Starting phenix.real_space_refine on Thu Sep 18 12:02:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vht_43241/09_2025/8vht_43241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vht_43241/09_2025/8vht_43241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vht_43241/09_2025/8vht_43241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vht_43241/09_2025/8vht_43241.map" model { file = "/net/cci-nas-00/data/ceres_data/8vht_43241/09_2025/8vht_43241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vht_43241/09_2025/8vht_43241.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 81 5.16 5 C 10815 2.51 5 N 2781 2.21 5 O 2904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16581 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5504 Classifications: {'peptide': 685} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5504 Classifications: {'peptide': 685} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5504 Classifications: {'peptide': 685} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.98, per 1000 atoms: 0.24 Number of scatterers: 16581 At special positions: 0 Unit cell: (106.92, 133.92, 133.92, 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 81 16.00 O 2904 8.00 N 2781 7.00 C 10815 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 Links applied BETA1-4 " BGC C 1 " - " BGC C 2 " " BGC E 1 " - " BGC E 2 " " BGC F 1 " - " BGC F 2 " Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 636.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3828 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 9 sheets defined 58.2% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 267 through 291 Processing helix chain 'A' and resid 299 through 320 removed outlier: 3.972A pdb=" N VAL A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.598A pdb=" N THR A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 395 through 420 removed outlier: 4.155A pdb=" N LYS A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 444 through 472 removed outlier: 3.920A pdb=" N ASP A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 549 Processing helix chain 'A' and resid 567 through 577 removed outlier: 3.874A pdb=" N PHE A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 613 through 620 removed outlier: 3.655A pdb=" N GLY A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 724 through 732 removed outlier: 3.526A pdb=" N LEU A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.623A pdb=" N LYS A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.549A pdb=" N TYR A 759 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU A 760 " --> pdb=" O CYS A 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 760' Processing helix chain 'A' and resid 778 through 788 removed outlier: 3.999A pdb=" N GLY A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 830 removed outlier: 3.698A pdb=" N ARG A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 857 Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 861 through 879 removed outlier: 3.515A pdb=" N ILE A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) Proline residue: A 872 - end of helix Processing helix chain 'A' and resid 887 through 913 removed outlier: 4.309A pdb=" N TRP A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 912 " --> pdb=" O GLU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 947 removed outlier: 4.346A pdb=" N HIS A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 977 No H-bonds generated for 'chain 'A' and resid 975 through 977' Processing helix chain 'A' and resid 978 through 1003 removed outlier: 3.676A pdb=" N THR A 982 " --> pdb=" O LEU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'B' and resid 267 through 291 Processing helix chain 'B' and resid 299 through 320 removed outlier: 3.973A pdb=" N VAL B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 377 removed outlier: 3.597A pdb=" N THR B 368 " --> pdb=" O PRO B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 395 through 420 removed outlier: 4.154A pdb=" N LYS B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Proline residue: B 414 - end of helix Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 444 through 472 removed outlier: 3.921A pdb=" N ASP B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 549 Processing helix chain 'B' and resid 567 through 577 removed outlier: 3.875A pdb=" N PHE B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 613 through 620 removed outlier: 3.655A pdb=" N GLY B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 714 through 721 Processing helix chain 'B' and resid 724 through 732 removed outlier: 3.526A pdb=" N LEU B 732 " --> pdb=" O VAL B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 removed outlier: 3.622A pdb=" N LYS B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.549A pdb=" N TYR B 759 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B 760 " --> pdb=" O CYS B 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 760' Processing helix chain 'B' and resid 778 through 788 removed outlier: 3.999A pdb=" N GLY B 783 " --> pdb=" O ASP B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 830 removed outlier: 3.698A pdb=" N ARG B 814 " --> pdb=" O ASN B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 857 Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 861 through 879 removed outlier: 3.514A pdb=" N ILE B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 887 through 913 removed outlier: 4.308A pdb=" N TRP B 893 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 912 " --> pdb=" O GLU B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 947 removed outlier: 4.345A pdb=" N HIS B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 935 " --> pdb=" O VAL B 931 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 977 No H-bonds generated for 'chain 'B' and resid 975 through 977' Processing helix chain 'B' and resid 978 through 1003 removed outlier: 3.676A pdb=" N THR B 982 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1006 No H-bonds generated for 'chain 'B' and resid 1004 through 1006' Processing helix chain 'B' and resid 1008 through 1024 Processing helix chain 'D' and resid 267 through 291 Processing helix chain 'D' and resid 299 through 320 removed outlier: 3.971A pdb=" N VAL D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 323 No H-bonds generated for 'chain 'D' and resid 321 through 323' Processing helix chain 'D' and resid 331 through 339 Processing helix chain 'D' and resid 364 through 377 removed outlier: 3.597A pdb=" N THR D 368 " --> pdb=" O PRO D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 395 through 420 removed outlier: 4.155A pdb=" N LYS D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) Proline residue: D 414 - end of helix Processing helix chain 'D' and resid 425 through 430 Processing helix chain 'D' and resid 444 through 472 removed outlier: 3.921A pdb=" N ASP D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 549 Processing helix chain 'D' and resid 567 through 577 removed outlier: 3.874A pdb=" N PHE D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 613 through 620 removed outlier: 3.654A pdb=" N GLY D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 639 Processing helix chain 'D' and resid 714 through 721 Processing helix chain 'D' and resid 724 through 732 removed outlier: 3.525A pdb=" N LEU D 732 " --> pdb=" O VAL D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 removed outlier: 3.622A pdb=" N LYS D 749 " --> pdb=" O GLU D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 760 removed outlier: 3.549A pdb=" N TYR D 759 " --> pdb=" O SER D 756 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 760 " --> pdb=" O CYS D 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 756 through 760' Processing helix chain 'D' and resid 778 through 788 removed outlier: 3.999A pdb=" N GLY D 783 " --> pdb=" O ASP D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 830 removed outlier: 3.698A pdb=" N ARG D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 857 Processing helix chain 'D' and resid 858 through 860 No H-bonds generated for 'chain 'D' and resid 858 through 860' Processing helix chain 'D' and resid 861 through 879 removed outlier: 3.515A pdb=" N ILE D 867 " --> pdb=" O ILE D 863 " (cutoff:3.500A) Proline residue: D 872 - end of helix Processing helix chain 'D' and resid 887 through 913 removed outlier: 4.308A pdb=" N TRP D 893 " --> pdb=" O LEU D 889 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 912 " --> pdb=" O GLU D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 947 removed outlier: 4.345A pdb=" N HIS D 934 " --> pdb=" O GLY D 930 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU D 935 " --> pdb=" O VAL D 931 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE D 936 " --> pdb=" O SER D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 977 No H-bonds generated for 'chain 'D' and resid 975 through 977' Processing helix chain 'D' and resid 978 through 1003 removed outlier: 3.676A pdb=" N THR D 982 " --> pdb=" O LEU D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1006 No H-bonds generated for 'chain 'D' and resid 1004 through 1006' Processing helix chain 'D' and resid 1008 through 1024 Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 262 Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 500 removed outlier: 3.661A pdb=" N ARG A 517 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 351 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N TYR A 388 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 353 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N SER A 390 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 355 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 631 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N CYS A 586 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG A 792 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR A 587 " --> pdb=" O ARG A 792 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 562 through 563 removed outlier: 4.083A pdb=" N ARG A 593 " --> pdb=" O PHE A 803 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AA5, first strand: chain 'B' and resid 497 through 500 removed outlier: 3.661A pdb=" N ARG B 517 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 351 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N TYR B 388 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE B 353 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER B 390 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 355 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS B 631 " --> pdb=" O ASN B 556 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N CYS B 586 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG B 792 " --> pdb=" O VAL B 585 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR B 587 " --> pdb=" O ARG B 792 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 562 through 563 removed outlier: 4.082A pdb=" N ARG B 593 " --> pdb=" O PHE B 803 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 258 through 262 Processing sheet with id=AA8, first strand: chain 'D' and resid 497 through 500 removed outlier: 3.661A pdb=" N ARG D 517 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL D 351 " --> pdb=" O SER D 386 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N TYR D 388 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE D 353 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER D 390 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL D 355 " --> pdb=" O SER D 390 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS D 631 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N CYS D 586 " --> pdb=" O ASN D 634 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG D 792 " --> pdb=" O VAL D 585 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR D 587 " --> pdb=" O ARG D 792 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 562 through 563 removed outlier: 4.082A pdb=" N ARG D 593 " --> pdb=" O PHE D 803 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2583 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: 2.83 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5177 1.35 - 1.46: 4272 1.46 - 1.58: 7489 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 17064 Sorted by residual: bond pdb=" C5 BGC F 1 " pdb=" O5 BGC F 1 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C5 BGC C 2 " pdb=" O5 BGC C 2 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C1 BGC E 2 " pdb=" O5 BGC E 2 " ideal model delta sigma weight residual 1.408 1.433 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C5 BGC C 1 " pdb=" O5 BGC C 1 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C5 BGC E 1 " pdb=" O5 BGC E 1 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.54e+00 ... (remaining 17059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 22760 1.75 - 3.51: 412 3.51 - 5.26: 54 5.26 - 7.01: 0 7.01 - 8.76: 3 Bond angle restraints: 23229 Sorted by residual: angle pdb=" CB MET A 452 " pdb=" CG MET A 452 " pdb=" SD MET A 452 " ideal model delta sigma weight residual 112.70 121.46 -8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" CB MET D 452 " pdb=" CG MET D 452 " pdb=" SD MET D 452 " ideal model delta sigma weight residual 112.70 121.44 -8.74 3.00e+00 1.11e-01 8.48e+00 angle pdb=" CB MET B 452 " pdb=" CG MET B 452 " pdb=" SD MET B 452 " ideal model delta sigma weight residual 112.70 121.40 -8.70 3.00e+00 1.11e-01 8.42e+00 angle pdb=" C PHE B1027 " pdb=" CA PHE B1027 " pdb=" CB PHE B1027 " ideal model delta sigma weight residual 116.63 113.73 2.90 1.16e+00 7.43e-01 6.24e+00 angle pdb=" C PHE D1027 " pdb=" CA PHE D1027 " pdb=" CB PHE D1027 " ideal model delta sigma weight residual 116.63 113.76 2.87 1.16e+00 7.43e-01 6.12e+00 ... (remaining 23224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8904 17.90 - 35.80: 939 35.80 - 53.70: 214 53.70 - 71.60: 44 71.60 - 89.50: 12 Dihedral angle restraints: 10113 sinusoidal: 4152 harmonic: 5961 Sorted by residual: dihedral pdb=" CA ASN A1001 " pdb=" C ASN A1001 " pdb=" N SER A1002 " pdb=" CA SER A1002 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASN D1001 " pdb=" C ASN D1001 " pdb=" N SER D1002 " pdb=" CA SER D1002 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASN B1001 " pdb=" C ASN B1001 " pdb=" N SER B1002 " pdb=" CA SER B1002 " ideal model delta harmonic sigma weight residual 180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 10110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1782 0.035 - 0.070: 542 0.070 - 0.106: 177 0.106 - 0.141: 40 0.141 - 0.176: 9 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CA VAL D 294 " pdb=" N VAL D 294 " pdb=" C VAL D 294 " pdb=" CB VAL D 294 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA VAL B 294 " pdb=" N VAL B 294 " pdb=" C VAL B 294 " pdb=" CB VAL B 294 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA VAL A 294 " pdb=" N VAL A 294 " pdb=" C VAL A 294 " pdb=" CB VAL A 294 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 2547 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 979 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A 980 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 980 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 980 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 979 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO D 980 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 980 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 980 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 979 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 980 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 980 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 980 " 0.024 5.00e-02 4.00e+02 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1885 2.75 - 3.29: 16725 3.29 - 3.83: 28308 3.83 - 4.36: 32433 4.36 - 4.90: 55101 Nonbonded interactions: 134452 Sorted by model distance: nonbonded pdb=" OE1 GLU B 760 " pdb=" OH TYR B 773 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLU A 760 " pdb=" OH TYR A 773 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLU D 760 " pdb=" OH TYR D 773 " model vdw 2.216 3.040 nonbonded pdb=" OE2 GLU A 457 " pdb=" OH TYR B 436 " model vdw 2.225 3.040 nonbonded pdb=" OE2 GLU B 457 " pdb=" OH TYR D 436 " model vdw 2.290 3.040 ... (remaining 134447 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.660 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 0.038 17067 Z= 0.123 Angle : 0.542 8.763 23238 Z= 0.278 Chirality : 0.040 0.176 2550 Planarity : 0.005 0.044 2922 Dihedral : 15.273 89.503 6285 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.23 (0.19), residues: 2037 helix: 1.31 (0.16), residues: 1098 sheet: 0.85 (0.37), residues: 162 loop : 0.24 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 720 TYR 0.014 0.001 TYR B 271 PHE 0.009 0.001 PHE A1016 TRP 0.024 0.001 TRP A 837 HIS 0.003 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00261 (17064) covalent geometry : angle 0.54101 (23229) hydrogen bonds : bond 0.13259 ( 867) hydrogen bonds : angle 5.18322 ( 2583) link_BETA1-4 : bond 0.00169 ( 3) link_BETA1-4 : angle 1.41489 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8269 (mm) cc_final: 0.8038 (mm) REVERT: A 396 MET cc_start: 0.8995 (ttm) cc_final: 0.8645 (ttm) REVERT: A 452 MET cc_start: 0.9298 (tpp) cc_final: 0.9022 (tpt) REVERT: A 612 ASP cc_start: 0.8666 (m-30) cc_final: 0.8324 (m-30) REVERT: A 918 GLU cc_start: 0.6643 (tp30) cc_final: 0.6226 (tp30) REVERT: D 290 ILE cc_start: 0.7812 (mm) cc_final: 0.7367 (tp) REVERT: D 309 ILE cc_start: 0.8156 (mm) cc_final: 0.7943 (mm) REVERT: D 452 MET cc_start: 0.9047 (tpp) cc_final: 0.8645 (tpt) REVERT: D 720 ARG cc_start: 0.8584 (ttt90) cc_final: 0.8372 (ttm170) REVERT: D 830 PHE cc_start: 0.7764 (m-80) cc_final: 0.7504 (m-80) REVERT: D 832 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7105 (ptt90) REVERT: D 868 TYR cc_start: 0.7126 (t80) cc_final: 0.6714 (t80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1494 time to fit residues: 53.8059 Evaluate side-chains 223 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0050 overall best weight: 0.7496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN A1005 GLN B1005 GLN D1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.165693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119889 restraints weight = 19096.281| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.48 r_work: 0.2778 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17067 Z= 0.162 Angle : 0.557 6.164 23238 Z= 0.285 Chirality : 0.043 0.158 2550 Planarity : 0.005 0.044 2922 Dihedral : 4.310 56.777 2373 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.35 % Allowed : 12.72 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.82 (0.19), residues: 2037 helix: 1.94 (0.16), residues: 1089 sheet: 1.29 (0.46), residues: 120 loop : 0.28 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 720 TYR 0.014 0.002 TYR D 587 PHE 0.012 0.001 PHE B 830 TRP 0.016 0.001 TRP A 837 HIS 0.004 0.001 HIS D 531 Details of bonding type rmsd covalent geometry : bond 0.00390 (17064) covalent geometry : angle 0.55622 (23229) hydrogen bonds : bond 0.04898 ( 867) hydrogen bonds : angle 3.93939 ( 2583) link_BETA1-4 : bond 0.00189 ( 3) link_BETA1-4 : angle 1.92413 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.679 Fit side-chains REVERT: A 396 MET cc_start: 0.9110 (ttm) cc_final: 0.8791 (ttm) REVERT: A 569 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 850 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7958 (t80) REVERT: B 733 MET cc_start: 0.8229 (mtp) cc_final: 0.7586 (mtp) REVERT: B 832 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7280 (ptt90) REVERT: D 309 ILE cc_start: 0.8337 (mm) cc_final: 0.8101 (mm) REVERT: D 814 ARG cc_start: 0.6144 (tpt-90) cc_final: 0.5885 (tpt-90) REVERT: D 832 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7006 (ptt90) REVERT: D 870 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7029 (mt) outliers start: 42 outliers final: 25 residues processed: 270 average time/residue: 0.1471 time to fit residues: 59.0822 Evaluate side-chains 265 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 904 THR Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 0.0670 chunk 38 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 607 ASN D 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.168352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.126540 restraints weight = 19213.509| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.47 r_work: 0.2784 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17067 Z= 0.140 Angle : 0.533 6.424 23238 Z= 0.271 Chirality : 0.042 0.157 2550 Planarity : 0.004 0.044 2922 Dihedral : 4.224 57.214 2373 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.69 % Allowed : 13.61 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.94 (0.19), residues: 2037 helix: 2.14 (0.16), residues: 1089 sheet: 1.28 (0.47), residues: 120 loop : 0.20 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 720 TYR 0.011 0.001 TYR A 288 PHE 0.012 0.001 PHE B1016 TRP 0.014 0.001 TRP A 911 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00337 (17064) covalent geometry : angle 0.53216 (23229) hydrogen bonds : bond 0.04307 ( 867) hydrogen bonds : angle 3.72199 ( 2583) link_BETA1-4 : bond 0.00186 ( 3) link_BETA1-4 : angle 1.88917 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.9148 (tpp) cc_final: 0.8876 (tpt) REVERT: A 569 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 733 MET cc_start: 0.8382 (mtp) cc_final: 0.8149 (mtt) REVERT: A 850 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7982 (t80) REVERT: A 984 LEU cc_start: 0.8004 (tt) cc_final: 0.7692 (tp) REVERT: B 392 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8848 (m-30) REVERT: B 718 GLU cc_start: 0.8230 (tt0) cc_final: 0.7957 (tt0) REVERT: B 733 MET cc_start: 0.8286 (mtp) cc_final: 0.7640 (mtp) REVERT: B 832 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7162 (ptt90) REVERT: D 290 ILE cc_start: 0.7841 (mm) cc_final: 0.7393 (tp) REVERT: D 309 ILE cc_start: 0.8283 (mm) cc_final: 0.8052 (mm) REVERT: D 714 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7296 (tm-30) REVERT: D 814 ARG cc_start: 0.6097 (tpt-90) cc_final: 0.5835 (tpt-90) REVERT: D 832 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7067 (ptt90) REVERT: D 916 ILE cc_start: 0.8683 (tp) cc_final: 0.8423 (mm) REVERT: D 924 GLN cc_start: 0.7851 (pt0) cc_final: 0.7261 (mt0) outliers start: 48 outliers final: 30 residues processed: 279 average time/residue: 0.1331 time to fit residues: 56.3845 Evaluate side-chains 265 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 904 THR Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 716 SER Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.162790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.115225 restraints weight = 19161.907| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.53 r_work: 0.2720 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17067 Z= 0.175 Angle : 0.564 7.177 23238 Z= 0.287 Chirality : 0.044 0.163 2550 Planarity : 0.005 0.049 2922 Dihedral : 4.330 59.193 2373 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.25 % Allowed : 13.28 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.78 (0.19), residues: 2037 helix: 2.00 (0.16), residues: 1098 sheet: 1.21 (0.46), residues: 120 loop : 0.10 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 635 TYR 0.012 0.002 TYR D 858 PHE 0.010 0.001 PHE A 415 TRP 0.014 0.001 TRP D 911 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00433 (17064) covalent geometry : angle 0.56299 (23229) hydrogen bonds : bond 0.04685 ( 867) hydrogen bonds : angle 3.78682 ( 2583) link_BETA1-4 : bond 0.00054 ( 3) link_BETA1-4 : angle 2.07893 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 241 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 569 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8711 (mp) REVERT: A 850 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8029 (t80) REVERT: B 392 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8852 (m-30) REVERT: B 396 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8717 (ttt) REVERT: B 714 GLN cc_start: 0.7519 (tp40) cc_final: 0.7282 (tm-30) REVERT: B 718 GLU cc_start: 0.8343 (tt0) cc_final: 0.8042 (tt0) REVERT: B 733 MET cc_start: 0.8240 (mtp) cc_final: 0.7673 (mtp) REVERT: B 832 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7157 (ptt90) REVERT: D 290 ILE cc_start: 0.7896 (mm) cc_final: 0.7492 (tp) REVERT: D 714 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7324 (tm-30) REVERT: D 832 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7197 (ptt90) REVERT: D 924 GLN cc_start: 0.7819 (pt0) cc_final: 0.7241 (mt0) outliers start: 58 outliers final: 43 residues processed: 280 average time/residue: 0.1349 time to fit residues: 57.2637 Evaluate side-chains 282 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 716 SER Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 831 SER Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A 816 ASN B 817 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.170757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.132054 restraints weight = 18819.472| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.35 r_work: 0.2797 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17067 Z= 0.172 Angle : 0.562 6.731 23238 Z= 0.285 Chirality : 0.044 0.164 2550 Planarity : 0.005 0.048 2922 Dihedral : 4.290 50.256 2373 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.14 % Allowed : 13.67 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.73 (0.19), residues: 2037 helix: 1.98 (0.16), residues: 1107 sheet: 1.11 (0.46), residues: 120 loop : 0.06 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 635 TYR 0.013 0.001 TYR D 858 PHE 0.010 0.001 PHE A 415 TRP 0.015 0.001 TRP B 837 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00427 (17064) covalent geometry : angle 0.56045 (23229) hydrogen bonds : bond 0.04545 ( 867) hydrogen bonds : angle 3.74101 ( 2583) link_BETA1-4 : bond 0.00076 ( 3) link_BETA1-4 : angle 2.02853 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8349 (mm) cc_final: 0.8089 (mm) REVERT: A 569 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8642 (mp) REVERT: A 612 ASP cc_start: 0.8807 (m-30) cc_final: 0.8471 (m-30) REVERT: A 850 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 855 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8384 (t) REVERT: B 392 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8811 (m-30) REVERT: B 714 GLN cc_start: 0.7510 (tp40) cc_final: 0.7306 (tm-30) REVERT: B 718 GLU cc_start: 0.8263 (tt0) cc_final: 0.7939 (tt0) REVERT: B 733 MET cc_start: 0.8262 (mtp) cc_final: 0.7793 (mtp) REVERT: B 832 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7107 (ptt90) REVERT: D 290 ILE cc_start: 0.7870 (mm) cc_final: 0.7490 (tp) REVERT: D 714 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7327 (tm-30) REVERT: D 832 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7212 (ptt90) REVERT: D 924 GLN cc_start: 0.7742 (pt0) cc_final: 0.7233 (mt0) outliers start: 56 outliers final: 43 residues processed: 268 average time/residue: 0.1310 time to fit residues: 53.3066 Evaluate side-chains 274 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 43 optimal weight: 0.6980 chunk 113 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 169 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN D 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.162873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.114566 restraints weight = 19187.493| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.52 r_work: 0.2718 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17067 Z= 0.151 Angle : 0.549 9.237 23238 Z= 0.278 Chirality : 0.043 0.161 2550 Planarity : 0.004 0.048 2922 Dihedral : 4.145 39.919 2373 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.31 % Allowed : 13.78 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.78 (0.19), residues: 2037 helix: 2.02 (0.16), residues: 1107 sheet: 1.10 (0.46), residues: 120 loop : 0.08 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 720 TYR 0.011 0.001 TYR B 858 PHE 0.011 0.001 PHE A 415 TRP 0.015 0.001 TRP B 911 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00369 (17064) covalent geometry : angle 0.54800 (23229) hydrogen bonds : bond 0.04373 ( 867) hydrogen bonds : angle 3.70102 ( 2583) link_BETA1-4 : bond 0.00056 ( 3) link_BETA1-4 : angle 1.95029 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8362 (mm) cc_final: 0.8109 (mm) REVERT: A 569 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8616 (mp) REVERT: A 612 ASP cc_start: 0.8830 (m-30) cc_final: 0.8498 (m-30) REVERT: A 714 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7371 (tm-30) REVERT: A 850 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8140 (t80) REVERT: A 855 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8392 (t) REVERT: B 356 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8016 (m) REVERT: B 392 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8907 (m-30) REVERT: B 476 GLU cc_start: 0.6096 (pm20) cc_final: 0.5784 (pm20) REVERT: B 583 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8282 (mmtm) REVERT: B 718 GLU cc_start: 0.8300 (tt0) cc_final: 0.7977 (tt0) REVERT: B 733 MET cc_start: 0.8264 (mtp) cc_final: 0.7798 (mtp) REVERT: B 832 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7242 (ptt90) REVERT: B 870 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7237 (mt) REVERT: B 1010 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7445 (pp) REVERT: D 290 ILE cc_start: 0.7925 (mm) cc_final: 0.7548 (tp) REVERT: D 714 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7281 (tm-30) REVERT: D 832 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7140 (ptt90) REVERT: D 924 GLN cc_start: 0.7654 (pt0) cc_final: 0.7160 (mt0) outliers start: 59 outliers final: 44 residues processed: 262 average time/residue: 0.1314 time to fit residues: 52.4518 Evaluate side-chains 271 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 89 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN D 592 GLN D 605 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.171228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.133067 restraints weight = 18749.659| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.32 r_work: 0.2809 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17067 Z= 0.148 Angle : 0.546 9.169 23238 Z= 0.277 Chirality : 0.043 0.166 2550 Planarity : 0.004 0.047 2922 Dihedral : 4.028 28.629 2373 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.31 % Allowed : 13.78 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.78 (0.19), residues: 2037 helix: 2.04 (0.16), residues: 1107 sheet: 1.05 (0.46), residues: 120 loop : 0.04 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 720 TYR 0.012 0.001 TYR D 858 PHE 0.010 0.001 PHE A 415 TRP 0.015 0.001 TRP B 911 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00360 (17064) covalent geometry : angle 0.54490 (23229) hydrogen bonds : bond 0.04290 ( 867) hydrogen bonds : angle 3.67847 ( 2583) link_BETA1-4 : bond 0.00101 ( 3) link_BETA1-4 : angle 1.89644 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 569 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8615 (mp) REVERT: A 612 ASP cc_start: 0.8784 (m-30) cc_final: 0.8480 (m-30) REVERT: A 714 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 850 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8115 (t80) REVERT: A 855 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8445 (t) REVERT: B 356 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7905 (m) REVERT: B 392 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8872 (m-30) REVERT: B 583 LYS cc_start: 0.8889 (mtpt) cc_final: 0.8296 (mmtm) REVERT: B 714 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7246 (tp40) REVERT: B 718 GLU cc_start: 0.8346 (tt0) cc_final: 0.8037 (tt0) REVERT: B 733 MET cc_start: 0.8255 (mtp) cc_final: 0.7751 (mtp) REVERT: B 832 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7257 (ptt90) REVERT: B 1010 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7493 (pp) REVERT: D 284 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.6889 (pt) REVERT: D 290 ILE cc_start: 0.7923 (mm) cc_final: 0.7549 (tp) REVERT: D 832 ARG cc_start: 0.7699 (ttp80) cc_final: 0.7127 (ptt90) REVERT: D 924 GLN cc_start: 0.7589 (pt0) cc_final: 0.7159 (mt0) outliers start: 59 outliers final: 49 residues processed: 266 average time/residue: 0.1295 time to fit residues: 52.5055 Evaluate side-chains 281 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 100 optimal weight: 0.9980 chunk 155 optimal weight: 0.0050 chunk 33 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN A 924 GLN B 817 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.115638 restraints weight = 19164.691| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.52 r_work: 0.2748 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17067 Z= 0.121 Angle : 0.526 8.475 23238 Z= 0.266 Chirality : 0.041 0.167 2550 Planarity : 0.004 0.047 2922 Dihedral : 3.875 25.248 2373 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.03 % Allowed : 14.51 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.89 (0.19), residues: 2037 helix: 2.13 (0.16), residues: 1107 sheet: 1.05 (0.46), residues: 120 loop : 0.10 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 720 TYR 0.010 0.001 TYR D 858 PHE 0.011 0.001 PHE A 415 TRP 0.017 0.001 TRP A 911 HIS 0.002 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00282 (17064) covalent geometry : angle 0.52553 (23229) hydrogen bonds : bond 0.03926 ( 867) hydrogen bonds : angle 3.59167 ( 2583) link_BETA1-4 : bond 0.00198 ( 3) link_BETA1-4 : angle 1.69495 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 0.675 Fit side-chains REVERT: A 356 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7726 (m) REVERT: A 569 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 612 ASP cc_start: 0.8788 (m-30) cc_final: 0.8468 (m-30) REVERT: A 714 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 850 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8032 (t80) REVERT: A 855 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8425 (t) REVERT: B 356 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7870 (m) REVERT: B 392 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8876 (m-30) REVERT: B 476 GLU cc_start: 0.6721 (pm20) cc_final: 0.6401 (pm20) REVERT: B 583 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8283 (mmtm) REVERT: B 714 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7266 (tm-30) REVERT: B 718 GLU cc_start: 0.8240 (tt0) cc_final: 0.7914 (tt0) REVERT: B 733 MET cc_start: 0.8230 (mtp) cc_final: 0.7719 (mtp) REVERT: B 832 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7248 (ptt90) REVERT: D 290 ILE cc_start: 0.7941 (mm) cc_final: 0.7578 (tp) REVERT: D 832 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7125 (ptt90) REVERT: D 924 GLN cc_start: 0.7520 (pt0) cc_final: 0.7222 (mt0) outliers start: 54 outliers final: 40 residues processed: 257 average time/residue: 0.1307 time to fit residues: 51.4263 Evaluate side-chains 264 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 975 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 115 optimal weight: 1.9990 chunk 184 optimal weight: 0.0050 chunk 203 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 110 optimal weight: 0.0980 chunk 172 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** 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 = 0.3754 r_free = 0.3754 target = 0.163118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.115216 restraints weight = 19182.317| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.54 r_work: 0.2731 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17067 Z= 0.139 Angle : 0.547 9.682 23238 Z= 0.275 Chirality : 0.042 0.176 2550 Planarity : 0.004 0.048 2922 Dihedral : 3.863 24.018 2373 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.19 % Allowed : 14.23 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.86 (0.19), residues: 2037 helix: 2.12 (0.16), residues: 1107 sheet: 1.08 (0.47), residues: 120 loop : 0.08 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 814 TYR 0.011 0.001 TYR D 858 PHE 0.010 0.001 PHE A 415 TRP 0.015 0.001 TRP D 911 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00337 (17064) covalent geometry : angle 0.54576 (23229) hydrogen bonds : bond 0.04112 ( 867) hydrogen bonds : angle 3.63231 ( 2583) link_BETA1-4 : bond 0.00124 ( 3) link_BETA1-4 : angle 1.74819 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.658 Fit side-chains REVERT: A 356 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7764 (m) REVERT: A 569 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 612 ASP cc_start: 0.8817 (m-30) cc_final: 0.8495 (m-30) REVERT: A 714 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 850 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8054 (t80) REVERT: A 855 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8425 (t) REVERT: B 356 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7944 (m) REVERT: B 392 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8895 (m-30) REVERT: B 476 GLU cc_start: 0.6786 (pm20) cc_final: 0.6359 (pm20) REVERT: B 583 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8296 (mmtm) REVERT: B 718 GLU cc_start: 0.8265 (tt0) cc_final: 0.7952 (tt0) REVERT: B 733 MET cc_start: 0.8254 (mtp) cc_final: 0.7745 (mtp) REVERT: B 832 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7259 (ptt90) REVERT: D 284 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.6843 (pt) REVERT: D 290 ILE cc_start: 0.7942 (mm) cc_final: 0.7584 (tp) REVERT: D 832 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7152 (ptt90) REVERT: D 924 GLN cc_start: 0.7481 (pt0) cc_final: 0.7235 (mt0) outliers start: 57 outliers final: 46 residues processed: 258 average time/residue: 0.1303 time to fit residues: 51.2641 Evaluate side-chains 272 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 831 SER Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 975 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS B 584 HIS B 605 ASN B 922 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.161682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.126769 restraints weight = 18988.224| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.22 r_work: 0.2877 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 17067 Z= 0.267 Angle : 0.651 11.342 23238 Z= 0.332 Chirality : 0.047 0.190 2550 Planarity : 0.005 0.048 2922 Dihedral : 4.346 33.090 2373 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.14 % Allowed : 14.29 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.56 (0.19), residues: 2037 helix: 1.91 (0.16), residues: 1107 sheet: 0.95 (0.45), residues: 120 loop : -0.13 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 635 TYR 0.016 0.002 TYR D 858 PHE 0.011 0.002 PHE A 501 TRP 0.012 0.002 TRP D 428 HIS 0.005 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00674 (17064) covalent geometry : angle 0.64969 (23229) hydrogen bonds : bond 0.05397 ( 867) hydrogen bonds : angle 3.97455 ( 2583) link_BETA1-4 : bond 0.00218 ( 3) link_BETA1-4 : angle 2.35726 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8313 (mm) cc_final: 0.8084 (mm) REVERT: A 476 GLU cc_start: 0.6310 (pm20) cc_final: 0.6076 (pm20) REVERT: A 569 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8631 (mp) REVERT: A 612 ASP cc_start: 0.8879 (m-30) cc_final: 0.8626 (m-30) REVERT: A 850 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8145 (t80) REVERT: A 855 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8545 (t) REVERT: B 392 ASP cc_start: 0.9221 (OUTLIER) cc_final: 0.8833 (m-30) REVERT: B 476 GLU cc_start: 0.6714 (pm20) cc_final: 0.6286 (pm20) REVERT: B 718 GLU cc_start: 0.8357 (tt0) cc_final: 0.8032 (tt0) REVERT: B 832 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7265 (ptt90) REVERT: D 284 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7026 (pt) REVERT: D 290 ILE cc_start: 0.7956 (mm) cc_final: 0.7616 (tp) REVERT: D 452 MET cc_start: 0.9023 (tpp) cc_final: 0.8701 (tpt) REVERT: D 714 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7329 (tm-30) REVERT: D 832 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7307 (ptt90) REVERT: D 924 GLN cc_start: 0.7646 (pt0) cc_final: 0.7344 (mt0) outliers start: 56 outliers final: 48 residues processed: 269 average time/residue: 0.1354 time to fit residues: 54.5174 Evaluate side-chains 269 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 875 CYS Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 831 SER Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 875 CYS Chi-restraints excluded: chain D residue 904 THR Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 975 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN A 924 GLN B 817 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.162314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.127177 restraints weight = 19084.013| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.26 r_work: 0.2912 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17067 Z= 0.169 Angle : 0.579 9.631 23238 Z= 0.293 Chirality : 0.044 0.173 2550 Planarity : 0.005 0.063 2922 Dihedral : 4.194 32.907 2373 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.86 % Allowed : 14.68 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 1.65 (0.19), residues: 2037 helix: 2.01 (0.16), residues: 1104 sheet: 0.92 (0.45), residues: 120 loop : -0.11 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 814 TYR 0.013 0.001 TYR D 858 PHE 0.011 0.001 PHE A 415 TRP 0.014 0.001 TRP A 911 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00416 (17064) covalent geometry : angle 0.57825 (23229) hydrogen bonds : bond 0.04587 ( 867) hydrogen bonds : angle 3.79512 ( 2583) link_BETA1-4 : bond 0.00076 ( 3) link_BETA1-4 : angle 2.00201 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4511.18 seconds wall clock time: 77 minutes 53.53 seconds (4673.53 seconds total)