0.8099 (mmm) REVERT: Av 414 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7998 (ttm170) REVERT: Av 427 ASP cc_start: 0.9073 (t0) cc_final: 0.8406 (p0) REVERT: Av 476 MET cc_start: 0.9030 (tmm) cc_final: 0.8425 (tmm) REVERT: Av 519 MET cc_start: 0.9383 (tmm) cc_final: 0.9063 (tmm) REVERT: Av 596 MET cc_start: 0.8713 (mtp) cc_final: 0.8471 (mtp) REVERT: Av 616 LYS cc_start: 0.9443 (mttt) cc_final: 0.9185 (mtpp) REVERT: Aw 519 MET cc_start: 0.9192 (ppp) cc_final: 0.8929 (ppp) REVERT: Aw 580 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8367 (mm-30) REVERT: Aw 616 LYS cc_start: 0.9223 (mttt) cc_final: 0.8837 (mtpp) outliers start: 49 outliers final: 27 residues processed: 225 average time/residue: 0.1810 time to fit residues: 64.1994 Evaluate side-chains 206 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 262 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 504 LEU Chi-restraints excluded: chain Ar residue 546 ILE Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain As residue 262 VAL Chi-restraints excluded: chain As residue 413 LEU Chi-restraints excluded: chain As residue 530 LEU Chi-restraints excluded: chain As residue 596 MET Chi-restraints excluded: chain At residue 415 VAL Chi-restraints excluded: chain At residue 530 LEU Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain Au residue 177 LYS Chi-restraints excluded: chain Au residue 262 VAL Chi-restraints excluded: chain Au residue 361 THR Chi-restraints excluded: chain Au residue 476 MET Chi-restraints excluded: chain Au residue 530 LEU Chi-restraints excluded: chain Au residue 546 ILE Chi-restraints excluded: chain Au residue 574 THR Chi-restraints excluded: chain Au residue 703 MET Chi-restraints excluded: chain Au residue 709 ARG Chi-restraints excluded: chain Av residue 214 LEU Chi-restraints excluded: chain Av residue 414 ARG Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 642 VAL Chi-restraints excluded: chain Aw residue 290 ILE Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 530 LEU Chi-restraints excluded: chain Aw residue 655 MET Chi-restraints excluded: chain Aw residue 703 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [73, 48, 213, 316, 263, 172, 269, 2, 147, 1, 57] chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 316 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... As 433 GLN As 651 ASN At 442 GLN Au 367 HIS Au 433 GLN Au 651 ASN Aw 367 HIS Aw 433 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.056125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.045156 restraints weight = 90501.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.047034 restraints weight = 43803.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.048305 restraints weight = 27046.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.049187 restraints weight = 19210.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.049793 restraints weight = 15002.777| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 28410 Z= 0.375 Angle : 0.728 7.183 38466 Z= 0.385 Chirality : 0.047 0.189 4314 Planarity : 0.005 0.044 5064 Dihedral : 5.219 56.891 3882 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.90 % Allowed : 7.76 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3486 helix: 1.04 (0.21), residues: 660 sheet: 0.04 (0.18), residues: 882 loop : -1.10 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAw 480 TYR 0.024 0.002 TYRAv 626 PHE 0.024 0.002 PHEAt 680 TRP 0.011 0.002 TRPAw 225 HIS 0.004 0.001 HISAu 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00878 / 0.38 (28410) covalent geometry : angle 0.72760 / 0.38 (38466) hydrogen bonds : bond 0.07938 / 5.31 ( 913) hydrogen bonds : angle 5.28998 / 3.62 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 159 time to evaluate : 1.136 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ar 224 ASP cc_start: 0.8936 (t0) cc_final: 0.8723 (t0) REVERT: Ar 413 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9305 (mt) REVERT: Ar 455 GLU cc_start: 0.8634 (tp30) cc_final: 0.8229 (tp30) REVERT: Ar 566 GLU cc_start: 0.8031 (mp0) cc_final: 0.7790 (mp0) REVERT: Ar 709 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7097 (tmt90) REVERT: As 177 LYS cc_start: 0.9213 (mttt) cc_final: 0.8894 (mmmt) REVERT: As 235 MET cc_start: 0.9504 (mtt) cc_final: 0.9291 (mtm) REVERT: As 354 GLU cc_start: 0.3239 (mm-30) cc_final: 0.2706 (tp30) REVERT: As 360 MET cc_start: 0.9020 (mtp) cc_final: 0.7767 (mmm) REVERT: As 455 GLU cc_start: 0.8919 (tt0) cc_final: 0.8571 (tt0) REVERT: As 476 MET cc_start: 0.8796 (ttp) cc_final: 0.8029 (pmm) REVERT: As 521 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8406 (mp0) REVERT: As 580 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8355 (mm-30) REVERT: At 167 MET cc_start: 0.8840 (mtp) cc_final: 0.7966 (mtp) REVERT: At 519 MET cc_start: 0.9464 (ppp) cc_final: 0.9225 (ppp) REVERT: At 521 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8902 (mt-10) REVERT: At 547 GLU cc_start: 0.8668 (tt0) cc_final: 0.8402 (tt0) REVERT: Au 235 MET cc_start: 0.9510 (mtp) cc_final: 0.9238 (mtp) REVERT: Au 566 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8061 (mp0) REVERT: Au 580 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8536 (mm-30) REVERT: Au 709 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6459 (tmt90) REVERT: Av 354 GLU cc_start: 0.3610 (tp30) cc_final: 0.3251 (tp30) REVERT: Av 360 MET cc_start: 0.9487 (mtp) cc_final: 0.9226 (mmm) REVERT: Av 427 ASP cc_start: 0.8913 (t0) cc_final: 0.8214 (p0) REVERT: Av 476 MET cc_start: 0.9124 (tmm) cc_final: 0.8511 (tmm) REVERT: Av 580 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: Av 596 MET cc_start: 0.8839 (mtp) cc_final: 0.8601 (mtp) REVERT: Av 616 LYS cc_start: 0.9492 (mttt) cc_final: 0.9270 (mtpp) REVERT: Aw 167 MET cc_start: 0.9018 (mtm) cc_final: 0.8722 (mtm) REVERT: Aw 168 MET cc_start: 0.9055 (ttp) cc_final: 0.8789 (ttp) REVERT: Aw 184 MET cc_start: 0.8851 (ttp) cc_final: 0.8615 (ttp) REVERT: Aw 519 MET cc_start: 0.9288 (ppp) cc_final: 0.8810 (ppp) REVERT: Aw 634 ASP cc_start: 0.7584 (t0) cc_final: 0.7377 (t0) outliers start: 58 outliers final: 41 residues processed: 210 average time/residue: 0.1832 time to fit residues: 61.7439 Evaluate side-chains 188 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 203 VAL Chi-restraints excluded: chain Ar residue 262 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 476 MET Chi-restraints excluded: chain Ar residue 504 LEU Chi-restraints excluded: chain Ar residue 518 LEU Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 642 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain Ar residue 702 THR Chi-restraints excluded: chain Ar residue 709 ARG Chi-restraints excluded: chain Ar residue 711 VAL Chi-restraints excluded: chain Ar residue 740 ASN Chi-restraints excluded: chain As residue 262 VAL Chi-restraints excluded: chain As residue 413 LEU Chi-restraints excluded: chain As residue 530 LEU Chi-restraints excluded: chain As residue 546 ILE Chi-restraints excluded: chain At residue 262 VAL Chi-restraints excluded: chain At residue 415 VAL Chi-restraints excluded: chain At residue 458 ILE Chi-restraints excluded: chain At residue 546 ILE Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain Au residue 262 VAL Chi-restraints excluded: chain Au residue 361 THR Chi-restraints excluded: chain Au residue 413 LEU Chi-restraints excluded: chain Au residue 476 MET Chi-restraints excluded: chain Au residue 530 LEU Chi-restraints excluded: chain Au residue 535 THR Chi-restraints excluded: chain Au residue 546 ILE Chi-restraints excluded: chain Au residue 703 MET Chi-restraints excluded: chain Au residue 709 ARG Chi-restraints excluded: chain Av residue 214 LEU Chi-restraints excluded: chain Av residue 295 ILE Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 580 GLU Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 642 VAL Chi-restraints excluded: chain Aw residue 290 ILE Chi-restraints excluded: chain Aw residue 361 THR Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 413 LEU Chi-restraints excluded: chain Aw residue 530 LEU Chi-restraints excluded: chain Aw residue 546 ILE Chi-restraints excluded: chain Aw residue 655 MET Chi-restraints excluded: chain Aw residue 703 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [293, 156, 344, 59, 96, 158, 252, 62, 157, 121, 100] chunk 293 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... As 433 GLN Au 433 GLN Aw 433 GLN Aw 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.059436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.048351 restraints weight = 86847.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.050356 restraints weight = 41176.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.051718 restraints weight = 25055.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.052657 restraints weight = 17569.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.053323 restraints weight = 13529.488| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28410 Z= 0.128 Angle : 0.498 9.652 38466 Z= 0.269 Chirality : 0.043 0.143 4314 Planarity : 0.004 0.036 5064 Dihedral : 4.660 58.253 3882 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.38 % Allowed : 8.38 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3486 helix: 1.88 (0.22), residues: 618 sheet: -0.36 (0.16), residues: 1008 loop : -0.62 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAu 435 TYR 0.012 0.001 TYRAr 602 PHE 0.011 0.001 PHEAw 680 TRP 0.005 0.001 TRPAv 557 HIS 0.002 0.000 HISAw 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (28410) covalent geometry : angle 0.49765 / 0.27 (38466) hydrogen bonds : bond 0.05428 / 3.65 ( 913) hydrogen bonds : angle 4.64813 / 3.16 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.914 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ar 224 ASP cc_start: 0.8922 (t0) cc_final: 0.8666 (t0) REVERT: Ar 360 MET cc_start: 0.9477 (mmt) cc_final: 0.8765 (mmm) REVERT: Ar 413 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9018 (mt) REVERT: Ar 421 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8121 (mm-30) REVERT: Ar 455 GLU cc_start: 0.8585 (tp30) cc_final: 0.8159 (tp30) REVERT: Ar 566 GLU cc_start: 0.8105 (mp0) cc_final: 0.7882 (mp0) REVERT: Ar 709 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7036 (tmt90) REVERT: As 177 LYS cc_start: 0.9186 (mttt) cc_final: 0.8860 (mmmt) REVERT: As 360 MET cc_start: 0.8746 (mtp) cc_final: 0.8020 (mmm) REVERT: As 455 GLU cc_start: 0.8857 (tt0) cc_final: 0.8463 (tt0) REVERT: As 476 MET cc_start: 0.8826 (ttp) cc_final: 0.8049 (pmm) REVERT: As 521 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8136 (mp0) REVERT: As 580 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8118 (mm-30) REVERT: At 167 MET cc_start: 0.8971 (mtp) cc_final: 0.8534 (mtp) REVERT: At 360 MET cc_start: 0.9644 (mmm) cc_final: 0.9215 (mmm) REVERT: At 521 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8919 (mt-10) REVERT: At 547 GLU cc_start: 0.8674 (tt0) cc_final: 0.8450 (tt0) REVERT: Au 235 MET cc_start: 0.9529 (mtp) cc_final: 0.9313 (mtp) REVERT: Au 314 ASP cc_start: 0.9121 (t0) cc_final: 0.8890 (t0) REVERT: Au 476 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7586 (pmm) REVERT: Au 521 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8464 (mt-10) REVERT: Au 566 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8098 (mp0) REVERT: Au 709 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6685 (tmt90) REVERT: Av 167 MET cc_start: 0.8805 (mtm) cc_final: 0.8565 (mtm) REVERT: Av 214 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8922 (pt) REVERT: Av 354 GLU cc_start: 0.3390 (tp30) cc_final: 0.3051 (tp30) REVERT: Av 476 MET cc_start: 0.9060 (tmm) cc_final: 0.8534 (tmm) REVERT: Av 519 MET cc_start: 0.9334 (tmm) cc_final: 0.9126 (tmm) REVERT: Av 616 LYS cc_start: 0.9467 (mttt) cc_final: 0.9221 (mtpp) REVERT: Av 709 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6351 (tmt90) REVERT: Aw 168 MET cc_start: 0.8997 (ttp) cc_final: 0.8773 (ttp) REVERT: Aw 519 MET cc_start: 0.9187 (ppp) cc_final: 0.8947 (ppp) REVERT: Aw 634 ASP cc_start: 0.7511 (t0) cc_final: 0.7249 (t0) outliers start: 42 outliers final: 22 residues processed: 194 average time/residue: 0.1772 time to fit residues: 54.5513 Evaluate side-chains 177 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 203 VAL Chi-restraints excluded: chain Ar residue 262 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 476 MET Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain Ar residue 709 ARG Chi-restraints excluded: chain As residue 262 VAL Chi-restraints excluded: chain At residue 415 VAL Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain Au residue 413 LEU Chi-restraints excluded: chain Au residue 476 MET Chi-restraints excluded: chain Au residue 518 LEU Chi-restraints excluded: chain Au residue 530 LEU Chi-restraints excluded: chain Au residue 535 THR Chi-restraints excluded: chain Au residue 546 ILE Chi-restraints excluded: chain Au residue 703 MET Chi-restraints excluded: chain Au residue 709 ARG Chi-restraints excluded: chain Av residue 214 LEU Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 642 VAL Chi-restraints excluded: chain Av residue 709 ARG Chi-restraints excluded: chain Aw residue 290 ILE Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 413 LEU Chi-restraints excluded: chain Aw residue 530 LEU Chi-restraints excluded: chain Aw residue 655 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [248, 246, 266, 122, 210, 167, 115, 11, 201, 259, 214] chunk 248 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 167 optimal weight: 0.0030 chunk 115 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.058239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.047297 restraints weight = 87887.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.049257 restraints weight = 41759.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.050591 restraints weight = 25444.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.051506 restraints weight = 17856.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.052147 restraints weight = 13770.507| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28410 Z= 0.195 Angle : 0.537 9.736 38466 Z= 0.287 Chirality : 0.043 0.140 4314 Planarity : 0.004 0.039 5064 Dihedral : 4.580 57.365 3879 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.38 % Allowed : 9.33 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 3486 helix: 1.52 (0.21), residues: 660 sheet: -0.17 (0.18), residues: 888 loop : -0.89 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAu 435 TYR 0.014 0.001 TYRAr 602 PHE 0.015 0.001 PHEAw 680 TRP 0.006 0.001 TRPAw 557 HIS 0.002 0.001 HISAu 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (28410) covalent geometry : angle 0.53738 / 0.29 (38466) hydrogen bonds : bond 0.05934 / 3.98 ( 913) hydrogen bonds : angle 4.67707 / 3.18 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.207 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: symmetry clash revert: symmetry clash REVERT: Ar 224 ASP cc_start: 0.8953 (t0) cc_final: 0.8694 (t0) REVERT: Ar 413 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9099 (mt) REVERT: Ar 421 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8195 (mm-30) REVERT: Ar 455 GLU cc_start: 0.8596 (tp30) cc_final: 0.8208 (tp30) REVERT: Ar 566 GLU cc_start: 0.8092 (mp0) cc_final: 0.7866 (mp0) REVERT: Ar 709 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.6859 (tmt90) REVERT: As 177 LYS cc_start: 0.9194 (mttt) cc_final: 0.8876 (mmmt) REVERT: As 354 GLU cc_start: 0.3503 (mm-30) cc_final: 0.3021 (tp30) REVERT: As 360 MET cc_start: 0.8890 (mtp) cc_final: 0.7962 (mmm) REVERT: As 455 GLU cc_start: 0.8883 (tt0) cc_final: 0.8507 (tt0) REVERT: As 476 MET cc_start: 0.8779 (ttp) cc_final: 0.8018 (pmm) REVERT: As 521 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8127 (mp0) REVERT: As 580 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8105 (mm-30) REVERT: At 167 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: At 521 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8910 (mt-10) REVERT: At 547 GLU cc_start: 0.8665 (tt0) cc_final: 0.8444 (tt0) REVERT: At 709 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7783 (ttt180) REVERT: Au 235 MET cc_start: 0.9527 (mtp) cc_final: 0.9310 (mtp) REVERT: Au 314 ASP cc_start: 0.9138 (t0) cc_final: 0.8806 (t70) REVERT: Au 566 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8039 (mp0) REVERT: Au 709 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6639 (tmt90) REVERT: Av 167 MET cc_start: 0.8874 (mtm) cc_final: 0.8595 (mtm) REVERT: Av 214 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8860 (pt) REVERT: Av 360 MET cc_start: 0.9415 (mtp) cc_final: 0.7919 (mmm) REVERT: Av 476 MET cc_start: 0.9024 (tmm) cc_final: 0.8514 (tmm) REVERT: Av 616 LYS cc_start: 0.9483 (mttt) cc_final: 0.9236 (mtpp) REVERT: Av 709 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.6313 (tmt90) REVERT: Aw 519 MET cc_start: 0.9229 (ppp) cc_final: 0.8929 (ppp) REVERT: Aw 634 ASP cc_start: 0.7634 (t0) cc_final: 0.7306 (t0) outliers start: 42 outliers final: 28 residues processed: 183 average time/residue: 0.1804 time to fit residues: 52.9077 Evaluate side-chains 179 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 203 VAL Chi-restraints excluded: chain Ar residue 262 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 476 MET Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain Ar residue 709 ARG Chi-restraints excluded: chain As residue 262 VAL Chi-restraints excluded: chain As residue 546 ILE Chi-restraints excluded: chain At residue 167 MET Chi-restraints excluded: chain At residue 262 VAL Chi-restraints excluded: chain At residue 415 VAL Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain At residue 709 ARG Chi-restraints excluded: chain Au residue 413 LEU Chi-restraints excluded: chain Au residue 476 MET Chi-restraints excluded: chain Au residue 530 LEU Chi-restraints excluded: chain Au residue 533 VAL Chi-restraints excluded: chain Au residue 535 THR Chi-restraints excluded: chain Au residue 546 ILE Chi-restraints excluded: chain Au residue 703 MET Chi-restraints excluded: chain Au residue 709 ARG Chi-restraints excluded: chain Av residue 214 LEU Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 596 MET Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 642 VAL Chi-restraints excluded: chain Av residue 709 ARG Chi-restraints excluded: chain Aw residue 290 ILE Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 413 LEU Chi-restraints excluded: chain Aw residue 530 LEU Chi-restraints excluded: chain Aw residue 533 VAL Chi-restraints excluded: chain Aw residue 655 MET Chi-restraints excluded: chain Aw residue 703 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [132, 51, 308, 292, 167, 89, 189, 9, 324, 22, 87] chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 308 optimal weight: 10.0000 chunk 292 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.057156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.046292 restraints weight = 88349.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.048210 restraints weight = 42369.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.049504 restraints weight = 25977.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.050405 restraints weight = 18358.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.051051 restraints weight = 14246.904| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 28410 Z= 0.243 Angle : 0.585 10.520 38466 Z= 0.312 Chirality : 0.044 0.140 4314 Planarity : 0.004 0.041 5064 Dihedral : 4.797 56.375 3879 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.87 % Allowed : 9.30 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 3486 helix: 1.45 (0.21), residues: 654 sheet: -0.33 (0.17), residues: 972 loop : -0.89 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAu 435 TYR 0.016 0.002 TYRAt 602 PHE 0.022 0.002 PHEAt 370 TRP 0.010 0.001 TRPAr 557 HIS 0.003 0.001 HISAu 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (28410) covalent geometry : angle 0.58541 / 0.31 (38466) hydrogen bonds : bond 0.06553 / 4.39 ( 913) hydrogen bonds : angle 4.83064 / 3.29 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 0.785 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: symmetry clash revert: symmetry clash REVERT: Ar 354 GLU cc_start: 0.3826 (tp30) cc_final: 0.3589 (tp30) REVERT: Ar 413 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9202 (mt) REVERT: Ar 455 GLU cc_start: 0.8592 (tp30) cc_final: 0.8256 (tp30) REVERT: Ar 709 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6889 (tmt90) REVERT: As 177 LYS cc_start: 0.9195 (mttt) cc_final: 0.8870 (mmmt) REVERT: As 354 GLU cc_start: 0.2646 (mm-30) cc_final: 0.2393 (tp30) REVERT: As 360 MET cc_start: 0.9058 (mtp) cc_final: 0.8671 (mtp) REVERT: As 455 GLU cc_start: 0.8906 (tt0) cc_final: 0.8546 (tt0) REVERT: As 476 MET cc_start: 0.8816 (ttp) cc_final: 0.8001 (pmm) REVERT: As 521 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8132 (mp0) REVERT: As 566 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8064 (mp0) REVERT: As 580 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8133 (mm-30) REVERT: At 167 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8591 (mtp) REVERT: At 521 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8923 (mt-10) REVERT: At 547 GLU cc_start: 0.8700 (tt0) cc_final: 0.8484 (tt0) REVERT: At 709 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7937 (ttt180) REVERT: Au 235 MET cc_start: 0.9535 (mtp) cc_final: 0.9324 (mtp) REVERT: Au 566 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8060 (mp0) REVERT: Au 709 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6608 (tmt90) REVERT: Av 167 MET cc_start: 0.8920 (mtm) cc_final: 0.8691 (mtm) REVERT: Av 360 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.7960 (mmm) REVERT: Av 476 MET cc_start: 0.9098 (tmm) cc_final: 0.8533 (tmm) REVERT: Av 616 LYS cc_start: 0.9498 (mttt) cc_final: 0.9253 (mtpp) REVERT: Av 709 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.6334 (tmt90) REVERT: Aw 168 MET cc_start: 0.9165 (ttp) cc_final: 0.8539 (ttp) REVERT: Aw 184 MET cc_start: 0.8871 (ttp) cc_final: 0.8612 (ttp) REVERT: Aw 519 MET cc_start: 0.9267 (ppp) cc_final: 0.8884 (ppp) REVERT: Aw 634 ASP cc_start: 0.7681 (t0) cc_final: 0.7292 (t0) outliers start: 57 outliers final: 38 residues processed: 190 average time/residue: 0.1862 time to fit residues: 56.1518 Evaluate side-chains 184 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 203 VAL Chi-restraints excluded: chain Ar residue 262 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 476 MET Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain Ar residue 698 VAL Chi-restraints excluded: chain Ar residue 709 ARG Chi-restraints excluded: chain Ar residue 711 VAL Chi-restraints excluded: chain As residue 262 VAL Chi-restraints excluded: chain As residue 546 ILE Chi-restraints excluded: chain At residue 167 MET Chi-restraints excluded: chain At residue 262 VAL Chi-restraints excluded: chain At residue 415 VAL Chi-restraints excluded: chain At residue 483 ILE Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain At residue 709 ARG Chi-restraints excluded: chain Au residue 262 VAL Chi-restraints excluded: chain Au residue 295 ILE Chi-restraints excluded: chain Au residue 413 LEU Chi-restraints excluded: chain Au residue 476 MET Chi-restraints excluded: chain Au residue 518 LEU Chi-restraints excluded: chain Au residue 530 LEU Chi-restraints excluded: chain Au residue 533 VAL Chi-restraints excluded: chain Au residue 535 THR Chi-restraints excluded: chain Au residue 546 ILE Chi-restraints excluded: chain Au residue 574 THR Chi-restraints excluded: chain Au residue 703 MET Chi-restraints excluded: chain Au residue 709 ARG Chi-restraints excluded: chain Av residue 214 LEU Chi-restraints excluded: chain Av residue 360 MET Chi-restraints excluded: chain Av residue 370 PHE Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 596 MET Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 642 VAL Chi-restraints excluded: chain Av residue 709 ARG Chi-restraints excluded: chain Aw residue 290 ILE Chi-restraints excluded: chain Aw residue 361 THR Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 530 LEU Chi-restraints excluded: chain Aw residue 533 VAL Chi-restraints excluded: chain Aw residue 574 THR Chi-restraints excluded: chain Aw residue 655 MET Chi-restraints excluded: chain Aw residue 703 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [223, 194, 263, 45, 229, 182, 4, 204, 5, 73, 327] chunk 223 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 327 optimal weight: 0.0980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** As 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.059488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.048544 restraints weight = 87174.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.050538 restraints weight = 41293.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.051896 restraints weight = 25143.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.052827 restraints weight = 17613.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.053477 restraints weight = 13543.722| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28410 Z= 0.117 Angle : 0.487 11.531 38466 Z= 0.260 Chirality : 0.043 0.144 4314 Planarity : 0.003 0.050 5064 Dihedral : 4.440 58.186 3879 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.54 % Allowed : 9.82 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3486 helix: 2.12 (0.22), residues: 612 sheet: -0.33 (0.17), residues: 1008 loop : -0.66 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGAs 435 TYR 0.011 0.001 TYRAr 602 PHE 0.019 0.001 PHEAt 370 TRP 0.006 0.001 TRPAr 557 HIS 0.001 0.000 HISAu 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (28410) covalent geometry : angle 0.48675 / 0.26 (38466) hydrogen bonds : bond 0.05083 / 3.41 ( 913) hydrogen bonds : angle 4.47617 / 3.04 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.174 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: symmetry clash REVERT: Ar 354 GLU cc_start: 0.3841 (tp30) cc_final: 0.3609 (tp30) REVERT: Ar 413 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9002 (mt) REVERT: Ar 455 GLU cc_start: 0.8594 (tp30) cc_final: 0.8204 (tp30) REVERT: Ar 655 MET cc_start: 0.9140 (mtp) cc_final: 0.8940 (ttm) REVERT: Ar 709 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.6871 (tmt90) REVERT: As 177 LYS cc_start: 0.9176 (mttt) cc_final: 0.8855 (mmmt) REVERT: As 354 GLU cc_start: 0.2291 (mm-30) cc_final: 0.1602 (tp30) REVERT: As 360 MET cc_start: 0.8836 (mtp) cc_final: 0.7913 (mmm) REVERT: As 455 GLU cc_start: 0.8864 (tt0) cc_final: 0.8468 (tt0) REVERT: As 460 ARG cc_start: 0.9483 (OUTLIER) cc_final: 0.8901 (ttp-170) REVERT: As 476 MET cc_start: 0.8781 (ttp) cc_final: 0.8013 (pmm) REVERT: As 521 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8151 (mp0) REVERT: As 566 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8052 (mp0) REVERT: As 580 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8091 (mm-30) REVERT: At 167 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8581 (mtp) REVERT: At 168 MET cc_start: 0.8847 (ttp) cc_final: 0.8611 (ttp) REVERT: At 519 MET cc_start: 0.9357 (ppp) cc_final: 0.9151 (ppp) REVERT: At 521 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8908 (mt-10) REVERT: At 547 GLU cc_start: 0.8685 (tt0) cc_final: 0.8477 (tt0) REVERT: At 709 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7878 (ttt-90) REVERT: Au 314 ASP cc_start: 0.9154 (t0) cc_final: 0.8832 (t70) REVERT: Au 476 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7633 (pmm) REVERT: Au 521 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8463 (mt-10) REVERT: Au 566 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8053 (mp0) REVERT: Au 709 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6656 (tmt90) REVERT: Av 167 MET cc_start: 0.8841 (mtm) cc_final: 0.8630 (mtm) REVERT: Av 214 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8940 (pt) REVERT: Av 354 GLU cc_start: 0.3608 (tp30) cc_final: 0.3198 (tp30) REVERT: Av 414 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7883 (ttm170) REVERT: Av 476 MET cc_start: 0.9057 (tmm) cc_final: 0.8536 (tmm) REVERT: Av 616 LYS cc_start: 0.9480 (mttt) cc_final: 0.9233 (mtpp) REVERT: Av 709 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.6228 (tmt90) REVERT: Aw 168 MET cc_start: 0.9131 (ttp) cc_final: 0.8518 (ttp) REVERT: Aw 519 MET cc_start: 0.9244 (ppp) cc_final: 0.8994 (ppp) REVERT: Aw 580 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7886 (mm-30) REVERT: Aw 634 ASP cc_start: 0.7699 (t0) cc_final: 0.7292 (t0) outliers start: 47 outliers final: 29 residues processed: 192 average time/residue: 0.1913 time to fit residues: 57.8974 Evaluate side-chains 186 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 203 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 476 MET Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain Ar residue 709 ARG Chi-restraints excluded: chain As residue 262 VAL Chi-restraints excluded: chain As residue 460 ARG Chi-restraints excluded: chain As residue 530 LEU Chi-restraints excluded: chain As residue 596 MET Chi-restraints excluded: chain At residue 167 MET Chi-restraints excluded: chain At residue 262 VAL Chi-restraints excluded: chain At residue 415 VAL Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain At residue 709 ARG Chi-restraints excluded: chain Au residue 262 VAL Chi-restraints excluded: chain Au residue 476 MET Chi-restraints excluded: chain Au residue 518 LEU Chi-restraints excluded: chain Au residue 530 LEU Chi-restraints excluded: chain Au residue 535 THR Chi-restraints excluded: chain Au residue 546 ILE Chi-restraints excluded: chain Au residue 703 MET Chi-restraints excluded: chain Au residue 709 ARG Chi-restraints excluded: chain Av residue 214 LEU Chi-restraints excluded: chain Av residue 370 PHE Chi-restraints excluded: chain Av residue 414 ARG Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 483 ILE Chi-restraints excluded: chain Av residue 596 MET Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 642 VAL Chi-restraints excluded: chain Av residue 709 ARG Chi-restraints excluded: chain Aw residue 361 THR Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 413 LEU Chi-restraints excluded: chain Aw residue 530 LEU Chi-restraints excluded: chain Aw residue 533 VAL Chi-restraints excluded: chain Aw residue 655 MET Chi-restraints excluded: chain Aw residue 703 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [299, 151, 175, 302, 194, 52, 241, 223, 239, 50, 252] chunk 299 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 241 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 239 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** As 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 713 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.061214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.050239 restraints weight = 85843.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.052279 restraints weight = 40674.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.053668 restraints weight = 24665.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.054617 restraints weight = 17196.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.055290 restraints weight = 13168.935| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28410 Z= 0.094 Angle : 0.470 12.113 38466 Z= 0.247 Chirality : 0.043 0.138 4314 Planarity : 0.003 0.048 5064 Dihedral : 4.140 59.299 3878 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 10.45 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.15), residues: 3486 helix: 2.35 (0.22), residues: 612 sheet: 0.02 (0.18), residues: 900 loop : -0.77 (0.15), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAs 435 TYR 0.010 0.001 TYRAr 602 PHE 0.019 0.001 PHEAt 370 TRP 0.005 0.001 TRPAv 557 HIS 0.002 0.000 HISAu 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (28410) covalent geometry : angle 0.46971 / 0.25 (38466) hydrogen bonds : bond 0.04227 / 2.85 ( 913) hydrogen bonds : angle 4.25911 / 2.89 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.151 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: symmetry clash REVERT: Ar 354 GLU cc_start: 0.3443 (tp30) cc_final: 0.3189 (tp30) REVERT: Ar 360 MET cc_start: 0.9551 (mmt) cc_final: 0.9020 (mmm) REVERT: Ar 413 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8963 (mt) REVERT: Ar 455 GLU cc_start: 0.8586 (tp30) cc_final: 0.8224 (tp30) REVERT: Ar 521 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8710 (mp0) REVERT: Ar 655 MET cc_start: 0.9213 (mtp) cc_final: 0.8996 (ttm) REVERT: Ar 709 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6724 (tmt90) REVERT: As 177 LYS cc_start: 0.9208 (mttt) cc_final: 0.8864 (mmmt) REVERT: As 354 GLU cc_start: 0.2270 (mm-30) cc_final: 0.1590 (tp30) REVERT: As 360 MET cc_start: 0.8583 (mtp) cc_final: 0.7898 (mmm) REVERT: As 455 GLU cc_start: 0.8806 (tt0) cc_final: 0.8106 (mt-10) REVERT: As 476 MET cc_start: 0.8818 (ttp) cc_final: 0.7934 (pmm) REVERT: As 566 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8006 (mp0) REVERT: As 580 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8039 (mm-30) REVERT: At 167 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: At 354 GLU cc_start: 0.3839 (tp30) cc_final: 0.3565 (tp30) REVERT: At 519 MET cc_start: 0.9368 (ppp) cc_final: 0.9155 (ppp) REVERT: At 521 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8911 (mt-10) REVERT: At 547 GLU cc_start: 0.8704 (tt0) cc_final: 0.8424 (tt0) REVERT: At 709 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7394 (ttt180) REVERT: Au 167 MET cc_start: 0.8566 (mtp) cc_final: 0.7430 (mtp) REVERT: Au 314 ASP cc_start: 0.9138 (t0) cc_final: 0.8812 (t70) REVERT: Au 566 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8019 (mp0) REVERT: Au 709 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6518 (tmt90) REVERT: Av 354 GLU cc_start: 0.3843 (tp30) cc_final: 0.3444 (tp30) REVERT: Av 414 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7843 (ttm170) REVERT: Av 476 MET cc_start: 0.8958 (tmm) cc_final: 0.8499 (tmm) REVERT: Av 547 GLU cc_start: 0.8536 (tt0) cc_final: 0.8085 (tt0) REVERT: Av 616 LYS cc_start: 0.9459 (mttt) cc_final: 0.9213 (mtpp) REVERT: Av 709 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6124 (tmt90) REVERT: Aw 168 MET cc_start: 0.9150 (ttp) cc_final: 0.8577 (ttp) REVERT: Aw 354 GLU cc_start: 0.3972 (mm-30) cc_final: 0.3748 (mm-30) REVERT: Aw 519 MET cc_start: 0.9303 (ppp) cc_final: 0.9066 (ppp) REVERT: Aw 616 LYS cc_start: 0.9203 (mttt) cc_final: 0.8830 (mtpp) REVERT: Aw 634 ASP cc_start: 0.7762 (t0) cc_final: 0.7328 (t0) outliers start: 33 outliers final: 18 residues processed: 186 average time/residue: 0.1812 time to fit residues: 53.6726 Evaluate side-chains 178 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 203 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 476 MET Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain Ar residue 709 ARG Chi-restraints excluded: chain As residue 262 VAL Chi-restraints excluded: chain At residue 167 MET Chi-restraints excluded: chain At residue 262 VAL Chi-restraints excluded: chain At residue 530 LEU Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain At residue 709 ARG Chi-restraints excluded: chain Au residue 262 VAL Chi-restraints excluded: chain Au residue 535 THR Chi-restraints excluded: chain Au residue 703 MET Chi-restraints excluded: chain Au residue 709 ARG Chi-restraints excluded: chain Av residue 370 PHE Chi-restraints excluded: chain Av residue 414 ARG Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 483 ILE Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 709 ARG Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 530 LEU Chi-restraints excluded: chain Aw residue 655 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [4, 68, 114, 95, 20, 123, 295, 164, 319, 238, 57] chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.060471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.049511 restraints weight = 86970.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.051534 restraints weight = 41196.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.052907 restraints weight = 24971.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.053850 restraints weight = 17412.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.054516 restraints weight = 13370.931| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28410 Z= 0.115 Angle : 0.479 12.487 38466 Z= 0.252 Chirality : 0.043 0.320 4314 Planarity : 0.003 0.045 5064 Dihedral : 4.106 59.350 3876 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.98 % Allowed : 10.64 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3486 helix: 2.34 (0.22), residues: 612 sheet: 0.07 (0.18), residues: 888 loop : -0.70 (0.15), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAs 435 TYR 0.011 0.001 TYRAr 602 PHE 0.019 0.001 PHEAt 370 TRP 0.004 0.001 TRPAv 557 HIS 0.002 0.000 HISAu 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (28410) covalent geometry : angle 0.47920 / 0.25 (38466) hydrogen bonds : bond 0.04558 / 3.07 ( 913) hydrogen bonds : angle 4.28283 / 2.90 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ar 360 MET cc_start: 0.9558 (mmt) cc_final: 0.9035 (mmm) REVERT: Ar 413 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9006 (mt) REVERT: Ar 455 GLU cc_start: 0.8586 (tp30) cc_final: 0.8240 (tp30) REVERT: Ar 521 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8711 (mp0) REVERT: Ar 709 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.6541 (tmt90) REVERT: As 177 LYS cc_start: 0.9174 (mttt) cc_final: 0.8862 (mmmt) REVERT: As 354 GLU cc_start: 0.2428 (mm-30) cc_final: 0.1729 (tp30) REVERT: As 360 MET cc_start: 0.8730 (mtp) cc_final: 0.8000 (mmm) REVERT: As 455 GLU cc_start: 0.8824 (tt0) cc_final: 0.8121 (mt-10) REVERT: As 476 MET cc_start: 0.8809 (ttp) cc_final: 0.7974 (pmm) REVERT: As 521 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8143 (mp0) REVERT: As 566 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8019 (mp0) REVERT: As 580 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8105 (mm-30) REVERT: As 655 MET cc_start: 0.8943 (mtp) cc_final: 0.8349 (ttm) REVERT: At 167 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8616 (mtp) REVERT: At 521 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8897 (mt-10) REVERT: At 547 GLU cc_start: 0.8716 (tt0) cc_final: 0.8438 (tt0) REVERT: At 709 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7482 (ttt180) REVERT: Au 167 MET cc_start: 0.8640 (mtp) cc_final: 0.7473 (mtp) REVERT: Au 168 MET cc_start: 0.8708 (ttm) cc_final: 0.8345 (ttp) REVERT: Au 314 ASP cc_start: 0.9142 (t0) cc_final: 0.8816 (t70) REVERT: Au 566 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8038 (mp0) REVERT: Au 709 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6542 (tmt90) REVERT: Av 167 MET cc_start: 0.8338 (mtm) cc_final: 0.8098 (ttm) REVERT: Av 476 MET cc_start: 0.9024 (tmm) cc_final: 0.8499 (tmm) REVERT: Av 521 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8885 (mt-10) REVERT: Av 547 GLU cc_start: 0.8512 (tt0) cc_final: 0.8016 (tt0) REVERT: Av 616 LYS cc_start: 0.9458 (mttt) cc_final: 0.9217 (mtpp) REVERT: Av 709 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6169 (tmt90) REVERT: Aw 168 MET cc_start: 0.9156 (ttp) cc_final: 0.8562 (ttp) REVERT: Aw 354 GLU cc_start: 0.3407 (mm-30) cc_final: 0.3191 (mm-30) REVERT: Aw 519 MET cc_start: 0.9251 (ppp) cc_final: 0.8964 (ppp) REVERT: Aw 616 LYS cc_start: 0.9203 (mttt) cc_final: 0.8830 (mtpp) REVERT: Aw 634 ASP cc_start: 0.7886 (t0) cc_final: 0.7522 (t0) outliers start: 30 outliers final: 19 residues processed: 177 average time/residue: 0.1836 time to fit residues: 51.9258 Evaluate side-chains 175 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ar residue 203 VAL Chi-restraints excluded: chain Ar residue 413 LEU Chi-restraints excluded: chain Ar residue 476 MET Chi-restraints excluded: chain Ar residue 640 VAL Chi-restraints excluded: chain Ar residue 693 THR Chi-restraints excluded: chain Ar residue 709 ARG Chi-restraints excluded: chain As residue 262 VAL Chi-restraints excluded: chain At residue 167 MET Chi-restraints excluded: chain At residue 262 VAL Chi-restraints excluded: chain At residue 530 LEU Chi-restraints excluded: chain At residue 640 VAL Chi-restraints excluded: chain At residue 709 ARG Chi-restraints excluded: chain Au residue 262 VAL Chi-restraints excluded: chain Au residue 535 THR Chi-restraints excluded: chain Au residue 703 MET Chi-restraints excluded: chain Au residue 709 ARG Chi-restraints excluded: chain Av residue 370 PHE Chi-restraints excluded: chain Av residue 415 VAL Chi-restraints excluded: chain Av residue 483 ILE Chi-restraints excluded: chain Av residue 640 VAL Chi-restraints excluded: chain Av residue 709 ARG Chi-restraints excluded: chain Aw residue 382 LYS Chi-restraints excluded: chain Aw residue 530 LEU Chi-restraints excluded: chain Aw residue 533 VAL Chi-restraints excluded: chain Aw residue 655 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [302, 257, 243, 22, 226, 10, 225, 160, 85, 3, 230] chunk 302 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 226 optimal weight: 3.9990 chunk 10 optimal weight: 0.0010 chunk 225 optimal weight: 0.4980 chunk 160 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 overall best weight: 1.1106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.061746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.050790 restraints weight = 85963.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.052848 restraints weight = 40652.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.054242 restraints weight = 24561.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.055176 restraints weight = 17064.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.055875 restraints weight = 13128.785| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28410 Z= 0.093 Angle : 0.465 12.655 38466 Z= 0.244 Chirality : 0.042 0.269 4314 Planarity : 0.003 0.044 5064 Dihedral : 3.975 59.984 3876 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.98 % Allowed : 10.74 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3486 helix: 2.39 (0.22), residues: 612 sheet: 0.09 (0.18), residues: 894 loop : -0.69 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAs 435 TYR 0.010 0.001 TYRAr 602 PHE 0.018 0.001 PHEAt 370 TRP 0.005 0.001 TRPAv 557 HIS 0.001 0.000 HISAr 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (28410) covalent geometry : angle 0.46479 / 0.24 (38466) hydrogen bonds : bond 0.04035 / 2.72 ( 913) hydrogen bonds : angle 4.17084 / 2.82 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.54 seconds wall clock time: 57 minutes 56.98 seconds (3476.98 seconds total)